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Sigmund LM, S SS, Albers A, Erdmann P, Paton RS, Greb L. Predicting Lewis Acidity: Machine Learning the Fluoride Ion Affinity of p-Block-Atom-Based Molecules. Angew Chem Int Ed Engl 2024; 63:e202401084. [PMID: 38452299 DOI: 10.1002/anie.202401084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
"How strong is this Lewis acid?" is a question researchers often approach by calculating its fluoride ion affinity (FIA) with quantum chemistry. Here, we present FIA49k, an extensive FIA dataset with 48,986 data points calculated at the RI-DSD-BLYP-D3(BJ)/def2-QZVPP//PBEh-3c level of theory, including 13 different p-block atoms as the fluoride accepting site. The FIA49k dataset was used to train FIA-GNN, two message-passing graph neural networks, which predict gas and solution phase FIA values of molecules excluded from training with a mean absolute error of 14 kJ mol-1 (r2=0.93) from the SMILES string of the Lewis acid as the only input. The level of accuracy is notable, given the wide energetic range of 750 kJ mol-1 spanned by FIA49k. The model's value was demonstrated with four case studies, including predictions for molecules extracted from the Cambridge Structural Database and by reproducing results from catalysis research available in the literature. Weaknesses of the model are evaluated and interpreted chemically. FIA-GNN and the FIA49k dataset can be reached via a free web app (www.grebgroup.de/fia-gnn).
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Affiliation(s)
- Lukas M Sigmund
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Department of Chemistry, Colorado State University, 1301 Center Avenue, Fort Collins, CO, 80523, USA
| | - Shree Sowndarya S
- Department of Chemistry, Colorado State University, 1301 Center Avenue, Fort Collins, CO, 80523, USA
| | - Andreas Albers
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Philipp Erdmann
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Robert S Paton
- Department of Chemistry, Colorado State University, 1301 Center Avenue, Fort Collins, CO, 80523, USA
| | - Lutz Greb
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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2
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Preuss A, Appel E, Gorb SN, Büsse S. Tanning of the tarsal and mandibular cuticle in adult Anax imperator (Insecta: Odonata) during the emergence sequence. Interface Focus 2024; 14:20230076. [PMID: 38618233 PMCID: PMC11008962 DOI: 10.1098/rsfs.2023.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/22/2024] [Indexed: 04/16/2024] Open
Abstract
The arthropod cuticle offers strength, protection, and lightweight. Due to its limit in expandability, arthropods have to moult periodically to grow. While moulting is beneficial in terms of parasite or toxin control, growth and adaptation to environmental conditions, it costs energy and leaves the soft animal's body vulnerable to injuries and desiccation directly after ecdysis. To investigate the temporal change in sclerotization and pigmentation during and after ecdysis, we combined macrophotography, confocal laser scanning microscopy, scanning electron microscopy and histological sectioning. We analysed the tarsal and mandibular cuticle of the blue emperor dragonfly to compare the progress of tanning for structures that are functionally involved during emergence (tarsus/tarsal claws) with structures whose functionality is required much later (mandibles). Our results show that: (i) the tanning of the tarsal and mandibular cuticle increases during emergence; (ii) the tarsal cuticle tans faster than the mandibular cuticle; (iii) the mandibles tan faster on the aboral than on the oral side; and (iv) both the exo- and the endocuticle are tanned. The change in the cuticle composition of the tarsal and mandibular cuticle reflects the demand for higher mechanical stability of these body parts when holding on to the substrate during emergence and during first walking or hunting attempts.
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Affiliation(s)
- Anika Preuss
- Department of Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Am Botanischen Garten 9, 24118 Kiel, Germany
| | - Esther Appel
- Department of Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Am Botanischen Garten 9, 24118 Kiel, Germany
| | - Stanislav N. Gorb
- Department of Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Am Botanischen Garten 9, 24118 Kiel, Germany
| | - Sebastian Büsse
- Department of Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Am Botanischen Garten 9, 24118 Kiel, Germany
- Department for Cytology and Evolutionary Biology, Zoological Institute and Museum, University of Greifswald, Soldmannstr. 23, 17489 Greifswald, Germany
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3
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Kairišs K, Sokolova N, Zilova L, Schlagheck C, Reinhardt R, Baumbach T, Faragó T, van de Kamp T, Wittbrodt J, Weinhardt V. Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach. Sci Rep 2024; 14:8543. [PMID: 38609416 PMCID: PMC11015006 DOI: 10.1038/s41598-024-58766-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The development of an organism is orchestrated by the spatial and temporal expression of genes. Accurate visualisation of gene expression patterns in the context of the surrounding tissues offers a glimpse into the mechanisms that drive morphogenesis. We developed correlative light-sheet fluorescence microscopy and X-ray computed tomography approach to map gene expression patterns to the whole organism`s 3D anatomy. We show that this multimodal approach is applicable to gene expression visualized by protein-specific antibodies and fluorescence RNA in situ hybridisation offering a detailed understanding of individual phenotypic variations in model organisms. Furthermore, the approach offers a unique possibility to identify tissues together with their 3D cellular and molecular composition in anatomically less-defined in vitro models, such as organoids. We anticipate that the visual and quantitative insights into the 3D distribution of gene expression within tissue architecture, by multimodal approach developed here, will be equally valuable for reference atlases of model organisms development, as well as for comprehensive screens, and morphogenesis studies of in vitro models.
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Affiliation(s)
- Kristaps Kairišs
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Lucie Zilova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
| | - Christina Schlagheck
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Robert Reinhardt
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tomáš Faragó
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Thomas van de Kamp
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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4
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Rossdam C, Brand S, Beimdiek J, Oberbeck A, Albers MD, Naujok O, Buettner FFR. Targeting the glycan epitope type I N-acetyllactosamine enables immunodepletion of human pluripotent stem cells from early differentiated cells. Glycobiology 2024; 34:cwae012. [PMID: 38349796 DOI: 10.1093/glycob/cwae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/15/2024] Open
Abstract
Cell surface biomarkers are fundamental for specific characterization of human pluripotent stem cells (hPSCs). Importantly, they can be applied for hPSC enrichment and/or purification but also to remove potentially teratoma-forming hPSCs from differentiated populations before clinical application. Several specific markers for hPSCs are glycoconjugates comprising the glycosphingolipid (GSL)-based glycans SSEA-3 and SSEA-4. We applied an analytical approach based on multiplexed capillary gel electrophoresis coupled to laser-induced fluorescence detection to quantitatively assess the GSL glycome of human embryonic stem cells and human induced pluripotent stem cells as well as during early stages of differentiation into mesoderm, endoderm, and ectoderm. Thereby, we identified the GSL lacto-N-tetraosylceramide (Lc4-Cer, Galβ1-3GlcNAcβ1-3Galβ1-4Glc-Cer), which comprises a terminal type 1 LacNAc (T1LN) structure (Galβ1-3GlcNAc), to be rapidly decreased upon onset of differentiation. Using a specific antibody, we could confirm a decline of T1LN-terminating glycans during the first four days of differentiation by live-cell staining and subsequent flow cytometry. We could further separate T1LN-positive and T1LN-negative cells out of a mixed population of pluripotent and differentiated cells by magnetic activated cell sorting. Notably, not only the T1LN-positive but also the T1LN-negative population was positive for SSEA-3, SSEA-4, and SSEA-5 while expression of nuclear pluripotency markers OCT4 and NANOG was highly reduced in the T1LN-negative population, exclusively. Our findings suggest T1LN as a pluripotent stem cell-specific glycan epitope that is more rapidly down-regulated upon differentiation than SSEA-3, SSEA-4, and SSEA-5.
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Affiliation(s)
- Charlotte Rossdam
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Smilla Brand
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Julia Beimdiek
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Astrid Oberbeck
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Marco Darius Albers
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Ortwin Naujok
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Falk F R Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
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5
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Liu Y, Wang L, Hübner R, Kresse J, Zhang X, Deconinick M, Vaynzof Y, Weidinger IM, Eychmüller A. Cobalt-based Co 3Mo 3N/Co 4N/Co Metallic Heterostructure as a Highly Active Electrocatalyst for Alkaline Overall Water Splitting. Angew Chem Int Ed Engl 2024; 63:e202319239. [PMID: 38314947 DOI: 10.1002/anie.202319239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
Alkaline water electrolysis holds promise for large-scale hydrogen production, yet it encounters challenges like high voltage and limited stability at higher current densities, primarily due to inefficient electron transport kinetics. Herein, a novel cobalt-based metallic heterostructure (Co3Mo3N/Co4N/Co) is designed for excellent water electrolysis. In operando Raman experiments reveal that the formation of the Co3Mo3N/Co4N heterointerface boosts the free water adsorption and dissociation, increasing the available protons for subsequent hydrogen production. Furthermore, the altered electronic structure of the Co3Mo3N/Co4N heterointerface optimizes ΔGH of the nitrogen atoms at the interface. This synergistic effect between interfacial nitrogen atoms and metal phase cobalt creates highly efficient active sites for the hydrogen evolution reaction (HER), thereby enhancing the overall HER performance. Additionally, the heterostructure exhibits a rapid OH- adsorption rate, coupled with great adsorption strength, leading to improved oxygen evolution reaction (OER) performance. Crucially, the metallic heterojunction accelerates electron transport, expediting the afore-mentioned reaction steps and enhancing water splitting efficiency. The Co3Mo3N/Co4N/Co electrocatalyst in the water electrolyzer delivers excellent performance, with a low 1.58 V cell voltage at 10 mA cm-2, and maintains 100 % retention over 100 hours at 200 mA cm-2, surpassing the Pt/C||RuO2 electrolyzer.
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Affiliation(s)
- Yuanwu Liu
- Physical Chemistry, TU Dresden, Zellescher Weg 19, 01069, Dresden, Germany
| | - Lirong Wang
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - René Hübner
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf e.V., Bautzner Landstrasse 400, 01328, Dresden, Germany
| | - Johannes Kresse
- Physical Chemistry, TU Dresden, Zellescher Weg 19, 01069, Dresden, Germany
| | - Xiaoming Zhang
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Marielle Deconinick
- Chair for Emerging Electronic Technologies, TU Dresden, Nöthnitzer Str. 61, Dresden, 01187 Sachsen, Germany
- Leibniz-Institute for Solid State and Materials Research Dresden, Helmholtzstraße 20, Dresden, 01069 Sachsen, Germany
| | - Yana Vaynzof
- Chair for Emerging Electronic Technologies, TU Dresden, Nöthnitzer Str. 61, Dresden, 01187 Sachsen, Germany
- Leibniz-Institute for Solid State and Materials Research Dresden, Helmholtzstraße 20, Dresden, 01069 Sachsen, Germany
| | - Inez M Weidinger
- Fakultät Chemie und Lebensmittelchemie, Technische Universität Dresden, Zellescher Weg 19, 01069, Dresden, Germany
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6
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Yazdi M, Hasanzadeh Kafshgari M, Khademi Moghadam F, Zarezade V, Oellinger R, Khosravi M, Haas S, Hoch CC, Pockley AG, Wagner E, Wollenberg B, Multhoff G, Bashiri Dezfouli A. Crosstalk Between NK Cell Receptors and Tumor Membrane Hsp70-Derived Peptide: A Combined Computational and Experimental Study. Adv Sci (Weinh) 2024; 11:e2305998. [PMID: 38298098 PMCID: PMC11005703 DOI: 10.1002/advs.202305998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/19/2023] [Indexed: 02/02/2024]
Abstract
Natural killer (NK) cells are central components of the innate immunity system against cancers. Since tumor cells have evolved a series of mechanisms to escape from NK cells, developing methods for increasing the NK cell antitumor activity is of utmost importance. It is previously shown that an ex vivo stimulation of patient-derived NK cells with interleukin (IL)-2 and Hsp70-derived peptide TKD (TKDNNLLGRFELSG, aa450-461) results in a significant upregulation of activating receptors including CD94 and CD69 which triggers exhausted NK cells to target and kill malignant solid tumors expressing membrane Hsp70 (mHsp70). Considering that TKD binding to an activating receptor is the initial step in the cytolytic signaling cascade of NK cells, herein this interaction is studied by molecular docking and molecular dynamics simulation computational modeling. The in silico results showed a crucial role of the heterodimeric receptor CD94/NKG2A and CD94/NKG2C in the TKD interaction with NK cells. Antibody blocking and CRISPR/Cas9-mediated knockout studies verified the key function of CD94 in the TKD stimulation and activation of NK cells which is characterized by an increased cytotoxic capacity against mHsp70 positive tumor cells via enhanced production and release of lytic granules and pro-inflammatory cytokines.
