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Hagihara H, Zaadnoordijk L, Cusack R, Kimura N, Tsuji S. Exploration of factors affecting webcam-based automated gaze coding. Behav Res Methods 2024:10.3758/s13428-024-02424-1. [PMID: 38693440 DOI: 10.3758/s13428-024-02424-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2024] [Indexed: 05/03/2024]
Abstract
Online experiments have been transforming the field of behavioral research, enabling researchers to increase sample sizes, access diverse populations, lower the costs of data collection, and promote reproducibility. The field of developmental psychology increasingly exploits such online testing approaches. Since infants cannot give explicit behavioral responses, one key outcome measure is infants' gaze behavior. In the absence of automated eyetrackers in participants' homes, automatic gaze classification from webcam data would make it possible to avoid painstaking manual coding. However, the lack of a controlled experimental environment may lead to various noise factors impeding automatic face detection or gaze classification. We created an adult webcam dataset that systematically reproduced noise factors from infant webcam studies which might affect automated gaze coding accuracy. We varied participants' left-right offset, distance to the camera, facial rotation, and the direction of the lighting source. Running two state-of-the-art classification algorithms (iCatcher+ and OWLET) revealed that facial detection performance was particularly affected by the lighting source, while gaze coding accuracy was consistently affected by the distance to the camera and lighting source. Morphing participants' faces to be unidentifiable did not generally affect the results, suggesting facial anonymization could be used when making online video data publicly available, for purposes of further study and transparency. Our findings will guide improving study design for infant and adult participants during online experiments. Moreover, training algorithms using our dataset will allow researchers to improve robustness and allow developmental psychologists to leverage online testing more efficiently.
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Affiliation(s)
- Hiromichi Hagihara
- Graduate School of Human Sciences, Osaka University 1-2 Yamadaoka, Suita-shi Osaka, 565-0871, Japan.
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan.
- The Institute for AI and Beyond, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Lorijn Zaadnoordijk
- Trinity College Institute of Neuroscience and School of Psychology, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Rhodri Cusack
- Trinity College Institute of Neuroscience and School of Psychology, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Nanako Kimura
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Sho Tsuji
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- The Institute for AI and Beyond, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
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2
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Smits MM, Galsgaard KD, Jepsen SL, Albrechtsen NW, Hartmann B, Holst JJ. In Vivo Inhibition of Dipeptidyl Peptidase 4 Allows Measurement of GLP-1 Secretion in Mice. Diabetes 2024; 73:671-681. [PMID: 38295385 DOI: 10.2337/db23-0848] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024]
Abstract
Dipeptidyl peptidase 4 (DPP-4) and neprilysin (NEP) rapidly degrade glucagon-like peptide 1 (GLP-1) in mice. Commercially available sandwich ELISA kits may not accurately detect the degradation products, leading to potentially misleading results. We aimed to stabilize GLP-1 in mice, allowing reliable measurement with sensitive commercially available ELISA kits. Nonanesthetized male C57Bl/6JRj mice were subjected to an oral glucose tolerance test (OGTT; 2 g/kg glucose), and plasma total and intact GLP-1 were measured (Mercodia and Alpco ELISA kits, respectively). No GLP-1 increases were seen in samples taken beyond 15 min after the glucose load. Samples taken at 5 and 10 min after the OGTT showed a minor increase in total, but not intact, GLP-1. We then administered saline (control), or a DPP-4 inhibitor (valine pyrrolidide or sitagliptin) with or without an NEP-inhibitor (sacubitril), 30 min before the OGTT. In the inhibitor groups only, intact GLP-1 increased significantly during the OGTT. After injecting male C57Bl/6JRj mice with a known dose of GLP-1(7-36)NH2, peak GLP-1 levels were barely detectable after saline but were 5- to 10-fold higher during sitagliptin and the combination of sitagliptin/sacubitril. The half-life of the GLP-1 plasma disappearance increased up to sevenfold during inhibitor treatment. We conclude that reliable measurement of GLP-1 secretion is not possible in mice in vivo with commercially available sandwich ELISA kits, unless degradation is prevented by inhibition of DPP-4 and perhaps NEP. The described approach allows improved estimates of GLP-1 secretion for future studies, although it is a limitation that these inhibitors additionally influence levels of insulin and glucagon. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Mark M Smits
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Katrine D Galsgaard
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sara Lind Jepsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Bolette Hartmann
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens J Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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3
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Gonzalez-de-Miguel J, Montero-Blay A, Ciampi L, Rodriguez-Arce I, Serrano L. Developing a platform for secretion of biomolecules in Mycoplasma feriruminatoris. Microb Cell Fact 2024; 23:124. [PMID: 38689251 DOI: 10.1186/s12934-024-02392-3] [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: 02/19/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Having a simple and fast dividing organism capable of producing and exposing at its surface or secreting functional complex biomolecules with disulphide bridges is of great interest. The mycoplasma bacterial genus offers a set of relevant properties that make it an interesting chassis for such purposes, the main one being the absence of a cell wall. However, due to their slow growth, they have rarely been considered as a potential platform in this respect. This notion may be challenged with the recent discovery of Mycoplasma feriruminatoris, a species with a dividing time close to that of common microbial workhorses. So far, no tools for heterologous protein expression nor secretion have been described for it. RESULTS The work presented here develops the fast-dividing M. feriruminatoris as a tool for secreting functional biomolecules of therapeutic interest that could be used for screening functional mutants as well as potentially for protein-protein interactions. Based on RNAseq, quantitative proteomics and promoter sequence comparison we have rationally designed optimal promoter sequences. Then, using in silico analysis, we have identified putative secretion signals that we validated using a luminescent reporter. The potential of the resulting secretion cassette has been shown with set of active clinically relevant proteins (interleukins and nanobodies). CONCLUSIONS We have engineered Mycoplasma feriruminatoris for producing and secreting functional proteins of medical interest.
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Affiliation(s)
- Javier Gonzalez-de-Miguel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
| | - Ariadna Montero-Blay
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
- Orikine Bio, Dr Aiguader 88, Barcelona, 08003, Spain
| | - Ludovica Ciampi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irene Rodriguez-Arce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain.
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain.
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Solà Colom M, Fu Z, Gunkel P, Güttler T, Trakhanov S, Srinivasan V, Gregor K, Pleiner T, Görlich D. A checkpoint function for Nup98 in nuclear pore formation suggested by novel inhibitory nanobodies. EMBO J 2024:10.1038/s44318-024-00081-w. [PMID: 38649536 DOI: 10.1038/s44318-024-00081-w] [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: 09/12/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/25/2024] Open
Abstract
Nuclear pore complex (NPC) biogenesis is a still enigmatic example of protein self-assembly. We now introduce several cross-reacting anti-Nup nanobodies for imaging intact nuclear pore complexes from frog to human. We also report a simplified assay that directly tracks postmitotic NPC assembly with added fluorophore-labeled anti-Nup nanobodies. During interphase, NPCs are inserted into a pre-existing nuclear envelope. Monitoring this process is challenging because newly assembled NPCs are indistinguishable from pre-existing ones. We overcame this problem by inserting Xenopus-derived NPCs into human nuclear envelopes and using frog-specific anti-Nup nanobodies for detection. We further asked whether anti-Nup nanobodies could serve as NPC assembly inhibitors. Using a selection strategy against conserved epitopes, we obtained anti-Nup93, Nup98, and Nup155 nanobodies that block Nup-Nup interfaces and arrest NPC assembly. We solved structures of nanobody-target complexes and identified roles for the Nup93 α-solenoid domain in recruiting Nup358 and the Nup214·88·62 complex, as well as for Nup155 and the Nup98 autoproteolytic domain in NPC scaffold assembly. The latter suggests a checkpoint linking pore formation to the assembly of the Nup98-dominated permeability barrier.
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Affiliation(s)
- Mireia Solà Colom
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- AI Proteins, 20 Overland St., Boston, MA, USA
| | - Zhenglin Fu
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Philip Gunkel
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Thomas Güttler
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Octapharma Biopharmaceuticals, Im Neuenheimer Feld 590, 69120, Heidelberg, Germany
| | - Sergei Trakhanov
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Vasundara Srinivasan
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Universität Hamburg, Hamburg, Germany
| | - Kathrin Gregor
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Tino Pleiner
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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Menaker Y, van den Munckhof I, Scarpa A, Placek K, Brandes-Leibovitz R, Glantzspiegel Y, Joosten LAB, Rutten JHW, Netea MG, Gat-Viks I, Riksen NP. Stratification of Atherosclerosis based on Plasma Metabolic States. J Clin Endocrinol Metab 2024; 109:1250-1262. [PMID: 38044551 DOI: 10.1210/clinem/dgad672] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 12/05/2023]
Abstract
CONTEXT Atherosclerosis is a dominant cause of cardiovascular disease (CVD), including myocardial infarction and stroke. OBJECTIVE To investigate metabolic states that are associated with the development of atherosclerosis. METHODS Cross-sectional cohort study at a university hospital in the Netherlands. A total of 302 adult subjects with a body mass index (BMI) ≥ 27 kg/m2 were included. We integrated plasma metabolomics with clinical metadata to quantify the "atherogenic state" of each individual, providing a continuous spectrum of atherogenic states that ranges between nonatherogenic states to highly atherogenic states. RESULTS Analysis of groups of individuals with different clinical conditions-such as metabolically healthy individuals with obesity, and individuals with metabolic syndrome-confirmed the generalizability of this spectrum; revealed a wide variation of atherogenic states within each condition; and allowed identification of metabolites that are associated with the atherogenic state regardless of the particular condition, such as gamma-glutamyl-glutamic acid and homovanillic acid sulfate. The analysis further highlighted metabolic pathways such as catabolism of phenylalanine and tyrosine and biosynthesis of estrogens and phenylpropanoids. Using validation cohorts, we confirmed variation in atherogenic states in healthy subjects (before atherosclerosis plaques become visible), and showed that metabolites associated with the atherogenic state were also associated with future CVD. CONCLUSION Our results provide a global view of atherosclerosis risk states using plasma metabolomics.