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Affiliation(s)
- Mina Yazdi
- Pharmaceutical BiotechnologyDepartment of PharmacyLudwig‐Maximilians‐Universität (LMU)81377MunichGermany
| | - Morteza Hasanzadeh Kafshgari
- Heinz‐Nixdorf‐Chair of Biomedical ElectronicsCampus Klinikum München rechts der IsarTranslaTUMTechnische Universität München81675MunichGermany
| | | | - Vahid Zarezade
- Behbahan Faculty of Medical SciencesBehbahan6361796819Iran
| | - Rupert Oellinger
- Institute of Molecular Oncology and Functional GenomicsSchool of MedicineTechnische Universität München81675MunichGermany
- Central Institute for Translational Cancer Research (TranslaTUM)School of MedicineTechnische Universität München81675MunichGermany
| | - Mohammad Khosravi
- Department of PathobiologyFaculty of Veterinary MedicineShahid Chamran University of AhvazAhvaz6135783151Iran
| | - Stefan Haas
- Department of Radiation OncologySchool of MedicineTechnische Universität München81675MunichGermany
- Department of OtorhinolaryngologySchool of MedicineTechnische Universität München81675MunichGermany
| | - Cosima C. Hoch
- Department of OtorhinolaryngologySchool of MedicineTechnische Universität München81675MunichGermany
| | - Alan Graham Pockley
- John van Geest Cancer Research CentreSchool of Science and TechnologyNottingham Trent UniversityNottinghamNG11 8NSUK
| | - Ernst Wagner
- Pharmaceutical BiotechnologyDepartment of PharmacyLudwig‐Maximilians‐Universität (LMU)81377MunichGermany
| | - Barbara Wollenberg
- Department of OtorhinolaryngologySchool of MedicineTechnische Universität München81675MunichGermany
| | - Gabriele Multhoff
- Central Institute for Translational Cancer Research (TranslaTUM)School of MedicineTechnische Universität München81675MunichGermany
- Department of Radiation OncologySchool of MedicineTechnische Universität München81675MunichGermany
| | - Ali Bashiri Dezfouli
- Central Institute for Translational Cancer Research (TranslaTUM)School of MedicineTechnische Universität München81675MunichGermany
- Department of Radiation OncologySchool of MedicineTechnische Universität München81675MunichGermany
- Department of OtorhinolaryngologySchool of MedicineTechnische Universität München81675MunichGermany
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7
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McGowran P, Mathews MA, Johns H, Harasym MC, Raju E, Ayeb-Karlsson S. Investigating the conditions of vulnerability experienced by migrant workers during the COVID-19 pandemic in Kerala, India. Disasters 2024; 48:e12614. [PMID: 37811865 DOI: 10.1111/disa.12614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
This paper analyses findings of the 'PROWELLMIGRANTS'2 project, which qualitatively investigated COVID-19 impacts on migrants' well-being and mental health in Kerala, India. It draws on a novel conceptual framework that combines assemblage-thinking with theories of social contracts in disasters. The paper first explores how past development processes and contemporary migration policies in Kerala, and India more widely, generated conditions of vulnerability for migrant workers in Kerala prior to the pandemic. Next it shows that Government of Kerala interventions, in some cases supported by the central Government of India, temporarily addressed these vulnerabilities during the pandemic. In acknowledging the helpful response of the Kerala government, we problematise its stance on migrant workers during 'normal' times and speculate that permanently addressing these conditions of vulnerability would be a more logical approach. We acknowledge this involves overcoming many wider barriers. Thus, the paper also contains national-level policy implications.
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Affiliation(s)
- Peter McGowran
- PhD is Senior Research Associate, United Nations University Institute for Environment and Human Security, Germany
- Lecturer in Development Geography, School of Law and Social Sciences, Oxford Brookes University, United Kingdom
| | - Mishal A Mathews
- Research Assistant, United Nations University Institute for Environment and Human Security, Germany
| | - Hannah Johns
- PhD is Senior Research Associate, United Nations University Institute for Environment and Human Security, Germany
| | - Mary C Harasym
- Research Assistant, United Nations University Institute for Environment and Human Security, Germany
| | - Emmanuel Raju
- Associate Professor, Global Health Section, University of Copenhagen, Denmark
- Director, Copenhagen Center for Disaster Research, Denmark
- Visiting Associate Professor, African Centre for Disaster Studies, North-West University, South Africa
| | - Sonja Ayeb-Karlsson
- PhD is Associate Professor, Institute for Risk and Disaster Reduction, University College London, United Kingdom
- Senior Researcher, United Nations University Institute for Environment and Human Security, United Kingdom
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8
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Rudszuck T, Nirschl H, Guthausen G. Combined nuclear magnetic resonance methods in quality control of lubricants in green energy production. Magn Reson Chem 2024; 62:212-221. [PMID: 36843335 DOI: 10.1002/mrc.5339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
NMR methods were applied for lubricant analysis. Different factors influence the real aging of lubricants on diverse length scales and are captured by NMR. Chemical conversion of additives is addressed by NMR spectroscopy. High-field NMR experiments allow the identification and quantification of chemical components and are transferred to benchtop devices. Molecular dynamics and contaminations like fuel or abrasion are addressed via NMR relaxation and diffusion. Quality parameters were extracted via suitable data analysis of NMR raw data, which allow the detection of aging and indicate changes in the oil composition. At the same time, the methodology is optimized to the conditions in quality control. The feasibility is shown the example of a series of lubricants from applications in regenerative energy production, namely, wind turbine oils and biogas motor oils.
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Affiliation(s)
- Thomas Rudszuck
- Institute for Mechanical Engineering and Mechanics, KIT, 76131, Karlsruhe, Germany
| | - Hermann Nirschl
- Institute for Mechanical Engineering and Mechanics, KIT, 76131, Karlsruhe, Germany
| | - Gisela Guthausen
- Institute for Mechanical Engineering and Mechanics, KIT, 76131, Karlsruhe, Germany
- Engler-Bunte Institut, Water Chemistry and Technology, KIT, 76131, Karlsruhe, Germany
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9
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Flosbach NT, Rasche B, Rochels L, Disch S, Wickleder C, Adlung M, Fischer P, Wickleder MS. The Divalent Lanthanoid Triflates Ln(CF 3SO 3) 2(CH 3CN) (Ln=Sm, Eu): Structure, Luminescence, and Magnetism. Chemistry 2024:e202400462. [PMID: 38501801 DOI: 10.1002/chem.202400462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/20/2024]
Abstract
The reaction of the trivalent lanthanoide triflates Ln(OTf)3 (Ln=Sm, Eu; OTf=CF3SO3 -) with the respective metals in acetonitrile leads to the Ln(II)-triflates Eu(OTf)2(CH3CN) (monoclinic, P21/n, Z=4, a=1053.54(1), b=610.28(5), c=1946.92(2) pm, β =98.611(4)) and Sm(OTf)2(CH3CN) (monoclinic, P21/n, Z=4, a=1054.41(4), b=612.16(2), c=1952.65(7) pm, β =98.524(2)). The isotypic strontium compound Sr(OTf)2(CH3CN) (monoclinic, P21/n, Z=4, a=1056.39(5), b=610.05(3), c=1950.1(1) pm, β =98.900(2)°) has been obtained from SrCO3 and triflic acid. The compounds have been investigated by X-ray diffraction, vibrational spectroscopy, luminescence spectroscopy, cyclic voltammetry, thermal analysis, and magnetic measurements.
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Affiliation(s)
- Niko T Flosbach
- Universität zu Köln, Institut für Anorganische Chemie, Greinstraße 6, 50939, Köln, Germany
| | - Bertold Rasche
- Universität Stuttgart, Institut für Anorganische Chemie, Pfaffenwaldring 55, 70569, Stuttgart
| | - Leonhard Rochels
- Universität Duisburg-Essen, Anorganische Chemie und Center for Nanointegration Duisburg-Essen (CENIDE), Universitätsstraße 5-7, 45141, Essen
| | - Sabrina Disch
- Universität Duisburg-Essen, Anorganische Chemie und Center for Nanointegration Duisburg-Essen (CENIDE), Universitätsstraße 5-7, 45141, Essen
| | - Claudia Wickleder
- Universität Siegen, Department Chemie/Biologie Anorganische Chemie, Adolf-Reichwein-Straße, 57068, Siegen
| | - Matthias Adlung
- Universität Siegen, Department Chemie/Biologie Anorganische Chemie, Adolf-Reichwein-Straße, 57068, Siegen
| | - Pia Fischer
- Universität Siegen, Department Chemie/Biologie Anorganische Chemie, Adolf-Reichwein-Straße, 57068, Siegen
| | - Mathias S Wickleder
- Universität zu Köln, Institut für Anorganische Chemie, Greinstraße 6, 50939, Köln, Germany
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10
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Matsuda A, Plewka J, Rawski M, Mourão A, Zajko W, Siebenmorgen T, Kresik L, Lis K, Jones AN, Pachota M, Karim A, Hartman K, Nirwal S, Sonani R, Chykunova Y, Minia I, Mak P, Landthaler M, Nowotny M, Dubin G, Sattler M, Suder P, Popowicz GM, Pyrć K, Czarna A. Despite the odds: formation of the SARS-CoV-2 methylation complex. Nucleic Acids Res 2024:gkae165. [PMID: 38499483 DOI: 10.1093/nar/gkae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
Coronaviruses modify their single-stranded RNA genome with a methylated cap during replication to mimic the eukaryotic mRNAs. The capping process is initiated by several nonstructural proteins (nsp) encoded in the viral genome. The methylation is performed by two methyltransferases, nsp14 and nsp16, while nsp10 acts as a co-factor to both. Additionally, nsp14 carries an exonuclease domain which operates in the proofreading system during RNA replication of the viral genome. Both nsp14 and nsp16 were reported to independently bind nsp10, but the available structural information suggests that the concomitant interaction between these three proteins would be impossible due to steric clashes. Here, we show that nsp14, nsp10, and nsp16 can form a heterotrimer complex upon significant allosteric change. This interaction is expected to encourage the formation of mature capped viral mRNA, modulating nsp14's exonuclease activity, and protecting the viral RNA. Our findings show that nsp14 is amenable to allosteric regulation and may serve as a novel target for therapeutic approaches.
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Affiliation(s)
- Alex Matsuda
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-387 Kraków, Poland
| | - Jacek Plewka
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Poland
| | - Michał Rawski
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland
| | - André Mourão
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Weronika Zajko
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | | | - Leanid Kresik
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Kinga Lis
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Faculty of Chemical Engineering and Technology, Kraków University of Technology, 31-155 Kraków, Poland
| | - Alisha N Jones
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Magdalena Pachota
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Abdulkarim Karim
- Department of Biology, College of Science, Salahaddin University-Erbil, 44002 Erbil, Kurdistan Region, Iraq
- Department of Community Health, College of Health Technology, Cihan University-Erbil, 44001 Erbil, Kurdistan Region, Iraq
| | - Kinga Hartman
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059 Kraków, Poland
| | - Shivlee Nirwal
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Ravi Sonani
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Yuliya Chykunova
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Igor Minia
- Laboratory for RNA Biology, Berlin Institute for Medical System Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Paweł Mak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Markus Landthaler
- Laboratory for RNA Biology, Berlin Institute for Medical System Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Grzegorz Dubin
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Michael Sattler
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Piotr Suder
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059 Kraków, Poland
| | - Grzegorz M Popowicz
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Krzysztof Pyrć
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Anna Czarna
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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11
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Steurer M, Ruther J, Pokorny T. Behavioural consequences of intraspecific variability in a mate recognition signal. Proc Biol Sci 2024; 291:20232518. [PMID: 38444335 PMCID: PMC10915540 DOI: 10.1098/rspb.2023.2518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/08/2024] [Indexed: 03/07/2024] Open
Abstract
Mate recognition is paramount for sexually reproducing animals, and many insects rely on cuticular hydrocarbons (CHCs) for close-range sexual communication. To ensure reliable mate recognition, intraspecific sex pheromone variability should be low. However, CHCs can be influenced by several factors, with the resulting variability potentially impacting sexual communication. While intraspecific CHC variability is a common phenomenon, the consequences thereof for mate recognition remain largely unknown. We investigated the effect of CHC variability on male responses in a parasitoid wasp showing a clear-cut within-population CHC polymorphism (three distinct female chemotypes, one thereof similar to male profiles). Males clearly discriminated between female and male CHCs, but not between female chemotypes in no-choice assays. When given a choice, a preference hierarchy emerged. Interestingly, the most attractive chemotype was the one most similar to male profiles. Mixtures of female CHCs were as attractive as chemotype-pure ones, while a female-male mixture negatively impacted male responses, indicating assessment of the entire, complex CHC profile composition. Our study reveals that the evaluation of CHC profiles can be strict towards 'undesirable' features, but simultaneously tolerant enough to cover a range of variants. This reconciles reliable mate recognition with naturally occurring variability.