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Affiliation(s)
- Yuval Menaker
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Inge van den Munckhof
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alice Scarpa
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | - Katarzyna Placek
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | - Rachel Brandes-Leibovitz
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yossef Glantzspiegel
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, 400000 Cluj-Napoca, Romania
| | - Joost H W Rutten
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | - Irit Gat-Viks
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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6
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Gargallo-Garriga A, Sardans J, Llusià J, Peguero G, Ayala-Roque M, Courtois EA, Stahl C, Urban O, Klem K, Nolis P, Pérez-Trujillo M, Parella T, Richter A, Janssens IA, Peñuelas J. Different profiles of soil phosphorous compounds depending on tree species and availability of soil phosphorus in a tropical rainforest in French Guiana. BMC Plant Biol 2024; 24:278. [PMID: 38609866 PMCID: PMC11010349 DOI: 10.1186/s12870-024-04907-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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/13/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND The availability of soil phosphorus (P) often limits the productivities of wet tropical lowland forests. Little is known, however, about the metabolomic profile of different chemical P compounds with potentially different uses and about the cycling of P and their variability across space under different tree species in highly diverse tropical rainforests. RESULTS We hypothesised that the different strategies of the competing tree species to retranslocate, mineralise, mobilise, and take up P from the soil would promote distinct soil 31P profiles. We tested this hypothesis by performing a metabolomic analysis of the soils in two rainforests in French Guiana using 31P nuclear magnetic resonance (NMR). We analysed 31P NMR chemical shifts in soil solutions of model P compounds, including inorganic phosphates, orthophosphate mono- and diesters, phosphonates, and organic polyphosphates. The identity of the tree species (growing above the soil samples) explained > 53% of the total variance of the 31P NMR metabolomic profiles of the soils, suggesting species-specific ecological niches and/or species-specific interactions with the soil microbiome and soil trophic web structure and functionality determining the use and production of P compounds. Differences at regional and topographic levels also explained some part of the the total variance of the 31P NMR profiles, although less than the influence of the tree species. Multivariate analyses of soil 31P NMR metabolomics data indicated higher soil concentrations of P biomolecules involved in the active use of P (nucleic acids and molecules involved with energy and anabolism) in soils with lower concentrations of total soil P and higher concentrations of P-storing biomolecules in soils with higher concentrations of total P. CONCLUSIONS The results strongly suggest "niches" of soil P profiles associated with physical gradients, mostly topographic position, and with the specific distribution of species along this gradient, which is associated with species-specific strategies of soil P mineralisation, mobilisation, use, and uptake.
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Affiliation(s)
- Albert Gargallo-Garriga
- Global Change Research Institute, The Czech Academy of Sciences, Belidla 986/4a, Brno, CZ-60300, Czech Republic.
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
| | - Jordi Sardans
- Global Ecology Unit, CSIC, CREAF-CSIC-UAB, Bellaterra, 08193, Catalonia, Spain
- CREAF, Cerdanyola del vallès, Barcelona, Catalonia, 08193, Spain
| | - Joan Llusià
- Global Ecology Unit, CSIC, CREAF-CSIC-UAB, Bellaterra, 08193, Catalonia, Spain
- CREAF, Cerdanyola del vallès, Barcelona, Catalonia, 08193, Spain
| | - Guille Peguero
- Global Ecology Unit, CSIC, CREAF-CSIC-UAB, Bellaterra, 08193, Catalonia, Spain
- CREAF, Cerdanyola del vallès, Barcelona, Catalonia, 08193, Spain
| | | | - Elodie A Courtois
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
- Laboratoire écologie, évolution, Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, Cayenne, France
| | - Clément Stahl
- UMR ECOFOG - Ecologie des forêts de Guyane, Kourou cedex, 97379, France
| | - Otmar Urban
- Global Ecology Unit, CSIC, CREAF-CSIC-UAB, Bellaterra, 08193, Catalonia, Spain
| | - Karel Klem
- Global Ecology Unit, CSIC, CREAF-CSIC-UAB, Bellaterra, 08193, Catalonia, Spain
| | - Pau Nolis
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Miriam Pérez-Trujillo
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstr. 14, Vienna, 1090, Austria
| | - Ivan A Janssens
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Josep Peñuelas
- Global Ecology Unit, CSIC, CREAF-CSIC-UAB, Bellaterra, 08193, Catalonia, Spain
- CREAF, Cerdanyola del vallès, Barcelona, Catalonia, 08193, Spain
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Fiorentino J, Armaos A, Colantoni A, Tartaglia G. Prediction of protein-RNA interactions from single-cell transcriptomic data. Nucleic Acids Res 2024; 52:e31. [PMID: 38364867 PMCID: PMC11014251 DOI: 10.1093/nar/gkae076] [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: 07/17/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024] Open
Abstract
Proteins are crucial in regulating every aspect of RNA life, yet understanding their interactions with coding and noncoding RNAs remains limited. Experimental studies are typically restricted to a small number of cell lines and a limited set of RNA-binding proteins (RBPs). Although computational methods based on physico-chemical principles can predict protein-RNA interactions accurately, they often lack the ability to consider cell-type-specific gene expression and the broader context of gene regulatory networks (GRNs). Here, we assess the performance of several GRN inference algorithms in predicting protein-RNA interactions from single-cell transcriptomic data, and propose a pipeline, called scRAPID (single-cell transcriptomic-based RnA Protein Interaction Detection), that integrates these methods with the catRAPID algorithm, which can identify direct physical interactions between RBPs and RNA molecules. Our approach demonstrates that RBP-RNA interactions can be predicted from single-cell transcriptomic data, with performances comparable or superior to those achieved for the well-established task of inferring transcription factor-target interactions. The incorporation of catRAPID significantly enhances the accuracy of identifying interactions, particularly with long noncoding RNAs, and enables the identification of hub RBPs and RNAs. Additionally, we show that interactions between RBPs can be detected based on their inferred RNA targets. The software is freely available at https://github.com/tartaglialabIIT/scRAPID.
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Affiliation(s)
- Jonathan Fiorentino
- Center for Life Nano- and Neuro-Science, RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Alexandros Armaos
- Centre for Human Technologies (CHT), RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Alessio Colantoni
- Center for Life Nano- and Neuro-Science, RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Gian Gaetano Tartaglia
- Center for Life Nano- and Neuro-Science, RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- Centre for Human Technologies (CHT), RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
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Benjamin L, Sablé-Meyer M, Fló A, Dehaene-Lambertz G, Al Roumi F. Long-Horizon Associative Learning Explains Human Sensitivity to Statistical and Network Structures in Auditory Sequences. J Neurosci 2024; 44:e1369232024. [PMID: 38408873 PMCID: PMC10993028 DOI: 10.1523/jneurosci.1369-23.2024] [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: 07/04/2023] [Revised: 01/16/2024] [Accepted: 02/07/2024] [Indexed: 02/28/2024] Open
Abstract
Networks are a useful mathematical tool for capturing the complexity of the world. In a previous behavioral study, we showed that human adults were sensitive to the high-level network structure underlying auditory sequences, even when presented with incomplete information. Their performance was best explained by a mathematical model compatible with associative learning principles, based on the integration of the transition probabilities between adjacent and nonadjacent elements with a memory decay. In the present study, we explored the neural correlates of this hypothesis via magnetoencephalography (MEG). Participants (N = 23, 16 females) passively listened to sequences of tones organized in a sparse community network structure comprising two communities. An early difference (∼150 ms) was observed in the brain responses to tone transitions with similar transition probability but occurring either within or between communities. This result implies a rapid and automatic encoding of the sequence structure. Using time-resolved decoding, we estimated the duration and overlap of the representation of each tone. The decoding performance exhibited exponential decay, resulting in a significant overlap between the representations of successive tones. Based on this extended decay profile, we estimated a long-horizon associative learning novelty index for each transition and found a correlation of this measure with the MEG signal. Overall, our study sheds light on the neural mechanisms underlying human sensitivity to network structures and highlights the potential role of Hebbian-like mechanisms in supporting learning at various temporal scales.
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Affiliation(s)
- Lucas Benjamin
- Cognitive Neuroimaging Unit, CNRS ERL 9003, INSERM U992, CEA, Université Paris-Saclay, NeuroSpin Center, 91190 Gif/Yvette, France
| | - Mathias Sablé-Meyer
- Cognitive Neuroimaging Unit, CNRS ERL 9003, INSERM U992, CEA, Université Paris-Saclay, NeuroSpin Center, 91190 Gif/Yvette, France
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, United Kingdom
| | - Ana Fló
- Cognitive Neuroimaging Unit, CNRS ERL 9003, INSERM U992, CEA, Université Paris-Saclay, NeuroSpin Center, 91190 Gif/Yvette, France
- Department of Developmental Psychology and Socialization, University of Padova, Padova 35131, Italy
| | - Ghislaine Dehaene-Lambertz
- Cognitive Neuroimaging Unit, CNRS ERL 9003, INSERM U992, CEA, Université Paris-Saclay, NeuroSpin Center, 91190 Gif/Yvette, France
| | - Fosca Al Roumi
- Cognitive Neuroimaging Unit, CNRS ERL 9003, INSERM U992, CEA, Université Paris-Saclay, NeuroSpin Center, 91190 Gif/Yvette, France
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Zhu Y, Zhang J, Cheng T, Tang J, Duan H, Hu Z, Shao J, Wang S, Wei M, Wu H, Li A, Li S, Balci O, Shinde SM, Ramezani H, Wang L, Lin L, Ferrari AC, Yakobson BI, Peng H, Jia K, Liu Z. Controlled Growth of Single-Crystal Graphene Wafers on Twin-Boundary-Free Cu(111) Substrates. Adv Mater 2024; 36:e2308802. [PMID: 37878366 DOI: 10.1002/adma.202308802] [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: 08/29/2023] [Revised: 10/05/2023] [Indexed: 10/26/2023]
Abstract
Single-crystal graphene (SCG) wafers are needed to enable mass-electronics and optoelectronics owing to their excellent properties and compatibility with silicon-based technology. Controlled synthesis of high-quality SCG wafers can be done exploiting single-crystal Cu(111) substrates as epitaxial growth substrates recently. However, current Cu(111) films prepared by magnetron sputtering on single-crystal sapphire wafers still suffer from in-plane twin boundaries, which degrade the SCG chemical vapor deposition. Here, it is shown how to eliminate twin boundaries on Cu and achieve 4 in. Cu(111) wafers with ≈95% crystallinity. The introduction of a temperature gradient on Cu films with designed texture during annealing drives abnormal grain growth across the whole Cu wafer. In-plane twin boundaries are eliminated via migration of out-of-plane grain boundaries. SCG wafers grown on the resulting single-crystal Cu(111) substrates exhibit improved crystallinity with >97% aligned graphene domains. As-synthesized SCG wafers exhibit an average carrier mobility up to 7284 cm2 V-1 s-1 at room temperature from 103 devices and a uniform sheet resistance with only 5% deviation in 4 in. region.