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Affiliation(s)
- Maximilian Steurer
- Institute of Zoology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Joachim Ruther
- Institute of Zoology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Tamara Pokorny
- Institute of Zoology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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12
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Schülke KH, Fröse JS, Klein A, Garcia-Borràs M, Hammer SC. Efficient Transferase Engineering for SAM Analog Synthesis from Iodoalkanes. Chembiochem 2024:e202400079. [PMID: 38477872 DOI: 10.1002/cbic.202400079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/14/2024]
Abstract
S-Adenosyl-l-methionine (SAM) is an important cosubstrate in various biochemical processes, including selective methyl transfer reactions. Simple methods for the (re)generation of SAM analogs could expand the chemistry accessible with SAM-dependent transferases and go beyond methylation reactions. Here we present an efficient enzyme engineering strategy to synthesize different SAM analogs from "off-the-shelf" iodoalkanes through enzymatic alkylation of S-adenosyl-l-homocysteine (SAH). This was achieved by mutating multiple hydrophobic and structurally dynamic amino acids simultaneously. Combinatorial mutagenesis was guided by the natural amino acid diversity and generated a highly functional mutant library. This approach increased the speed as well as the scale of enzyme engineering by providing a panel of optimized enzymes with orders of magnitude higher activities for multiple substrates in just one round of enzyme engineering. The optimized enzymes exhibit catalytic efficiencies up to 31 M-1 s-1, convert various iodoalkanes, including substrates bearing cyclopropyl or aromatic moieties, and catalyze S-alkylation of SAH with very high stereoselectivities (>99 % de). We further report a high throughput chromatographic screening system for reliable and rapid SAM analog analysis. We believe that the methods and enzymes described herein will further advance the field of selective biocatalytic alkylation chemistry by enabling SAM analog regeneration with "off-the-shelf" reagents.
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Affiliation(s)
- Kai H Schülke
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Jana S Fröse
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Alina Klein
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Marc Garcia-Borràs
- Department Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, 17003, Girona, Catalonia, Spain
| | - Stephan C Hammer
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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13
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John M, Rüttger F. Multinuclear Residual Quadrupolar Couplings for Structure and Assignment. Chemphyschem 2024:e202400068. [PMID: 38465709 DOI: 10.1002/cphc.202400068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 03/12/2024]
Abstract
Most stable isotopes have a nuclear spin >1/2, but the quadrupole interaction poses challenge on their detection by nuclear magnetic resonance (NMR). On the other hand, the quadrupole interaction is a rich source of structural information that may be exploited for solution NMR in the form of residual quadrupolar couplings (RQCs) of weakly oriented samples. While 2H RQCs are now well established for structure verification and enantiomeric discrimination of organic molecules, we will in this article highlight some recent work on RQCs of other nuclei (especially 7Li and 11B).
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Affiliation(s)
- Michael John
- Fakultät für Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077, Göttingen
| | - Franziska Rüttger
- Fakultät für Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077, Göttingen
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14
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Wang Y, Crumpton AE, Ellwanger MA, McManus C, Aldridge S. Boryl Ancillary Ligands: Influencing Stability and Reactivity of Amidinato-Silanone and Germanone Systems in Ammonia Activation. Angew Chem Int Ed Engl 2024:e202402795. [PMID: 38465783 DOI: 10.1002/anie.202402795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/12/2024]
Abstract
While the nucleophilic addition of ammonia to ketones is an archetypal reaction in classical organic chemistry, the reactivity of heavier group 14 carbonyl analogues (R2E=O; E=Si, Ge, Sn, or Pb) with NH3 remains sparsely investigated, primarily due to the synthetic difficulties in accessing heavier ketone congeners. Herein, we present a room-temperature stable boryl-substituted amidinato-silanone {(HCDippN)2B}{PhC(tBuN)2}Si=O (Dipp=2,6-iPr2C6H3) (together with its germanone analogue), formed from the corresponding silylene under a N2O atmosphere. This system reacts cleanly with ammonia in 1,2-fashion to give an isolable sila-hemiaminal complex {(HCDippN)2B}{PhC(tBuN)2}Si(OH)(NH2). Quantum chemical calculations reveal that the formation of this sila-hemiaminal is crucially dependent on the nature of the ancillary ligand scaffold. It is facilitated thermodynamically by the hemi-lability of the amidinate ligand (which allows for the formation of an energetically critical intramolecular N⋅⋅⋅HO hydrogen bond within the product) and is enabled mech-anistically by a process in which the silanone initially acts in umpolung fashion as a base (rather than an acid), due to the strongly electron-releasing and sterically bulky nature of the ancillary boryl ligand.
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Affiliation(s)
- Yuwen Wang
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, P. R. China
| | - Agamemnon E Crumpton
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - Mathias A Ellwanger
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - Caitilín McManus
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - Simon Aldridge
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
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AbuAlia KFN, Damm E, Ullrich KK, Mukaj A, Parvanov E, Forejt J, Odenthal-Hesse L. Natural variation in the zinc-finger-encoding exon of Prdm9 affects hybrid sterility phenotypes in mice. Genetics 2024; 226:iyae004. [PMID: 38217871 PMCID: PMC10917509 DOI: 10.1093/genetics/iyae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/15/2024] Open
Abstract
PRDM9-mediated reproductive isolation was first described in the progeny of Mus musculus musculus (MUS) PWD/Ph and Mus musculus domesticus (DOM) C57BL/6J inbred strains. These male F1 hybrids fail to complete chromosome synapsis and arrest meiosis at prophase I, due to incompatibilities between the Prdm9 gene and hybrid sterility locus Hstx2. We identified 14 alleles of Prdm9 in exon 12, encoding the DNA-binding domain of the PRDM9 protein in outcrossed wild mouse populations from Europe, Asia, and the Middle East, 8 of which are novel. The same allele was found in all mice bearing introgressed t-haplotypes encompassing Prdm9. We asked whether 7 novel Prdm9 alleles in MUS populations and the t-haplotype allele in 1 MUS and 3 DOM populations induce Prdm9-mediated reproductive isolation. The results show that only combinations of the dom2 allele of DOM origin and the MUS msc1 allele ensure complete infertility of intersubspecific hybrids in outcrossed wild populations and inbred mouse strains examined so far. The results further indicate that MUS mice may share the erasure of PRDM9msc1 binding motifs in populations with different Prdm9 alleles, which implies that erased PRDM9 binding motifs may be uncoupled from their corresponding Prdm9 alleles at the population level. Our data corroborate the model of Prdm9-mediated hybrid sterility beyond inbred strains of mice and suggest that sterility alleles of Prdm9 may be rare.
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Affiliation(s)
- Khawla F N AbuAlia
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Elena Damm
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Kristian K Ullrich
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Amisa Mukaj
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Emil Parvanov
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, 9002 Varna, Bulgaria
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, 1090 Vienna, Austria
| | - Jiri Forejt
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Linda Odenthal-Hesse
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
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16
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Klug C, Spiekman SNF, Bastiaans D, Scheffold B, Scheyer TM. The marine conservation deposits of Monte San Giorgio (Switzerland, Italy): the prototype of Triassic black shale Lagerstätten. Swiss J Palaeontol 2024; 143:11. [PMID: 38450287 PMCID: PMC10912274 DOI: 10.1186/s13358-024-00308-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/23/2024] [Indexed: 03/08/2024]
Abstract
Marine conservation deposits ('Konservat-Lagerstätten') are characterized by their mode of fossil preservation, faunal composition and sedimentary facies. Here, we review these characteristics with respect to the famous conservation deposit of the Besano Formation (formerly Grenzbitumenzone; including the Anisian-Ladinian boundary), and the successively younger fossil-bearing units Cava inferiore, Cava superiore, Cassina beds and the Kalkschieferzone of Monte San Giorgio (Switzerland and Italy). We compare these units to a selection of important black shale-type Lagerstätten of the global Phanerozoic plus the Ediacaran in order to detect commonalities in their facies, genesis, and fossil content using principal component and hierarchical cluster analyses. Further, we put the Monte San Giorgio type Fossillagerstätten into the context of other comparable Triassic deposits worldwide based on their fossil content. The results of the principal component and cluster analyses allow a subdivision of the 45 analysed Lagerstätten into four groups, for which we suggest the use of the corresponding pioneering localities: Burgess type for the early Palaeozoic black shales, Monte San Giorgio type for the Triassic black shales, Holzmaden type for the pyrite-rich black shales and Solnhofen type for platy limestones.
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Affiliation(s)
- Christian Klug
- Universität Zürich, Paläontologisches Institut, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
| | | | - Dylan Bastiaans
- Universität Zürich, Paläontologisches Institut, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
| | - Beat Scheffold
- Universität Zürich, Paläontologisches Institut, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
| | - Torsten M. Scheyer
- Universität Zürich, Paläontologisches Institut, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
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17
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Blickhan R, Andrada E, Hirasaki E, Ogihara N. Differential leg and trunk operation during skipping without and with hurdles in bipedal Japanese macaque. J Exp Zool A Ecol Integr Physiol 2024. [PMID: 38436123 DOI: 10.1002/jez.2803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 03/05/2024]
Abstract
When locomoting bipedally at higher speeds, macaques preferred unilateral skipping (galloping). The same skipping pattern was maintained while hurdling across two low obstacles at the distance of a stride within our experimental track. The present study investigated leg and trunk joint rotations and leg joint moments, with the aim of clarifying the differential leg and trunk operation during skipping in bipedal macaques. Especially at the hip, the range of joint rotation and extension at lift off was larger in the leading than in the trailing leg. The flexing knee absorbed energy and the extending ankle generated work during each step. The trunk showed only minor deviations from symmetry. Hurdling amplified the differences and notably resulted in a quasi-elastic use of the leading knee and in an asymmetric operation of the trunk.
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Affiliation(s)
| | - Emanuel Andrada
- Faculty of Social and Behavioural Sciences, Institute of Zoology and Evolutionary Research, Friedrich-Schiller-University, Jena, Germany
| | - Eishi Hirasaki
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
| | - Naomichi Ogihara
- Department of Mechanical Engineering, Keio University, Yokohama, Japan
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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18
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Zhao H, Wang Y, Chen Q, Liu Y, Gao Y, Müllen K, Li S, Narita A. A Nanographene-Porphyrin Hybrid for Near-Infrared-Ii Phototheranostics. Adv Sci (Weinh) 2024:e2309131. [PMID: 38430537 DOI: 10.1002/advs.202309131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/20/2024] [Indexed: 03/04/2024]
Abstract
Photoacoustic imaging (PAI)-guided photothermal therapy (PTT) in the second near-infrared (NIR-II, 1000-1700 nm) window has been attracting attention as a promising cancer theranostic platform. Here, it is reported that the π-extended porphyrins fused with one or two nanographene units (NGP-1 and NGP-2) can serve as a new class of NIR-responsive organic agents, displaying absorption extending to ≈1000 and ≈1400 nm in the NIR-I and NIR-II windows, respectively. NGP-1 and NGP-2 are dispersed in water through encapsulation into self-assembled nanoparticles (NPs), achieving high photothermal conversion efficiency of 60% and 69%, respectively, under 808 and 1064 nm laser irradiation. Moreover, the NIR-II-active NGP-2-NPs demonstrated promising photoacoustic responses, along with high photostability and biocompatibility, enabling PAI and efficient NIR-II PTT of cancer in vivo.
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Affiliation(s)
- Hao Zhao
- Organic and Carbon Nanomaterials Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Yu Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, P. R. China
| | - Qiang Chen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Ying Liu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, P. R. China
| | - Yijian Gao
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, P. R. China
| | - Klaus Müllen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Shengliang Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, P. R. China
| | - Akimitsu Narita
- Organic and Carbon Nanomaterials Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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19
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Kiss AE, Venkatasubramani AV, Pathirana D, Krause S, Sparr AC, Hasenauer J, Imhof A, Müller M, Becker PB. Processivity and specificity of histone acetylation by the male-specific lethal complex. Nucleic Acids Res 2024:gkae123. [PMID: 38407474 DOI: 10.1093/nar/gkae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/29/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
Acetylation of lysine 16 of histone H4 (H4K16ac) stands out among the histone modifications, because it decompacts the chromatin fiber. The metazoan acetyltransferase MOF (KAT8) regulates transcription through H4K16 acetylation. Antibody-based studies had yielded inconclusive results about the selectivity of MOF to acetylate the H4 N-terminus. We used targeted mass spectrometry to examine the activity of MOF in the male-specific lethal core (4-MSL) complex on nucleosome array substrates. This complex is part of the Dosage Compensation Complex (DCC) that activates X-chromosomal genes in male Drosophila. During short reaction times, MOF acetylated H4K16 efficiently and with excellent selectivity. Upon longer incubation, the enzyme progressively acetylated lysines 12, 8 and 5, leading to a mixture of oligo-acetylated H4. Mathematical modeling suggests that MOF recognizes and acetylates H4K16 with high selectivity, but remains substrate-bound and continues to acetylate more N-terminal H4 lysines in a processive manner. The 4-MSL complex lacks non-coding roX RNA, a critical component of the DCC. Remarkably, addition of RNA to the reaction non-specifically suppressed H4 oligo-acetylation in favor of specific H4K16 acetylation. Because RNA destabilizes the MSL-nucleosome interaction in vitro we speculate that RNA accelerates enzyme-substrate turn-over in vivo, thus limiting the processivity of MOF, thereby increasing specific H4K16 acetylation.