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Affiliation(s)
- Yeshu Zhu
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Jincan Zhang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Ting Cheng
- Department of Materials Science & NanoEngineering, Rice University, Houston, TX, 77005, USA
| | - Jilin Tang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Hongwei Duan
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, School of Integrated Circuits, Peking University, Beijing, 100871, P. R. China
| | - Zhaoning Hu
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P. R. China
| | - Jiaxin Shao
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Shiwei Wang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Mingyue Wei
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Haotian Wu
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P. R. China
| | - Ang Li
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- College of Science, China University of Petroleum, Beijing, 102249, P. R. China
| | - Sheng Li
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Osman Balci
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Sachin M Shinde
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Hamideh Ramezani
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Luda Wang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, School of Integrated Circuits, Peking University, Beijing, 100871, P. R. China
| | - Li Lin
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P. R. China
| | - Andrea C Ferrari
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Boris I Yakobson
- Department of Materials Science & NanoEngineering, Rice University, Houston, TX, 77005, USA
- Department of Chemistry, Rice University, Houston, TX, 77005, USA
| | - Hailin Peng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Kaicheng Jia
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Zhongfan Liu
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
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10
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Du T, Li S, Ganisetti S, Bauchy M, Yue Y, Smedskjaer MM. Deciphering the controlling factors for phase transitions in zeolitic imidazolate frameworks. Natl Sci Rev 2024; 11:nwae023. [PMID: 38560493 PMCID: PMC10980346 DOI: 10.1093/nsr/nwae023] [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: 09/04/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 04/04/2024] Open
Abstract
Zeolitic imidazolate frameworks (ZIFs) feature complex phase transitions, including polymorphism, melting, vitrification, and polyamorphism. Experimentally probing their structural evolution during transitions involving amorphous phases is a significant challenge, especially at the medium-range length scale. To overcome this challenge, here we first train a deep learning-based force field to identify the structural characteristics of both crystalline and non-crystalline ZIF phases. This allows us to reproduce the structural evolution trend during the melting of crystals and formation of ZIF glasses at various length scales with an accuracy comparable to that of ab initio molecular dynamics, yet at a much lower computational cost. Based on this approach, we propose a new structural descriptor, namely, the ring orientation index, to capture the propensity for crystallization of ZIF-4 (Zn(Im)2, Im = C3H3N2-) glasses, as well as for the formation of ZIF-zni (Zn(Im)2) out of the high-density amorphous phase. This crystal formation process is a result of the reorientation of imidazole rings by sacrificing the order of the structure around the zinc-centered tetrahedra. The outcomes of this work are useful for studying phase transitions in other metal-organic frameworks (MOFs) and may thus guide the development of MOF glasses.
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Affiliation(s)
- Tao Du
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Shanwu Li
- Department of Mechanical Engineering-Engineering Mechanics, Michigan Technological University, Houghton MI 49931, USA
| | - Sudheer Ganisetti
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Mathieu Bauchy
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuanzheng Yue
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Morten M Smedskjaer
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
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11
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Abbona CC, Lebrasseur O, Prevosti FJ, Peralta E, González Venanzi L, Frantz L, Larson G, Gil AF, Neme GA. Patagonian partnerships: the extinct Dusicyon avus and its interaction with prehistoric human communities. R Soc Open Sci 2024; 11:231835. [PMID: 38601034 PMCID: PMC11004678 DOI: 10.1098/rsos.231835] [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: 11/29/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 04/12/2024]
Abstract
The southern Mendoza province, located in the northern region of Patagonia, was inhabited by hunter-gatherer groups until historic times. Previous archaeological studies have reported canid remains among faunal assemblages, which were assumed to be part of the human diet. However, the taxonomic identification and significance of these canids within human groups have raised questions. In this study, we used ancient DNA analysis, morphological examination and stable isotope analysis (δ13Ccol and δ15N) to re-evaluate the taxonomic assignment of a canid discovered at the Late Holocene burial site of Cañada Seca. Previous morphological identifications suggested that it belonged to the genus Lycalopex, but our results conclusively demonstrate that the individual belongs to the extinct fox species Dusicyon avus. This finding expands Dusicyon avus' known geographical distribution to Patagonia's northern extremity. Furthermore, statistical predictions based on genetic divergence undermine the hypothesis that hybridization between Canis and Dusicyon, facilitated by the introduction of domestic dogs, played a role in the extinction of Dusicyon species. On the other hand, our findings indicate that a Dusicyon avus individual shared a similar diet and was probably buried alongside humans, suggesting a close relationship between the two species during their lives and deaths.
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Affiliation(s)
- Cinthia C. Abbona
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Ophélie Lebrasseur
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, OxfordOX1 3TG, UK
| | - Francisco J. Prevosti
- Museo de Ciencias Antropológicas y Naturales, Universidad Nacional de La Rioja (UNLaR), Avenue Luis M. de la Fuente S/N, La Rioja5300, Argentina
| | - Eva Peralta
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Lucio González Venanzi
- Div. Arqueología, Anexo Museo, Laboratory 128 (FCNyM-UNLP), La Plata, Argentina, FHumyAr (UNR), Rosario, Argentina
| | - Laurent Frantz
- Graduate School Life Science Munich, Faculty of Biology/Biocenter, Grosshadernerstr, 2-4, 82152 Planegg-Martinsried, Munich, Germany
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, OxfordOX1 3TG, UK
| | - Adolfo F. Gil
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Gustavo A. Neme
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
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12
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van Bemmelen RSA, Moe B, Schekkerman H, Hansen SA, Snell KRS, Humphreys EM, Mäntylä E, Hallgrimsson GT, Gilg O, Ehrich D, Calladine J, Hammer S, Harris S, Lang J, Vignisson SR, Kolbeinsson Y, Nuotio K, Sillanpää M, Sittler B, Sokolov A, Klaassen RHG, Phillips RA, Tulp I. Synchronous timing of return to breeding sites in a long-distance migratory seabird with ocean-scale variation in migration schedules. Mov Ecol 2024; 12:22. [PMID: 38520007 PMCID: PMC10960466 DOI: 10.1186/s40462-024-00459-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/12/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Migratory birds generally have tightly scheduled annual cycles, in which delays can have carry-over effects on the timing of later events, ultimately impacting reproductive output. Whether temporal carry-over effects are more pronounced among migrations over larger distances, with tighter schedules, is a largely unexplored question. METHODS We tracked individual Arctic Skuas Stercorarius parasiticus, a long-distance migratory seabird, from eight breeding populations between Greenland and Siberia using light-level geolocators. We tested whether migration schedules among breeding populations differ as a function of their use of seven widely divergent wintering areas across the Atlantic Ocean, Mediterranean Sea and Indian Ocean. RESULTS Breeding at higher latitudes led not only to later reproduction and migration, but also faster spring migration and shorter time between return to the breeding area and clutch initiation. Wintering area was consistent within individuals among years; and more distant areas were associated with more time spent on migration and less time in the wintering areas. Skuas adjusted the period spent in the wintering area, regardless of migration distance, which buffered the variation in timing of autumn migration. Choice of wintering area had only minor effects on timing of return at the breeding area and timing of breeding and these effects were not consistent between breeding populations. CONCLUSION The lack of a consistent effect of wintering area on timing of return between breeding areas indicates that individuals synchronize their arrival with others in their population despite extensive individual differences in migration strategies.
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Affiliation(s)
- Rob S A van Bemmelen
- Wageningen Marine Research, Haringkade 1, 1976 CP, IJmuiden, The Netherlands.
- Waardenburg Ecology, Culemborg, The Netherlands.
| | - Børge Moe
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | | | | | - Katherine R S Snell
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Constance, Germany
| | - Elizabeth M Humphreys
- British Trust for Ornithology (BTO), Scotland, Stirling University Innovation Park, Stirling, FK9 4NF, UK
| | - Elina Mäntylä
- Section of Ecology, Department of Biology, University of Turku, Turku, Finland
- Applied Zoology/Animal Ecology, Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Olivier Gilg
- UMR 6249 Chrono-Environnement, CNRS, Université de Bourgogne Franche Comté, 25000, Besançon, France
- Groupe de Recherche en Ecologie Arctique, 16 Rue de Vernot, 21440, Francheville, France
| | | | - John Calladine
- British Trust for Ornithology (BTO), Scotland, Stirling University Innovation Park, Stirling, FK9 4NF, UK
| | - Sjúrður Hammer
- Faculty of Science and Technology, University of the Faroe Islands, Vestarabryggja 15, 100, Tórshavn, Faroe Islands
| | - Sarah Harris
- British Trust for Ornithology (BTO), The Nunnery, Thetford, Norfolk, IP24 2PU, UK
| | - Johannes Lang
- Groupe de Recherche en Ecologie Arctique, 16 Rue de Vernot, 21440, Francheville, France
- University of Giessen, Giessen, Germany
| | | | | | - Kimmo Nuotio
- Pori Ornithological Society, Pori, Finland
- Environmental Agency, Pori, Finland
| | | | - Benoît Sittler
- Groupe de Recherche en Ecologie Arctique, 16 Rue de Vernot, 21440, Francheville, France
- University of Freiburg, Freiburg, Germany
| | - Aleksandr Sokolov
- Arctic Research Station of Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Labytnangi, Russia
| | - Raymond H G Klaassen
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences (GELIFES), Groningen University, Groningen, The Netherlands
| | - Richard A Phillips
- British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Cambridge, UK
| | - Ingrid Tulp
- Wageningen Marine Research, Haringkade 1, 1976 CP, IJmuiden, The Netherlands.
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13
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Valentini C, Montes-García V, Ciesielski A, Samorì P. Boosting Zinc Hybrid Sup ercapacitor Performance via Thiol Functionalization of Graphene-Based Cathodes. Adv Sci (Weinh) 2024:e2309041. [PMID: 38509829 DOI: 10.1002/advs.202309041] [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: 01/02/2024] [Revised: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Zinc hybrid supercapacitors (Zn-HSCs) hold immense potential toward the next-generation energy storage systems, effectively spanning the divide between conventional lithium-ion batteries (LIBs) and supercapacitors. Unfortunately, the energy density of most of Zn-HSCs has not yet rivalled the levels observed in LIBs. The electrochemical performance of aqueous Zn-HSCs can be enhanced through the chemical functionalization of graphene-based cathode materials with thiol moieties as they will be highly suitable for favoring Zn2+ adsorption/desorption. Here, a single-step reaction is employed to synthesize thiol-functionalized reduced graphene oxide (rGOSH), incorporating both oxygen functional groups (OFGs) and thiol functionalities, as demonstrated by X-ray photoelectron spectroscopy (XPS) studies. Electrochemical analysis reveals that rGOSH cathodes exhibit a specific capacitance (540 F g-1) and specific capacity (139 mAh g-1) at 0.1 A g-1 as well as long-term stability, with over 92% capacitance retention after 10 000 cycles, outperforming chemically reduced graphene oxide (CrGO). Notably, rGOSH electrodes displayed an exceptional maximum energy density of 187.6 Wh kg-1 and power density of 48.6 kW kg-1. Overall, this study offers an unprecedented powerful strategy for the design and optimization of cathode materials, paving the way for efficient and sustainable energy storage solutions to meet the increasing demands of modern energy applications.