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Affiliation(s)
- Anna E Kiss
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Anuroop V Venkatasubramani
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Dilan Pathirana
- Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Silke Krause
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Aline Campos Sparr
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Jan Hasenauer
- Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Axel Imhof
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Marisa Müller
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Peter B Becker
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
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20
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Sailaja STN, Maisuls I, Hepp A, Brünink D, Doltsinis NL, Faust A, Hermann S, Strassert CA. Dual Emissive Zn(II) Naphthalocyanines: Synthesis, Structural and Photophysical Characterization with Theory-Supported Insights towards Soluble Coordination Compounds with Visible and Near-Infrared Emission. Int J Mol Sci 2024; 25:2605. [PMID: 38473852 DOI: 10.3390/ijms25052605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Metal phthalocyaninates and their higher homologues are recognized as deep-red luminophores emitting from their lowest excited singlet state. Herein, we report on the design, synthesis, and in-depth characterization of a new class of dual-emissive (visible and NIR) metal naphthalocyaninates. A 4-N,N-dimethylaminophen-4-yl-substituted naphthalocyaninato zinc(II) complex (Zn-NMe2Nc) and the derived water-soluble coordination compound (Zn-NMe3Nc) exhibit a near-infrared fluorescence from the lowest ligand-centered state, along with a unique push-pull-supported luminescence in the visible region of the electromagnetic spectrum. An unprecedentedly broad structural (2D-NMR spectroscopy and mass spectrometry) as well as photophysical characterization (steady-state state and time-resolved photoluminescence spectroscopy) is presented. The unique dual emission was assigned to two independent sets of singlet states related to the intrinsic Q-band of the macrocycle and to the push-pull substituents in the molecular periphery, respectively, as predicted by TD-DFT calculations. In general, the elusive chemical aspects of these macrocyclic compounds are addressed, involving both reaction conditions, thorough purification, and in-depth characterization. Besides the fundamental aspects that are investigated herein, the photoacoustic properties were exemplarily examined using phantom gels to assess their tomographic imaging capabilities. Finally, the robust luminescence in the visible range arising from the push-pull character of the peripheral moieties demonstrated a notable independence from aggregation and was exemplarily implemented for optical imaging (FLIM) through time-resolved multiphoton micro(spectro)scopy.
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Affiliation(s)
- Sidharth Thulaseedharan Nair Sailaja
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstraße 28/30, 48149 Münster, Germany
- CeNTech, CiMIC, SoN, Universität Münster, Heisenbergstraße 11, 48149 Münster, Germany
| | - Iván Maisuls
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstraße 28/30, 48149 Münster, Germany
- CeNTech, CiMIC, SoN, Universität Münster, Heisenbergstraße 11, 48149 Münster, Germany
| | - Alexander Hepp
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstraße 28/30, 48149 Münster, Germany
| | - Dana Brünink
- Institute for Solid State Theory and Center for Multiscale Theory and Computation, Universität Münster, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany
| | - Nikos L Doltsinis
- Institute for Solid State Theory and Center for Multiscale Theory and Computation, Universität Münster, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany
| | - Andreas Faust
- European Institute for Molecular Imaging, Universität Münster, Röntgenstraße 16, 48149 Münster, Germany
- Department of Nuclear Medicine, University Hospital Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Sven Hermann
- European Institute for Molecular Imaging, Universität Münster, Röntgenstraße 16, 48149 Münster, Germany
- Department of Nuclear Medicine, University Hospital Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Cristian A Strassert
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstraße 28/30, 48149 Münster, Germany
- CeNTech, CiMIC, SoN, Universität Münster, Heisenbergstraße 11, 48149 Münster, Germany
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21
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Pournajar M, Moretti P, Hosseini SA, Zaiser M. Creep failure of hierarchical materials. Sci Rep 2024; 14:4238. [PMID: 38378777 PMCID: PMC10879160 DOI: 10.1038/s41598-024-54908-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/18/2024] [Indexed: 02/22/2024] Open
Abstract
Creep failure of hierarchical materials is investigated by simulation of beam network models. Such models are idealizations of hierarchical fibrous materials where bundles of load-carrying fibers are held together by multi-level (hierarchical) cross-links. Failure of individual beams is assumed to be governed by stress-assisted thermal activation over local barriers, and beam stresses are computed by solving the global balance equations of linear and angular momentum across the network. Disorder is mimicked by a statistical distribution of barrier heights. Both initially intact samples and samples containing side notches of various length are considered. Samples with hierarchical cross-link patterns are simulated alongside reference samples where cross-links are placed randomly without hierarchical organization. The results demonstrate that hierarchical patterning may strongly increase creep strain and creep lifetime while reducing the lifetime variation. This is due to the fact that hierarchical patterning induces a failure mode that differs significantly from the standard scenario of failure by nucleation and growth of a critical crack. Characterization of this failure mode demonstrates good agreement between the present simulations and experimental findings on hierarchically patterned paper sheets.
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Affiliation(s)
- Mahshid Pournajar
- Department of Materials Science, WW8-Materials Simulation, FAU Universität Erlangen-Nürnberg, Dr.-Mack-Straße 77, 90762, Fürth, Germany
| | - Paolo Moretti
- Department of Materials Science, WW8-Materials Simulation, FAU Universität Erlangen-Nürnberg, Dr.-Mack-Straße 77, 90762, Fürth, Germany.
| | - Seyyed Ahmad Hosseini
- Department of Materials Science, WW8-Materials Simulation, FAU Universität Erlangen-Nürnberg, Dr.-Mack-Straße 77, 90762, Fürth, Germany
| | - Michael Zaiser
- Department of Materials Science, WW8-Materials Simulation, FAU Universität Erlangen-Nürnberg, Dr.-Mack-Straße 77, 90762, Fürth, Germany
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22
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Malgaretti P, Pagonabarraga I, Harting J. Local electroneutrality breakdown for electrolytes within varying-section nanopores. Eur Phys J E Soft Matter 2024; 47:15. [PMID: 38372943 DOI: 10.1140/epje/s10189-024-00408-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/25/2024] [Indexed: 02/20/2024]
Abstract
We determine the local charge dynamics of a [Formula: see text] electrolyte embedded in a varying-section channel. By means of an expansion based on the length scale separation between the axial and transverse direction of the channel, we derive closed formulas for the local excess charge for both, dielectric and conducting walls, in 2D (planar geometry) as well as in 3D (cylindrical geometry). Our results show that, even at equilibrium, the local charge electroneutrality is broken whenever the section of the channel is not homogeneous for both dielectric and conducting walls as well as for 2D and 3D channels. Interestingly, even within our expansion, the local excess charge in the fluid can be comparable to the net charge on the walls. We critically discuss the onset of such local electroneutrality breakdown in particular with respect to the correction that it induces on the effective free energy profile experienced by tracer ions.
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Affiliation(s)
- Paolo Malgaretti
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Erlangen, Germany.
| | - Ignacio Pagonabarraga
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franqués 1, 08028, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Jens Harting
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Erlangen, Germany
- Department of Chemical and Biological Engineering and Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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23
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Döbel T, Schäkel K. Transcriptional landscape of macrophages in cutaneous graft-versus-host disease. Br J Dermatol 2024; 190:298. [PMID: 38014744 DOI: 10.1093/bjd/ljad458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/08/2023] [Indexed: 11/29/2023]
Abstract
We are submitting a comment on a study authored by: J. Strobel, L. M. Gail, L. Krecu, S. Madad, L. Kleissl, L. Unterluggauer, A. Redl, K. Brazdilova, S. Saluzzo, P. Wohlfarth, H. A. Knaus, M. Mitterbauer, W. Rabitsch, M. Haniffa and G. Stary, "Diverse macrophage populations contribute to distinct manifestations of human cutaneous graft-versus-host disease," British Journal of Dermatology, 2023.
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Affiliation(s)
- Thomas Döbel
- Department of Dermatology, University Hospital, Heidelberg,Germany
| | - Knut Schäkel
- Department of Dermatology, University Hospital, Heidelberg,Germany
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24
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Heldmann M, Rinckens C, Brüggemann N, Al-Khaled M, Münte TF. Creative thinking and cognitive estimation in Parkinson's disease. Neurol Res Pract 2024; 6:9. [PMID: 38355739 PMCID: PMC10868033 DOI: 10.1186/s42466-023-00304-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/16/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Patients with Parkinson's disease (PD) have been reported to exhibit unusual bouts of creativity (e.g., painting, writing), in particular in the context of treatment with dopaminergic agents. Here we investigated divergent and convergent thinking thought to underlie creativity. In addition we assessed cognitive estimation. METHOD Twenty PD patients and 20 matched healthy control participants were subjected to the Guilford Alternate Uses task (divergent thinking), the remote associates task (convergent thinking) and two tests of cognitive estimation. RESULTS No group differences were found for the convergent thinking task, while the Guilford Alternate Uses task revealed a decreased number of correct responses and a reduced originality for PD patients. Originality in PD was correlated to total daily dose of dopaminergic medication. Moreover, both tasks of cognitive estimation showed an impairment in PD. CONCLUSION Only minor effects were found for psychometric indices of subprocesses of creative thinking, while estimation, relying on executive functioning, is impaired in PD. We suggest to take a product oriented view of creativity in further research on altered creative processes in PD.
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Affiliation(s)
- Marcus Heldmann
- Department of Neurology, University of Lübeck, Lübeck, Germany
- Center for Brain, Behavior and Metabolism, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Celia Rinckens
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Norbert Brüggemann
- Department of Neurology, University of Lübeck, Lübeck, Germany
- Center for Brain, Behavior and Metabolism, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | | | - Thomas F Münte
- Center for Brain, Behavior and Metabolism, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
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25
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Zenthöfer A, Ilani A, Schmitt C, Rammelsberg P, Hetzler S, Rues S. Biaxial flexural strength of 3D-printed 3Y-TZP zirconia using a novel ceramic printer. Clin Oral Investig 2024; 28:145. [PMID: 38351386 PMCID: PMC10864574 DOI: 10.1007/s00784-024-05533-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
OBJECTIVES To compare the strength and reliability of 3D-printed 3Y-TZP zirconia manufactured with various printing orientations and staining. MATERIALS AND METHODS A total of one-hundred cylindrical zirconia specimens were designed and fabricated using 3D printing and processed according to ISO 6872 standards. Of these specimens, 80 were 3D printed using the new ZIPRO-D (ZD) 3D ceramic printer. In this ZD group, 60 specimens were printed in a vertical orientation and were either stained after debinding (ZD1, x-orientation, n = 20) or not stained (ZD2, x-orientation, n = 20; ZD3, y-orientation, n = 20) and the remaining 20 specimens out of n = 80 were printed in a horizontal orientation (ZD4). Further 20 specimens out of the entire sample N = 100 were printed vertically with the CeraFab7500 3D ceramic printer (LC). All completed specimens were loaded until fracture using a universal testing machine. Biaxial flexural strengths and Weibull parameters were computed for the ZD groups and for the LC group. Group and sub-group effects were evaluated using Welch ANOVA (alpha = 0.05). RESULTS The mean (standard deviation, SD) biaxial flexural strengths of vertically oriented ZD samples with (ZD1) and without (ZD2/ZD3) staining were 811 (197) and 850 (152) MPa, respectively (p > 0.05). The ZD4 (horizontally printed), 1107 (144) MPa, and LC (1238 (327)) MPa samples had higher mean (SD) flexural strengths than the ZD1-3 specimens. No difference was observed between the ZD4 and LC group (p > 0.05). Weibull moduli were between m = 4.6 (ZD1) and 9.1 (ZD4) in the ZD group and m = 3.5 in the LC group. CONCLUSIONS All tested 3D-printed zirconia specimens exceeded the flexural strengths required for class 5 restorations according to ISO 6872 standards. While the flexural strengths of zirconia printed using the novel ZD device in the vertical orientation are lower than those of zirconia printed using the LC printer, the ZD printer shows at least comparable reliability. CLINICAL RELEVANCE 3D-printing of zirconia is a new technology in dental application. Based on the presented strengths values, clinical application of 3D-printed zirconia for fixed dental protheses can be recommended.