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Affiliation(s)
- Cataldo Valentini
- Université de Strasbourg and CNRS, ISIS, 8 allée Gaspard Monge, Strasbourg, 67000, France
- Centre for Advanced Technologies, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, Poznań, 61-614, Poland
| | - Verónica Montes-García
- Université de Strasbourg and CNRS, ISIS, 8 allée Gaspard Monge, Strasbourg, 67000, France
| | - Artur Ciesielski
- Université de Strasbourg and CNRS, ISIS, 8 allée Gaspard Monge, Strasbourg, 67000, France
- Centre for Advanced Technologies, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, Poznań, 61-614, Poland
| | - Paolo Samorì
- Université de Strasbourg and CNRS, ISIS, 8 allée Gaspard Monge, Strasbourg, 67000, France
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14
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Bosteels V, Van Duyse J, Ruyssinck E, Van der Borght K, Nguyen L, Gavel J, Janssens S, Van Isterdael G. Automated antibody dispensing to improve high-parameter flow cytometry throughput and analysis. Cytometry A 2024. [PMID: 38456613 DOI: 10.1002/cyto.a.24835] [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: 10/12/2023] [Revised: 02/02/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024]
Abstract
Over the past decade, the flow cytometry field has witnessed significant advancements in the number of fluorochromes that can be detected. This enables researchers to analyze more than 40 markers simultaneously on thousands of cells per second. However, with this increased complexity and multiplicity of markers, the manual dispensing of antibodies for flow cytometry experiments has become laborious, time-consuming, and prone to errors. An automated antibody dispensing system could provide a potential solution by enhancing the efficiency, and by improving data quality by faithfully dispensing the fluorochrome-conjugated antibodies and by enabling the easy addition of extra controls. In this study, a comprehensive comparison of different liquid handlers for dispensing fluorochrome-labeled antibodies was conducted for the preparation of flow cytometry stainings. The evaluation focused on key criteria including dispensing time, dead volume, and reliability of dispensing. After benchmarking, the I.DOT, a non-contact liquid handler, was selected and optimized in more detail. In the end, the I.DOT was able to prepare a 25-marker panel in 20 min, including the full stain, all FMOs and all single stain controls for cells and beads. Having all these controls improved the validation of the panel, visualization, and analysis of the data. Thus, automated antibody dispensing by dispensers such as the I.DOT reduces time and errors, enhances data quality, and can be easily integrated in an automated workflow to prepare samples for flow cytometry.
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Affiliation(s)
- Victor Bosteels
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Laboratory for ER Stress and Inflammation, VIB Center for Inflammation Research, Ghent, Belgium
| | - Julie Van Duyse
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
| | - Elien Ruyssinck
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
| | - Katrien Van der Borght
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
| | - Long Nguyen
- VIB Screening Core, VIB, Ghent, Belgium
- Center for Bioassay Development and Screening, Ghent University, Ghent, Belgium
| | - Jannes Gavel
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Immunoregulation and Mucosal Immunology Lab, VIB Center for Inflammation Research, Ghent, Belgium
| | - Sophie Janssens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Laboratory for ER Stress and Inflammation, VIB Center for Inflammation Research, Ghent, Belgium
| | - Gert Van Isterdael
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
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15
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Flinn B, Rance GA, Cull WJ, Cardillo-Zallo I, Pitcairn J, Cliffe MJ, Fay MW, Tyler AJ, Weare BL, Stoppiello CT, Davies ES, Mather ML, Khlobystov AN. Sensing the Spin State of Room-Temperature Switchable Cyanometallate Frameworks with Nitrogen-Vacancy Centers in Nanodiamonds. ACS Nano 2024; 18:7148-7160. [PMID: 38383159 PMCID: PMC10919078 DOI: 10.1021/acsnano.3c11820] [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: 11/26/2023] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
Room-temperature magnetically switchable materials play a vital role in current and upcoming quantum technologies, such as spintronics, molecular switches, and data storage devices. The increasing miniaturization of device architectures produces a need to develop analytical tools capable of precisely probing spin information at the single-particle level. In this work, we demonstrate a methodology using negatively charged nitrogen vacancies (NV-) in fluorescent nanodiamond (FND) particles to probe the magnetic switching of a spin crossover (SCO) metal-organic framework (MOF), [Fe(1,6-naphthyridine)2(Ag(CN)2)2] material (1), and a single-molecule photomagnet [X(18-crown-6)(H2O)3]Fe(CN)6·2H2O, where X = Eu and Dy (materials 2a and 2b, respectively), in response to heat, light, and electron beam exposure. We employ correlative light-electron microscopy using transmission electron microscopy (TEM) finder grids to accurately image and sense spin-spin interacting particles down to the single-particle level. We used surface-sensitive optically detected magnetic resonance (ODMR) and magnetic modulation (MM) of FND photoluminescence (PL) to sense spins to a distance of ca. 10-30 nm. We show that ODMR and MM sensing was not sensitive to the temperature-induced SCO of FeII in 1 as formation of paramagnetic FeIII through surface oxidation (detected by X-ray photoelectron spectroscopy) on heating obscured the signal of bulk SCO switching. We found that proximal FNDs could effectively sense the chemical transformations induced by the 200 keV electron beam in 1, namely, AgI → Ag0 and FeII → FeIII. However, transformations induced by the electron beam are irreversible as they substantially disrupt the structure of MOF particles. Finally, we demonstrate NV- sensing of reversible photomagnetic switching, FeIII + (18-crown-6) ⇆ FeII + (18-crown-6)+ •, triggered in 2a and 2b by 405 nm light. The photoredox process of 2a and 2b proved to be the best candidate for room-temperature single-particle magnetic switching utilizing FNDs as a sensor, which could have applications into next-generation quantum technologies.