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Affiliation(s)
- Andreas Zenthöfer
- Department of Prosthodontics, University Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany.
| | - Ali Ilani
- Department of Prosthodontics, University Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
| | - Clemens Schmitt
- Department of Prosthodontics, University Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
| | - Peter Rammelsberg
- Department of Prosthodontics, University Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
| | - Sebastian Hetzler
- Department of Prosthodontics, University Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
| | - Stefan Rues
- Department of Prosthodontics, University Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
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26
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Tolentino-Castro JW, Schroeger A, Cañal-Bruland R, Raab M. Increasing auditory intensity enhances temporal but deteriorates spatial accuracy in a virtual interception task. Exp Brain Res 2024:10.1007/s00221-024-06787-x. [PMID: 38334793 DOI: 10.1007/s00221-024-06787-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/15/2024] [Indexed: 02/10/2024]
Abstract
Humans are quite accurate and precise in interception performance. So far, it is still unclear what role auditory information plays in spatiotemporal accuracy and consistency during interception. In the current study, interception performance was measured as the spatiotemporal accuracy and consistency of when and where a virtual ball was intercepted on a visible line displayed on a screen based on auditory information alone. We predicted that participants would more accurately indicate when the ball would cross a target line than where it would cross the line, because human hearing is particularly sensitive to temporal parameters. In a within-subject design, we manipulated auditory intensity (52, 61, 70, 79, 88 dB) using a sound stimulus programmed to be perceived over the screen in an inverted C-shape trajectory. Results showed that the louder the sound, the better was temporal accuracy, but the worse was spatial accuracy. We argue that louder sounds increased attention toward auditory information when performing interception judgments. How balls are intercepted and practically how intensity of sound may add to temporal accuracy and consistency is discussed from a theoretical perspective of modality-specific interception behavior.
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Affiliation(s)
- J Walter Tolentino-Castro
- Department of Performance Psychology, Institute of Psychology, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany
| | - Anna Schroeger
- Department for General Psychology, Justus Liebig University Giessen, Giessen, Germany
| | - Rouwen Cañal-Bruland
- Department for the Psychology of Human Movement and Sport, Institute of Sport Science, Friedrich Schiller University Jena, Jena, Germany
| | - Markus Raab
- Department of Performance Psychology, Institute of Psychology, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany.
- School of Applied Sciences, London South Bank University, London, England.
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27
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Brocks C, Das CK, Duan J, Yadav S, Apfel UP, Ghosh S, Hofmann E, Winkler M, Engelbrecht V, Schäfer LV, Happe T. A Dynamic Water Channel Affects O 2 Stability in [FeFe]-Hydrogenases. ChemSusChem 2024; 17:e202301365. [PMID: 37830175 DOI: 10.1002/cssc.202301365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/14/2023]
Abstract
[FeFe]-hydrogenases are capable of reducing protons at a high rate. However, molecular oxygen (O2 ) induces the degradation of their catalytic cofactor, the H-cluster, which consists of a cubane [4Fe4S] subcluster (4FeH ) and a unique diiron moiety (2FeH ). Previous attempts to prevent O2 -induced damage have focused on enhancing the protein's sieving effect for O2 by blocking the hydrophobic gas channels that connect the protein surface and the 2FeH . In this study, we aimed to block an O2 diffusion pathway and shield 4FeH instead. Molecular dynamics (MD) simulations identified a novel water channel (WH ) surrounding the H-cluster. As this hydrophilic path may be accessible for O2 molecules we applied site-directed mutagenesis targeting amino acids along WH in proximity to 4FeH to block O2 diffusion. Protein film electrochemistry experiments demonstrate increased O2 stabilities for variants G302S and S357T, and MD simulations based on high-resolution crystal structures confirmed an enhanced local sieving effect for O2 in the environment of the 4FeH in both cases. The results strongly suggest that, in wild type proteins, O2 diffuses from the 4FeH to the 2FeH . These results reveal new strategies for improving the O2 stability of [FeFe]-hydrogenases by focusing on the O2 diffusion network near the active site.
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Affiliation(s)
- Claudia Brocks
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Chandan K Das
- Faculty of Chemistry and Biochemistry, Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Jifu Duan
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Shanika Yadav
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Ulf-Peter Apfel
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Subhasri Ghosh
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Eckhard Hofmann
- Faculty of Biology and Biotechnology, X-ray structure analysis of proteins, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Martin Winkler
- Electrobiotechnology, TUM Campus Straubing, Schulgasse 22, Straubing, 94315, Germany
| | - Vera Engelbrecht
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Lars V Schäfer
- Faculty of Chemistry and Biochemistry, Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Thomas Happe
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
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28
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Huang X, Xiong R, Hao C, Beck P, Sa B, Wiebe J, Wiesendanger R. 2D Lateral Heterojunction Arrays with Tailored Interface Band Bending. Adv Mater 2024:e2308007. [PMID: 38315969 DOI: 10.1002/adma.202308007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/24/2023] [Indexed: 02/07/2024]
Abstract
Two-dimensional (2D) lateral heterojunction arrays, characterized by well-defined electronic interfaces, hold significant promise for advancing next-generation electronic devices. Despite this potential, the efficient synthesis of high-density lateral heterojunctions with tunable interfacial band alignment remains a challenging. Here, a novel strategy is reported for the fabrication of lateral heterojunction arrays between monolayer Si2 Te2 grown on Sb2 Te3 (ML-Si2 Te2 @Sb2 Te3 ) and one-quintuple-layer Sb2 Te3 grown on monolayer Si2 Te2 (1QL-Sb2 Te3 @ML-Si2 Te2 ) on a p-doped Sb2 Te3 substrate. The site-specific formation of numerous periodically arranged 2D ML-Si2 Te2 @Sb2 Te3 /1QL-Sb2 Te3 @ML-Si2 Te2 lateral heterojunctions is realized solely through three epitaxial growth steps of thick-Sb2 Te3 , ML-Si2 Te2 , and 1QL-Sb2 Te3 films, sequentially. More importantly, the precisely engineering of the interfacial band alignment is realized, by manipulating the substrate's p-doping effect with lateral spatial dependency, on each ML-Si2 Te2 @Sb2 Te3 /1QL-Sb2 Te3 @ML-Si2 Te2 junction. Atomically sharp interfaces of the junctions with continuous lattices are observed by scanning tunneling microscopy. Scanning tunneling spectroscopy measurements directly reveal the tailored type-II band bending at the interface. This reported strategy opens avenues for advancing lateral epitaxy technology, facilitating practical applications of 2D in-plane heterojunctions.
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Affiliation(s)
- Xiaochun Huang
- Department of Physics, University of Hamburg, D-20355, Hamburg, Germany
| | - Rui Xiong
- Multiscale Computational Materials Facility & Materials Genome Institute, School of Materials Science and Engineering, Fuzhou University, Fuzhou, 350108, P. R. China
| | - Chunxue Hao
- Department of Physics, University of Hamburg, D-20355, Hamburg, Germany
| | - Philip Beck
- Department of Physics, University of Hamburg, D-20355, Hamburg, Germany
| | - Baisheng Sa
- Multiscale Computational Materials Facility & Materials Genome Institute, School of Materials Science and Engineering, Fuzhou University, Fuzhou, 350108, P. R. China
| | - Jens Wiebe
- Department of Physics, University of Hamburg, D-20355, Hamburg, Germany
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29
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Christophel T, Weber S, Yan C, Stopak L, Hetzer S, Haynes JD. Nonfrontal Control of Working Memory. J Cogn Neurosci 2024:1-11. [PMID: 38319895 DOI: 10.1162/jocn_a_02127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Items held in visual working memory can be quickly updated, replaced, removed, and even manipulated in accordance with current behavioral goals. Here, we use multivariate pattern analyses to identify the patterns of neuronal activity that realize the executive control processes supervising these flexible stores. We find that portions of the middle temporal gyrus and the intraparietal sulcus represent what item is cued for continued memorization independently of representations of the item itself. Importantly, this selection-specific activity could not be explained by sensory representations of the cue and is only present when control is exerted. Our results suggest that the selection of memorized items might be controlled in a distributed and decentralized fashion. This evidence provides an alternative perspective to the notion of "domain general" central executive control over memory function.
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Affiliation(s)
| | - Simon Weber
- Berlin Institute of Health
- Humboldt Universität, Berlin, Germany
| | | | | | | | - John-Dylan Haynes
- Berlin Institute of Health
- Humboldt Universität, Berlin, Germany
- Technische Universität Dresden
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30
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Chia-Gil A, Floege J, Stamellou E, Moeller MJ. Perihilar FSGS lesions originate from flat parietal epithelial cells. J Nephrol 2024:10.1007/s40620-024-01886-y. [PMID: 38300433 DOI: 10.1007/s40620-024-01886-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/01/2024] [Indexed: 02/02/2024]
Abstract
Graphical Abstract
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Affiliation(s)
- Arnaldo Chia-Gil
- Division of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Jürgen Floege
- Division of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Eleni Stamellou
- Division of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.
- Department of Nephrology, University Hospital of Ioannina, Ioannina, Greece.
| | - Marcus J Moeller
- Division of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
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31
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Lüer L, Wang R, Liu C, Dube H, Heumüller T, Hauch J, Brabec CJ. Maximizing Performance and Stability of Organic Solar Cells at Low Driving Force for Charge Separation. Adv Sci (Weinh) 2024; 11:e2305948. [PMID: 38039433 PMCID: PMC10853714 DOI: 10.1002/advs.202305948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/19/2023] [Indexed: 12/03/2023]
Abstract
Thanks to the development of novel electron acceptor materials, the power conversion efficiencies (PCE) of organic photovoltaic (OPV) devices are now approaching 20%. Further improvement of PCE is complicated by the need for a driving force to split strongly bound excitons into free charges, causing voltage losses. This review discusses recent approaches to finding efficient OPV systems with minimal driving force, combining near unity quantum efficiency (maximum short circuit currents) with optimal energy efficiency (maximum open circuit voltages). The authors discuss apparently contradicting results on the amount of exciton binding in recent literature, and approaches to harmonize the findings. A comprehensive view is then presented on motifs providing a driving force for charge separation, namely hybridization at the donor:acceptor interface and polarization effects in the bulk, of which quadrupole moments (electrostatics) play a leading role. Apart from controlling the energies of the involved states, these motifs also control the dynamics of recombination processes, which are essential to avoid voltage and fill factor losses. Importantly, all motifs are shown to depend on both molecular structure and process conditions. The resulting high dimensional search space advocates for high throughput (HT) workflows. The final part of the review presents recent HT studies finding consolidated structure-property relationships in OPV films and devices from various deposition methods, from research to industrial upscaling.
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Affiliation(s)
- Larry Lüer
- Institute of Materials for Electronics and Energy Technology (i‐MEET)Friedrich‐Alexander‐Universität Erlangen‐NürnbergMartensstrasse 791058ErlangenGermany
| | - Rong Wang
- Institute of Materials for Electronics and Energy Technology (i‐MEET)Friedrich‐Alexander‐Universität Erlangen‐NürnbergMartensstrasse 791058ErlangenGermany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT)Paul‐Gordan‐Straße 691052ErlangenGermany
| | - Chao Liu
- Institute of Materials for Electronics and Energy Technology (i‐MEET)Friedrich‐Alexander‐Universität Erlangen‐NürnbergMartensstrasse 791058ErlangenGermany
| | - Henry Dube
- Department Chemistry and PharmacyFriedrich‐Alexander‐Universität Erlangen‐NürnbergNikolaus‐Fiebiger‐Straße 1091058ErlangenGermany
| | - Thomas Heumüller
- Institute of Materials for Electronics and Energy Technology (i‐MEET)Friedrich‐Alexander‐Universität Erlangen‐NürnbergMartensstrasse 791058ErlangenGermany
| | - Jens Hauch
- Helmholtz‐Institute Erlangen‐Nürnberg (HI‐ERN)Immerwahrstraße 291058ErlangenGermany
| | - Christoph J. Brabec
- Institute of Materials for Electronics and Energy Technology (i‐MEET)Friedrich‐Alexander‐Universität Erlangen‐NürnbergMartensstrasse 791058ErlangenGermany
- Helmholtz‐Institute Erlangen‐Nürnberg (HI‐ERN)Immerwahrstraße 291058ErlangenGermany
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Immler F, Schneider T, Kovermann M. Targeted Preparation and NMR Spectroscopic Characterization of Lys11-Linked Ubiquitin Trimers. Chembiochem 2024; 25:e202300670. [PMID: 37983597 DOI: 10.1002/cbic.202300670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023]
Abstract
Ubiquitylation refers to the attachment of mono- or poly-ubiquitin molecules to a substrate protein. To shield ubiquitin chains against potential hydrolysis, a facile, click-chemistry based approach was recently established for the generation of site-specifically conjugated ubiquitin dimers relying on triazole-linkage. Here, the preparation of such ubiquitin chains was advanced by the generation of homotypic Lys11-linked ubiquitin trimers considering an isotopic labeling scheme in a moiety-wise manner. The structural and dynamical impact on the ubiquitin unit at proximal, central, or distal position that is potentially invoked by the respective other two moieties was systematically probed by heteronuclear high-resolution NMR spectroscopic approaches. As a result, conjugating a third ubiquitin moiety to the proximal or distal site of a ubiquitin dimer does not alter structural and dynamical characteristics as it has been seen for ubiquitin dimers. This observation suggests that recognition of a homotypically assembled ubiquitin chain by a potential substrate is primarily done by screening the length of a ubiquitin chain rather than relying on subtle changes in structure or dynamic properties of single ubiquitin moieties composing the chain.
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Affiliation(s)
- Fabian Immler
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
| | - Tobias Schneider
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
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Gebler R, Lehmann M, Löwe M, Gruhl M, Wolfien M, Goldammer M, Bathelt F, Karschau J, Hasselberg A, Bierbaum V, Lange T, Polotzek K, Held HC, Albrecht M, Schmitt J, Sedlmayr M. Supporting regional pandemic management by enabling self-service reporting-A case report. PLoS One 2024; 19:e0297039. [PMID: 38295046 PMCID: PMC10829976 DOI: 10.1371/journal.pone.0297039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/26/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic revealed a need for better collaboration among research, care, and management in Germany as well as globally. Initially, there was a high demand for broad data collection across Germany, but as the pandemic evolved, localized data became increasingly necessary. Customized dashboards and tools were rapidly developed to provide timely and accurate information. In Saxony, the DISPENSE project was created to predict short-term hospital bed capacity demands, and while it was successful, continuous adjustments and the initial monolithic system architecture of the application made it difficult to customize and scale. METHODS To analyze the current state of the DISPENSE tool, we conducted an in-depth analysis of the data processing steps and identified data flows underlying users' metrics and dashboards. We also conducted a workshop to understand the different views and constraints of specific user groups, and brought together and clustered the information according to content-related service areas to determine functionality-related service groups. Based on this analysis, we developed a concept for the system architecture, modularized the main services by assigning specialized applications and integrated them into the existing system, allowing for self-service reporting and evaluation of the expert groups' needs. RESULTS We analyzed the applications' dataflow and identified specific user groups. The functionalities of the monolithic application were divided into specific service groups for data processing, data storage, predictions, content visualization, and user management. After composition and implementation, we evaluated the new system architecture against the initial requirements by enabling self-service reporting to the users. DISCUSSION By modularizing the monolithic application and creating a more flexible system, the challenges of rapidly changing requirements, growing need for information, and high administrative efforts were addressed. CONCLUSION We demonstrated an improved adaptation towards the needs of various user groups, increased efficiency, and reduced burden on administrators, while also enabling self-service functionalities and specialization of single applications on individual service groups.
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Affiliation(s)
- Richard Gebler
- Institute for Medical Informatics and Biometry, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Martin Lehmann
- Institute for Medical Informatics and Biometry, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Maik Löwe
- Institute for Medical Informatics and Biometry, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Mirko Gruhl
- Institute for Medical Informatics and Biometry, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Markus Wolfien
- Institute for Medical Informatics and Biometry, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Miriam Goldammer
- Institute for Medical Informatics and Biometry, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Franziska Bathelt
- Institute for Medical Informatics and Biometry, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
- Thiem-Research GmbH at Carl-Thiem-Clinic, Cottbus, Germany
| | - Jens Karschau
- Center for Evidence-Based Healthcare, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Andreas Hasselberg
- Center for Evidence-Based Healthcare, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Veronika Bierbaum
- Center for Evidence-Based Healthcare, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Toni Lange
- Center for Evidence-Based Healthcare, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Katja Polotzek
- Center for Evidence-Based Healthcare, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Hanns-Christoph Held
- Clinic and Polyclinic for Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | | | - Jochen Schmitt
- Center for Evidence-Based Healthcare, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Martin Sedlmayr
- Institute for Medical Informatics and Biometry, University Hospital Dresden and Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
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Schneider N, Hermann PC, Eiseler T, Seufferlein T. Emerging Roles of Small Extracellular Vesicles in Gastrointestinal Cancer Research and Therapy. Cancers (Basel) 2024; 16:567. [PMID: 38339318 PMCID: PMC10854789 DOI: 10.3390/cancers16030567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Discovered in the late eighties, sEVs are small extracellular nanovesicles (30-150 nm diameter) that gained increasing attention due to their profound roles in cancer, immunology, and therapeutic approaches. They were initially described as cellular waste bins; however, in recent years, sEVs have become known as important mediators of intercellular communication. They are secreted from cells in substantial amounts and exert their influence on recipient cells by signaling through cell surface receptors or transferring cargos, such as proteins, RNAs, miRNAs, or lipids. A key role of sEVs in cancer is immune modulation, as well as pro-invasive signaling and formation of pre-metastatic niches. sEVs are ideal biomarker platforms, and can be engineered as drug carriers or anti-cancer vaccines. Thus, sEVs further provide novel avenues for cancer diagnosis and treatment. This review will focus on the role of sEVs in GI-oncology and delineate their functions in cancer progression, diagnosis, and therapeutic use.
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Affiliation(s)
- Nora Schneider
- Department for Internal Medicine 1, University Clinic Ulm, 89081 Ulm, Germany; (P.C.H.); (T.S.)
| | | | - Tim Eiseler
- Correspondence: (N.S.); (T.E.); Tel.: +49-731-500-44678 (N.S.); +49-731-500-44523 (T.E.)
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Gessler L, Huraskin D, Jian Y, Eiber N, Hu Z, Prószyński T, Hashemolhosseini S. The YAP1/TAZ-TEAD transcriptional network regulates gene expression at neuromuscular junctions in skeletal muscle fibers. Nucleic Acids Res 2024; 52:600-624. [PMID: 38048326 PMCID: PMC10810223 DOI: 10.1093/nar/gkad1124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
We examined YAP1/TAZ-TEAD signaling pathway activity at neuromuscular junctions (NMJs) of skeletal muscle fibers in adult mice. Our investigations revealed that muscle-specific knockouts of Yap1 or Taz, or both, demonstrate that these transcriptional coactivators regulate synaptic gene expression, the number and morphology of NMJs, and synaptic nuclei. Yap1 or Taz single knockout mice display reduced grip strength, fragmentation of NMJs, and accumulation of synaptic nuclei. Yap1/Taz muscle-specific double knockout mice do not survive beyond birth and possess almost no NMJs, the few detectable show severely impaired morphology and are organized in widened endplate bands; and with motor nerve endings being mostly absent. Myogenic gene expression is significantly impaired in the denervated muscles of knockout mice. We found that Tead1 and Tead4 transcription rates were increased upon incubation of control primary myotubes with AGRN-conditioned medium. Reduced AGRN-dependent acetylcholine receptor clustering and synaptic gene transcription were observed in differentiated primary Tead1 and Tead4 knockout myotubes. In silico analysis of previously reported genomic occupancy sites of TEAD1/4 revealed evolutionary conserved regions of potential TEAD binding motifs in key synaptic genes, the relevance of which was functionally confirmed by reporter assays. Collectively, our data suggest a role for YAP1/TAZ-TEAD1/TEAD4 signaling, particularly through TAZ-TEAD4, in regulating synaptic gene expression and acetylcholine receptor clustering at NMJs.
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Affiliation(s)
- Lea Gessler
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Danyil Huraskin
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Yongzhi Jian
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Nane Eiber
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Zhaoyong Hu
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Tomasz J Prószyński
- Łukasiewicz Research Network-PORT Polish Center for Technology Development, Wrocław, Poland
| | - Said Hashemolhosseini
- Institute of Biochemistry, Medical Faculty, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
- Muscle Research Center, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany
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Küderle A, Ullrich M, Roth N, Ollenschläger M, Ibrahim AA, Moradi H, Richer R, Seifer AK, Zürl M, Sîmpetru RC, Herzer L, Prossel D, Kluge F, Eskofier BM. Gaitmap-An Open Ecosystem for IMU-Based Human Gait Analysis and Algorithm Benchmarking. IEEE Open J Eng Med Biol 2024; 5:163-172. [PMID: 38487091 PMCID: PMC10939318 DOI: 10.1109/ojemb.2024.3356791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/15/2023] [Accepted: 01/17/2024] [Indexed: 03/17/2024] Open
Abstract
Goal: Gait analysis using inertial measurement units (IMUs) has emerged as a promising method for monitoring movement disorders. However, the lack of public data and easy-to-use open-source algorithms hinders method comparison and clinical application development. To address these challenges, this publication introduces the gaitmap ecosystem, a comprehensive set of open source Python packages for gait analysis using foot-worn IMUs. Methods: This initial release includes over 20 state-of-the-art algorithms, enables easy access to seven datasets, and provides eight benchmark challenges with reference implementations. Together with its extensive documentation and tooling, it enables rapid development and validation of new algorithm and provides a foundation for novel clinical applications. Conclusion: The published software projects represent a pioneering effort to establish an open-source ecosystem for IMU-based gait analysis. We believe that this work can democratize the access to high-quality algorithm and serve as a driver for open and reproducible research in the field of human gait analysis and beyond.
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Affiliation(s)
- Arne Küderle
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Martin Ullrich
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Nils Roth
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Malte Ollenschläger
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Alzhraa A. Ibrahim
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
- Department of Molecular NeurologyFAU Erlangen91054ErlangenGermany
- Computer Science Department, Faculty of Computers and InformationAssiut UniversityAssiut Governorate71515Egypt
| | - Hamid Moradi
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Robert Richer
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Ann-Kristin Seifer
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Matthias Zürl
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Raul C. Sîmpetru
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Liv Herzer
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Dominik Prossel
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Felix Kluge
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
| | - Bjoern M. Eskofier
- Machine Learning and Data Analytics LabFriedrich-Alexander Universität Erlangen-Nürnberg (FAU)91054ErlangenGermany
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37
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Gavrilović S, Brüggenthies GA, Weck JM, Heuer-Jungemann A, Schwille P. Protein-Assisted Large-Scale Assembly and Differential Patterning of DNA Origami Lattices. Small 2024:e2309680. [PMID: 38229553 DOI: 10.1002/smll.202309680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/20/2023] [Indexed: 01/18/2024]
Abstract
Nanofabrication has experienced a big boost with the invention of DNA origami, enabling the production and assembly of complex nanoscale structures that may be able to unlock fully new functionalities in biology and beyond. The remarkable precision with which these structures can be designed and produced is, however, not yet matched by their assembly dynamics, which can be extremely slow, particularly when attached to biological templates, such as membranes. Here, the rapid and controlled formation of DNA origami lattices on the scale of hundreds of micrometers in as little as 30 minutes is demonstrated, utilizing active patterning by the E.coli Min protein system, thereby yielding a remarkable improvement over conventional passive diffusion-based assembly methods. Various patterns, including spots, inverse spots, mazes, and meshes can be produced at different scales, tailored through the shape and density of the assembled structures. The differential positioning accomplished by Min-induced diffusiophoresis even allows the introduction of "pseudo-colors", i.e., complex core-shell patterns, by simultaneously patterning different DNA origami species. Beyond the targeted functionalization of biological surfaces, this approach may also be promising for applications in plasmonics, catalysis, and molecular sensing.
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Affiliation(s)
- Svetozar Gavrilović
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | | | - Johann Moritz Weck
- Research Group DNA Hybridnanomaterials, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Amelie Heuer-Jungemann
- Research Group DNA Hybridnanomaterials, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
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Abylgazina L, Senkovska I, Engemann R, Bönisch N, Gorelik TE, Bachetzky C, Kaiser U, Brunner E, Kaskel S. Chemoselectivity Inversion of Responsive Metal-Organic Frameworks by Particle Size Tuning in the Micrometer Regime. Small 2024:e2307285. [PMID: 38225688 DOI: 10.1002/smll.202307285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/30/2023] [Indexed: 01/17/2024]
Abstract
Gated adsorption is one of the unique physical properties of flexible metal-organic frameworks with high application potential in selective adsorption and sensing of molecules. Despite recent studies that have provided some guidelines in understanding and designing structural flexibility for controlling gate opening by chemical modification of the secondary building units, currently, there is no established strategy to design a flexible MOF showing selective gated adsorption for a specific guest molecule. In a present contribution it is demonstrated for the first time, that the selectivity in the gate opening of a particular compound can be tuned, changed, and even reversed using particle size engineering DUT-8(Zn) ([Zn2 (2,6-ndc)2 (dabco)]n , 2,6-ndc = 2,6-naphthalenedicarboxylate, dabco = 1,4-diazabicyclo-[2.2.2]-octane, DUT = Dresden University of Technology) experiences phase transition from open (op) to closed (cp) pore phase upon removal of solvent from the pores. Microcrystals show selective reopening in the presence of dichloromethane (DCM) over alcohols. Crystal downsizing to micron size unexpectedly reverses the gate opening selectivity, causing DUT-8(Zn) to open its nanosized pores for alcohols but suppressing the responsivity toward DCM.
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Affiliation(s)
- Leila Abylgazina
- Technische Universität Dresden, Bergstr. 66, 01069, Dresden, Germany
| | - Irena Senkovska
- Technische Universität Dresden, Bergstr. 66, 01069, Dresden, Germany
| | - Richard Engemann
- Technische Universität Dresden, Bergstr. 66, 01069, Dresden, Germany
| | - Nadine Bönisch
- Technische Universität Dresden, Bergstr. 66, 01069, Dresden, Germany
| | - Tatiana E Gorelik
- Electron Microscopy Group of Materials Science (EMMS), Central Facility for Electron Microscopy, Universität Ulm, Oberberghof 3/1, 89081, Ulm, Germany
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Department of Pharmacy, Saarland University, Universitätscampus E8 1, 66123, Saarbrücken, Germany
| | | | - Ute Kaiser
- Electron Microscopy Group of Materials Science (EMMS), Central Facility for Electron Microscopy, Universität Ulm, Oberberghof 3/1, 89081, Ulm, Germany
| | - Eike Brunner
- Technische Universität Dresden, Bergstr. 66, 01069, Dresden, Germany
| | - Stefan Kaskel
- Technische Universität Dresden, Bergstr. 66, 01069, Dresden, Germany
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Ugrina M, Burkhart I, Müller D, Schwalbe H, Schwierz N. RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy. Nucleic Acids Res 2024; 52:87-100. [PMID: 37986217 PMCID: PMC10783511 DOI: 10.1093/nar/gkad1065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 09/25/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023] Open
Abstract
The kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes (rG4s). Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates are stabilized by transient Hoogsteen interactions. Each pathway passes through two on-pathway intermediates. We hypothesize that conformational entropy is a hallmark of rG4 folding. Conformational entropy leads to the observed branched multi-pathway folding process for TERRA25. We corroborate this hypothesis by presenting the free energy landscapes and folding pathways of four rG4 systems with varying loop length.
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Affiliation(s)
- Marijana Ugrina
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Ines Burkhart
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
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40
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Schwarzl T, Sahadevan S, Lang B, Miladi M, Backofen R, Huber W, Hentze MW, Tartaglia GG. Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq. Nucleic Acids Res 2024; 52:e1. [PMID: 37962298 PMCID: PMC10783507 DOI: 10.1093/nar/gkad998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 09/04/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Enhanced crosslinking and immunoprecipitation (eCLIP) sequencing is a method for transcriptome-wide detection of binding sites of RNA-binding proteins (RBPs). However, identified crosslink sites can deviate from experimentally established functional elements of even well-studied RBPs. Current peak-calling strategies result in low replication and high false positive rates. Here, we present the R/Bioconductor package DEWSeq that makes use of replicate information and size-matched input controls. We benchmarked DEWSeq on 107 RBPs for which both eCLIP data and RNA sequence motifs are available and were able to more than double the number of motif-containing binding regions relative to standard eCLIP processing. The improvement not only relates to the number of binding sites (3.1-fold with known motifs for RBFOX2), but also their subcellular localization (1.9-fold of mitochondrial genes for FASTKD2) and structural targets (2.2-fold increase of stem-loop regions for SLBP. On several orthogonal CLIP-seq datasets, DEWSeq recovers a larger number of motif-containing binding sites (3.3-fold). DEWSeq is a well-documented R/Bioconductor package, scalable to adequate numbers of replicates, and tends to substantially increase the proportion and total number of RBP binding sites containing biologically relevant features.
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Affiliation(s)
- Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Sudeep Sahadevan
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Benjamin Lang
- Department of Structural Biology and Center of Excellence for Data-Driven Discovery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79098 Freiburg im Breisgau, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79098 Freiburg im Breisgau, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Gian Gaetano Tartaglia
- Center for Life Nano & Neuroscience, Italian Institute of Technology, 00161 Rome, Italy and Department of Biology, Sapienza University of Rome, 00185 Rome, Italy
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41
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Burgert BB, Sun X, Hauser A, Wingering PMR, Breher F, Roesky PW. Bi- and tridentate coordination behaviour of a novel bis(phosphinimino)methanide ligand. Chem Asian J 2024:e202301084. [PMID: 38197668 DOI: 10.1002/asia.202301084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/11/2024]
Abstract
Herein, we report the synthesis of a novel ferrocenyl-functionalized bis(phosphinimino)methane ligand (CH2 (PPh2 NFc)2 ). Deprotonation of CH2 (PPh2 NFc)2 with KN(SiMe3 )2 gave the dimeric species [K{CH(PPh2 NFc)2 }]2 , which was further reacted with ECl2 (E=Ge, Sn) to yield the tetrylene compounds [{CH(PPh2 NFc)2 }ECl]. The ligand and the resulting tetrylenes were examined for their electrochemical properties with the aid of cyclic voltammetry. Furthermore, the reaction of the tetrylenes [{CH(PPh2 NFc)2 }ECl] with [AuC6 F5 (tht)] resulted in the bimetallic complexes [{(AuC6 F5 )CH(PPh2 NFc)2 }ECl] with an unusual Au coordination on the ligand backbone.
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Affiliation(s)
- Bastian B Burgert
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
| | - Xiaofei Sun
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
| | - Adrian Hauser
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
| | - Perrine M R Wingering
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
| | - Frank Breher
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
| | - Peter W Roesky
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
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42
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Flotho M, Amand J, Hirsch P, Grandke F, Wyss-Coray T, Keller A, Kern F. ZEBRA: a hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution. Nucleic Acids Res 2024; 52:D1089-D1096. [PMID: 37941147 PMCID: PMC10767845 DOI: 10.1093/nar/gkad990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/02/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023] Open
Abstract
The molecular causes and mechanisms of neurodegenerative diseases remain poorly understood. A growing number of single-cell studies have implicated various neural, glial, and immune cell subtypes to affect the mammalian central nervous system in many age-related disorders. Integrating this body of transcriptomic evidence into a comprehensive and reproducible framework poses several computational challenges. Here, we introduce ZEBRA, a large single-cell and single-nucleus RNA-seq database. ZEBRA integrates and normalizes gene expression and metadata from 33 studies, encompassing 4.2 million human and mouse brain cells sampled from 39 brain regions. It incorporates samples from patients with neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, and Multiple sclerosis, as well as samples from relevant mouse models. We employed scVI, a deep probabilistic auto-encoder model, to integrate the samples and curated both cell and sample metadata for downstream analysis. ZEBRA allows for cell-type and disease-specific markers to be explored and compared between sample conditions and brain regions, a cell composition analysis, and gene-wise feature mappings. Our comprehensive molecular database facilitates the generation of data-driven hypotheses, enhancing our understanding of mammalian brain function during aging and disease. The data sets, along with an interactive database are freely available at https://www.ccb.uni-saarland.de/zebra.
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Affiliation(s)
- Matthias Flotho
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123 Saarbrücken, Germany
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jérémy Amand
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123 Saarbrücken, Germany
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Pascal Hirsch
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Friederike Grandke
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
| | - Andreas Keller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123 Saarbrücken, Germany
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123 Saarbrücken, Germany
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
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43
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Bascón-Cardozo K, Bours A, Manthey G, Durieux G, Dutheil JY, Pruisscher P, Odenthal-Hesse L, Liedvogel M. Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap. Genome Biol Evol 2024; 16:evad233. [PMID: 38198800 PMCID: PMC10781513 DOI: 10.1093/gbe/evad233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack the protein PR domain-containing protein 9, a key determinant of recombination dynamics in most metazoans. Historical recombination maps in birds show an apparent stasis in positioning recombination events. This highly conserved recombination pattern over long timescales may constrain the evolution of recombination in birds. At the same time, extensive variation in recombination rate is observed across the genome and between different species of birds. Here, we characterize the fine-scale historical recombination map of an iconic migratory songbird, the Eurasian blackcap (Sylvia atricapilla), using a linkage disequilibrium-based approach that accounts for population demography. Our results reveal variable recombination rates among and within chromosomes, which associate positively with nucleotide diversity and GC content and negatively with chromosome size. Recombination rates increased significantly at regulatory regions but not necessarily at gene bodies. CpG islands are associated strongly with recombination rates, though their specific position and local DNA methylation patterns likely influence this relationship. The association with retrotransposons varied according to specific family and location. Our results also provide evidence of heterogeneous intrachromosomal conservation of recombination maps between the blackcap and its closest sister taxon, the garden warbler. These findings highlight the considerable variability of recombination rates at different scales and the role of specific genomic features in shaping this variation. This study opens the possibility of further investigating the impact of recombination on specific population-genomic features.
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Affiliation(s)
- Karen Bascón-Cardozo
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Andrea Bours
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Georg Manthey
- Institute of Avian Research “Vogelwarte Helgoland”, Wilhelmshaven 26386, Germany
| | - Gillian Durieux
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Julien Y Dutheil
- Department for Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Peter Pruisscher
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Department of Zoology, Stockholm University, Stockholm SE-106 91, Sweden
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Miriam Liedvogel
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Institute of Avian Research “Vogelwarte Helgoland”, Wilhelmshaven 26386, Germany
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg 26129, Germany
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Hirsch P, Tagirdzhanov A, Kushnareva A, Olkhovskii I, Graf S, Schmartz GP, Hegemann JD, Bozhüyük KAJ, Müller R, Keller A, Gurevich A. ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome. Nucleic Acids Res 2024; 52:D579-D585. [PMID: 37994699 PMCID: PMC10767846 DOI: 10.1093/nar/gkad1086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/18/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.
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Affiliation(s)
- Pascal Hirsch
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Azat Tagirdzhanov
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Aleksandra Kushnareva
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Ilia Olkhovskii
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken 66123, Germany
| | - Simon Graf
- Department of Computer Science, Saarland University, Saarbrücken 66123, Germany
| | - Georges P Schmartz
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Saarbrücken 66123, Germany
| | - Kenan A J Bozhüyük
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Saarbrücken 66123, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Alexey Gurevich
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Computer Science, Saarland University, Saarbrücken 66123, Germany
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45
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Kliem CV, Schaub B. The role of regulatory B cells in immune regulation and childhood allergic asthma. Mol Cell Pediatr 2024; 11:1. [PMID: 38172451 PMCID: PMC10764675 DOI: 10.1186/s40348-023-00174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND As the most common chronic disease in childhood, asthma displays a major public health problem worldwide with the incidence of those affected rising. As there is currently no cure for allergic asthma, it is mandatory to get a better understanding of the underlying molecular mechanism. MAIN BODY By producing IgE antibodies upon allergen contact, B cells play a pivotal role in allergic asthma. Besides that, IL-10-secreting B cell subsets, namely regulatory B cells (Bregs), are reported in mice and humans to play a role in allergic asthma. In humans, several Breg subsets with distinct phenotypic and functional properties are identified among B cells at different maturational and differentiation stages that exert anti-inflammatory functions by expressing several suppressor molecules. Emerging research has focused on the role of Bregs in allergic asthma as well as their role for future diagnostic and preventive strategies. CONCLUSION Knowledge about the exact function of human Bregs in allergic asthma is still very limited. This review aims to summarize the current knowledge on Bregs. We discuss different human Breg subsets, several ways of Breg induction as well as the mechanisms through which they exert immunoregulatory functions, and their role in (childhood) allergic asthma.
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Affiliation(s)
- Caroline Vanessa Kliem
- Pediatric Allergology, Department of Pediatrics, Dr. Von Hauner Children´S Hospital, University Hospital, Lindwurmstraße 4, 80337, LMU, Munich, Germany
| | - Bianca Schaub
- Pediatric Allergology, Department of Pediatrics, Dr. Von Hauner Children´S Hospital, University Hospital, Lindwurmstraße 4, 80337, LMU, Munich, Germany.
- Member of German Center for Lung Research - DZL, LMU, Munich, Germany.
- Member of German Center for Child and Adolescent Health-DZKJ, LMU, Munich, Germany.
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46
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Khodadadi M, Helluy X, Güntürkün O, Behroozi M. Segmented spin-echo echo-planar imaging improves whole-brain BOLD functional MRI in awake pigeon brains. NMR Biomed 2024; 37:e5034. [PMID: 37681398 DOI: 10.1002/nbm.5034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 08/10/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023]
Abstract
Functional magnetic resonance imaging (fMRI) in awake small animals such as pigeons or songbirds opens a new window into the neural fundaments of cognitive behavior. However, high-field fMRI in the avian brain is challenging due to strong local magnetic field inhomogeneities caused by air cavities in the skull. A spoiled gradient-echo fMRI sequence has already been used to map the auditory network in songbirds, but due to susceptibility artifacts only 50% of the whole brain could be recorded. Since whole-brain fMRI coverage is vital to reveal whole-brain networks, an MRI sequence that is less susceptible to these artifacts was required. This was recently achieved in various bird species by using a rapid acquisition with relaxation enhancement (RARE) sequence. Weak blood oxygen level-dependent (BOLD) sensitivity, low temporal resolution, and heat caused by the long train of RF refocusing pulses are the main limits of RARE fMRI at high magnetic fields. To go beyond some of these limitations, we here describe the implementation of a two-segmented spin-echo echo-planar imaging (SE-EPI). The proposed sequence covers the whole brain of awake pigeons. The sequence was applied to investigate the auditory network in awake pigeons and assessed the relative merits of this method in comparison with the single-shot RARE sequence. At the same imaging resolution but with a volume acquisition of 3 s versus 4 s for RARE, the two-segmented SE-EPI provided twice the strength of BOLD activity compared with the single-shot RARE sequence, while the image signal-to-noise ratio (SNR) and in particular the temporal SNR were very similar for the two sequences. In addition, the activation patterns in two-segmented SE-EPI data are more symmetric and larger than single-shot RARE results. Two-segmented SE-EPI represents a valid alternative to the RARE sequence in avian fMRI research since it yields more than twice the BOLD sensitivity per unit of time with much less energy deposition and better temporal resolution, particularly for event-related experiments.
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Affiliation(s)
- Mina Khodadadi
- Department of Biopsychology, Institute of Cognitive Neuroscience, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
- Department of Basic Sciences, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Xavier Helluy
- Department of Biopsychology, Institute of Cognitive Neuroscience, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
- Department of Neurophysiology, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Onur Güntürkün
- Department of Biopsychology, Institute of Cognitive Neuroscience, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
- Research Center One Health Ruhr, Research Alliance Ruhr, Ruhr University Bochum, Bochum, Germany
| | - Mehdi Behroozi
- Department of Biopsychology, Institute of Cognitive Neuroscience, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
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Vernin A, Schrittenlocher S, Matthaei M, Roters S, Siebelmann S, Bachmann B, Schiller P, Cursiefen C, Schlereth SL. Excimer Laser Phototherapeutic Keratectomy for Anterior Corneal Opacification After Descemet Membrane Endothelial Keratoplasty. Cornea 2024; 43:95-104. [PMID: 37772880 DOI: 10.1097/ico.0000000000003396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 08/19/2023] [Indexed: 09/30/2023]
Abstract
PURPOSE The aim of this study was to assess the long-term outcome of excimer laser phototherapeutic keratectomy (PTK) for treating remaining anterior corneal opacities after Descemet membrane endothelial keratoplasty (DMEK). METHODS This cohort study analyzed 67 eyes of 66 patients undergoing PTK in addition to and after DMEK between 2012 and 2021 at the Department of Ophthalmology, University of Cologne. Patients who were treated by PTK after previous DMEK on the same eye were included. The outcome parameters were best corrected visual acuity (BCVA), changes in refraction, endothelial cell density, corneal densitometry, central corneal thickness, and total corneal higher order aberrations. Patients with visual limitations in addition to anterior opacification were analyzed separately for their visual outcome. Eyes with severe visual limitations that have a very limited visual potential were excluded from the study. In addition, patients with not at least 1 postoperative follow-up examination were excluded from the study. RESULTS In this study, 67 eyes of 66 patients met all inclusion criteria. The median follow-up period was 13.1 (quartiles: 4.1; 30.7; interquartile range 26.6) months. The mean (±SD) BCVA improved from (logarithm of the minimum angle of resolution) 0.54 (±0.32) to 0.38 (±0.27) at the first postoperative visit ( P < 0.001) and remained significantly improved at all follow-up examinations compared with preoperative BCVA. Refraction and endothelial cell density did not change significantly after PTK. There was a significant decrease in corneal backscatter in the anterior corneal layer ( P < 0.001), and the total higher order aberration ( P = 0.02) and central corneal thickness were significantly reduced at the most recent postoperative visit ( P < 0.001). No immune reactions were observed. CONCLUSIONS Excimer laser PTK after DMEK for persisting anterior corneal opacities has the potential to significantly improve patients' vision without affecting refractive parameters or endothelial cell density.
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Affiliation(s)
- Alice Vernin
- Department of Ophthalmology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
- Faculty of Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Silvia Schrittenlocher
- Department of Ophthalmology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Mario Matthaei
- Department of Ophthalmology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Sigrid Roters
- Department of Ophthalmology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Sebastian Siebelmann
- Department of Ophthalmology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
- EyeCenter Solingen, Solingen Germany
- Schumpeter School of Health and Economics, University of Wuppertal, Wuppertal, Germany
| | - Björn Bachmann
- Department of Ophthalmology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Petra Schiller
- Faculty of Medicine, Institute of Medical Statistics and Computational Biology, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Claus Cursiefen
- Department of Ophthalmology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
- CECAD, Cluster of Excellence, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; and
- Center of Molecular Medicine Cologne, CMMC, University of Cologne, Cologne, Germany
| | - Simona L Schlereth
- Department of Ophthalmology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
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Du Z, Gupta M, Xu F, Zhang K, Zhang J, Zhou Y, Liu Y, Wang Z, Wrachtrup J, Wong N, Li C, Chu Z. Widefield Diamond Quantum Sensing with Neuromorphic Vision Sensors. Adv Sci (Weinh) 2024; 11:e2304355. [PMID: 37939304 PMCID: PMC10787069 DOI: 10.1002/advs.202304355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/04/2023] [Indexed: 11/10/2023]
Abstract
Despite increasing interest in developing ultrasensitive widefield diamond magnetometry for various applications, achieving high temporal resolution and sensitivity simultaneously remains a key challenge. This is largely due to the transfer and processing of massive amounts of data from the frame-based sensor to capture the widefield fluorescence intensity of spin defects in diamonds. In this study, a neuromorphic vision sensor to encode the changes of fluorescence intensity into spikes in the optically detected magnetic resonance (ODMR) measurements is adopted, closely resembling the operation of the human vision system, which leads to highly compressed data volume and reduced latency. It also results in a vast dynamic range, high temporal resolution, and exceptional signal-to-background ratio. After a thorough theoretical evaluation, the experiment with an off-the-shelf event camera demonstrated a 13× improvement in temporal resolution with comparable precision of detecting ODMR resonance frequencies compared with the state-of-the-art highly specialized frame-based approach. It is successfully deploy this technology in monitoring dynamically modulated laser heating of gold nanoparticles coated on a diamond surface, a recognizably difficult task using existing approaches. The current development provides new insights for high-precision and low-latency widefield quantum sensing, with possibilities for integration with emerging memory devices to realize more intelligent quantum sensors.
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Affiliation(s)
- Zhiyuan Du
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Madhav Gupta
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Feng Xu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Kai Zhang
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, 999077, P. R. China
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, 518000, China
| | - Jiahua Zhang
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Yan Zhou
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, 518000, China
| | - Yiyao Liu
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou, 510006, China
| | - Zhenyu Wang
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou, 510006, China
- Frontier Research Institute for Physics, South China Normal University, Guangzhou, 510006, China
| | - Jörg Wrachtrup
- 3rd Institute of Physics, Research Center SCoPE and IQST, University of Stuttgart, 70569, Stuttgart, Germany
- Max Planck Institute for Solid State Research, 70569, Stuttgart, Germany
| | - Ngai Wong
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Can Li
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Zhiqin Chu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, 999077, P. R. China
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, 999077, P. R. China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Hong Kong, 999077, P. R. China
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49
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Li C, Bhandary R, Marinow A, Bachmann S, Pöppler AC, Binder WH. Stability of Quadruple Hydrogen Bonds in an Ionic Liquid Environment. Macromol Rapid Commun 2024; 45:e2300464. [PMID: 37796474 DOI: 10.1002/marc.202300464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/02/2023] [Indexed: 10/06/2023]
Abstract
Hydrogen bonds (H-bonds) are highly sensitive to the surrounding environments owing to their dipolar nature, with polar solvents kown to significantly weaken H-bonds. Herein, the stability of the H-bonding motif ureidopyrimidinone (UPy) is investigated, embedded into a highly polar polymeric ionic liquid (PIL) consisting of pendant pyrrolidinium bis(trifluoromethylsulfonyl)imide (IL) moieties, to study the influence of such ionic environments on the UPy H-bonds. The content of the surrounding IL is changed by addition of an additional low molecular weight IL to further boost the IL content around the UPy moieties in molar ratios of UPy/IL ranging from 1/4 up to 1/113, thereby promoting the polar microenvironment around the UPy-H-bonds. Variable-temperature solid-state MAS NMR spectroscopy and FT-IR spectroscopy demonstrate that the UPy H-bonds are largely present as (UPy-) dimers, but sensitive to elevated temperatures (>70 °C). Subsequent rheology and DSC studies reveal that the ILs only solvate the polymeric chains but do not interfere with the UPy-dimer H-bonds, thus accounting for their high stability and applicability in many material systems.
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Affiliation(s)
- Chenming Li
- Macromolecular Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, D-06120, Halle (Saale), Germany
| | - Rajesh Bhandary
- Macromolecular Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, D-06120, Halle (Saale), Germany
| | - Anja Marinow
- Macromolecular Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, D-06120, Halle (Saale), Germany
| | - Stephanie Bachmann
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ann-Christin Pöppler
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Wolfgang H Binder
- Macromolecular Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, D-06120, Halle (Saale), Germany
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50
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Idesis S, Geli S, Faskowitz J, Vohryzek J, Sanz Perl Y, Pieper F, Galindo-Leon E, Engel AK, Deco G. Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex. PLoS Comput Biol 2024; 20:e1011818. [PMID: 38241383 PMCID: PMC10836715 DOI: 10.1371/journal.pcbi.1011818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 02/02/2024] [Accepted: 01/09/2024] [Indexed: 01/21/2024] Open
Abstract
Brain signal irreversibility has been shown to be a promising approach to study neural dynamics. Nevertheless, the relation with cortical hierarchy and the influence of different electrophysiological features is not completely understood. In this study, we recorded local field potentials (LFPs) during spontaneous behavior, including awake and sleep periods, using custom micro-electrocorticographic (μECoG) arrays implanted in ferrets. In contrast to humans, ferrets remain less time in each state across the sleep-wake cycle. We deployed a diverse set of metrics in order to measure the levels of complexity of the different behavioral states. In particular, brain irreversibility, which is a signature of non-equilibrium dynamics, captured by the arrow of time of the signal, revealed the hierarchical organization of the ferret's cortex. We found different signatures of irreversibility and functional hierarchy of large-scale dynamics in three different brain states (active awake, quiet awake, and deep sleep), showing a lower level of irreversibility in the deep sleep stage, compared to the other. Irreversibility also allowed us to disentangle the influence of different cortical areas and frequency bands in this process, showing a predominance of the parietal cortex and the theta band. Furthermore, when inspecting the embedded dynamic through a Hidden Markov Model, the deep sleep stage was revealed to have a lower switching rate and lower entropy production. These results suggest functional hierarchies in organization that can be revealed through thermodynamic features and information theory metrics.
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Affiliation(s)
- Sebastian Idesis
- Center for Brain and Cognition (CBC), Department of Information Technologies and Communications (DTIC), Pompeu Fabra University, Edifici Mercè Rodoreda, Barcelona, Catalonia, Spain
| | - Sebastián Geli
- Center for Brain and Cognition (CBC), Department of Information Technologies and Communications (DTIC), Pompeu Fabra University, Edifici Mercè Rodoreda, Barcelona, Catalonia, Spain
| | - Joshua Faskowitz
- Department of Psychological and Brain Sciences, Indiana University Bloomington, Bloomington, Indiana, United States of America
| | - Jakub Vohryzek
- Center for Brain and Cognition (CBC), Department of Information Technologies and Communications (DTIC), Pompeu Fabra University, Edifici Mercè Rodoreda, Barcelona, Catalonia, Spain
- Centre for Eudaimonia and Human Flourishing, Linacre College, University of Oxford, Oxford, United Kingdom
| | - Yonatan Sanz Perl
- Center for Brain and Cognition (CBC), Department of Information Technologies and Communications (DTIC), Pompeu Fabra University, Edifici Mercè Rodoreda, Barcelona, Catalonia, Spain
- National Scientific and Technical Research Council, Buenos Aires, Argentina
- Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Florian Pieper
- Department of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Edgar Galindo-Leon
- Department of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas K. Engel
- Department of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gustavo Deco
- Center for Brain and Cognition (CBC), Department of Information Technologies and Communications (DTIC), Pompeu Fabra University, Edifici Mercè Rodoreda, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
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