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Affiliation(s)
- Bradley
T. Flinn
- School
of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Graham A. Rance
- Nanoscale
and Microscale Research Centre, University
of Nottingham, Nottingham, NG7 2RD, United
Kingdom
| | - William J. Cull
- School
of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Ian Cardillo-Zallo
- School
of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Jem Pitcairn
- School
of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
- School
of Chemistry, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Matthew J. Cliffe
- School
of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Michael W. Fay
- Nanoscale
and Microscale Research Centre, University
of Nottingham, Nottingham, NG7 2RD, United
Kingdom
| | - Ashley J. Tyler
- Optics
and Photonics Group, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, United
Kingdom
| | - Benjamin L. Weare
- Nanoscale
and Microscale Research Centre, University
of Nottingham, Nottingham, NG7 2RD, United
Kingdom
| | - Craig T. Stoppiello
- Centre
for Microscopy and Microanalysis, University
of Queensland, St. Lucia, 4072, Australia
| | - E. Stephen Davies
- School
of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Melissa L. Mather
- Optics
and Photonics Group, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, United
Kingdom
| | - Andrei N. Khlobystov
- School
of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
- Nanoscale
and Microscale Research Centre, University
of Nottingham, Nottingham, NG7 2RD, United
Kingdom
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16
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Abbas N, Haas JA, Xiao K, Fuchs M, Just A, Pich A, Perbellini F, Werlein C, Ius F, Ruhparwar A, Fiedler J, Weber N, Thum T. Inhibition of miR-21: cardioprotective effects in human failing myocardium ex vivo. Eur Heart J 2024:ehae102. [PMID: 38442291 DOI: 10.1093/eurheartj/ehae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/30/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Affiliation(s)
- Naisam Abbas
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
- Fraunhofer Institute of Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - Jonas A Haas
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Ke Xiao
- Fraunhofer Institute of Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - Maximilian Fuchs
- Fraunhofer Institute of Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - Annette Just
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Andreas Pich
- Institute of Toxicology and Core Unit Proteomics, Hannover Medical School, Hannover, Germany
| | - Filippo Perbellini
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | | | - Fabio Ius
- Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, Hannover, Germany
| | - Arjang Ruhparwar
- Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, Hannover, Germany
| | - Jan Fiedler
- Fraunhofer Institute of Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - Natalie Weber
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
- Center for Translational Regenerative Medicine, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
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17
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Yang S, Wen X, Wagner D, Strauss J, Kallmeyer J, Anthony SE, Liebner S. Microbial assemblages in Arctic coastal thermokarst lakes and lagoons. FEMS Microbiol Ecol 2024; 100:fiae014. [PMID: 38308515 PMCID: PMC10883142 DOI: 10.1093/femsec/fiae014] [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: 07/09/2023] [Revised: 11/22/2023] [Accepted: 02/01/2024] [Indexed: 02/04/2024] Open
Abstract
Several studies have investigated changes in microbial community composition in thawing permafrost landscapes, but microbial assemblages in the transient ecosystems of the Arctic coastline remain poorly understood. Thermokarst lakes, abrupt permafrost thaw features, are widespread along the pan-Arctic coast and transform into thermokarst lagoons upon coastal erosion and sea-level rise. This study looks at the effect of marine water inundation (imposing a sulfate-rich, saline environment on top of former thermokarst lake sediments) on microbial community composition and the processes potentially driving microbial community assembly. In the uppermost lagoon sediment influenced from marine water inflow, the microbial structures were significantly different from those deeper in the lagoon sediment and from those of the lakes. In addition, they became more similar along depth compared with lake communities. At the same time, the diversity of core microbial consortia community decreased compared with the lake sediments. This work provides initial observational evidence that Arctic thermokarst lake to lagoon transitions do not only substantially alter microbial communities but also that this transition has a larger effect than permafrost thaw and lake formation history.
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Affiliation(s)
- Sizhong Yang
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
- Cyrosphere Research Station on the Qinghai-Tibet Plateau, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Donggang West Road 320, Lanzhou 730000, China
| | - Xi Wen
- College of Electrical Engineering, Northwest Minzu University, Xibei Xincun 1, Lanzhou 730070, China
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Jens Strauss
- Permafrost Research Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Telegrafenberg, Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
| | - Sara E Anthony
- Institute of Geology and Mineralogy, University of Cologne, Zülpicher Str. 49a, 50674 Cologne, Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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18
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Zhang Z, Shi Z, Ahmed D. SonoTransformers: Transformable acoustically activated wireless microscale machines. Proc Natl Acad Sci U S A 2024; 121:e2314661121. [PMID: 38289954 PMCID: PMC10861920 DOI: 10.1073/pnas.2314661121] [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: 08/26/2023] [Accepted: 12/22/2023] [Indexed: 02/01/2024] Open
Abstract
Shape transformation, a key mechanism for organismal survival and adaptation, has gained importance in developing synthetic shape-shifting systems with diverse applications ranging from robotics to bioengineering. However, designing and controlling microscale shape-shifting materials remains a fundamental challenge in various actuation modalities. As materials and structures are scaled down to the microscale, they often exhibit size-dependent characteristics, and the underlying physical mechanisms can be significantly affected or rendered ineffective. Additionally, surface forces such as van der Waals forces and electrostatic forces become dominant at the microscale, resulting in stiction and adhesion between small structures, making them fracture and more difficult to deform. Furthermore, despite various actuation approaches, acoustics have received limited attention despite their potential advantages. Here, we introduce "SonoTransformer," the acoustically activated micromachine that delivers shape transformability using preprogrammed soft hinges with different stiffnesses. When exposed to an acoustic field, these hinges concentrate sound energy through intensified oscillation and provide the necessary force and torque for the transformation of the entire micromachine within milliseconds. We have created machine designs to predetermine the folding state, enabling precise programming and customization of the acoustic transformation. Additionally, we have shown selective shape transformable microrobots by adjusting acoustic power, realizing high degrees of control and functional versatility. Our findings open new research avenues in acoustics, physics, and soft matter, offering new design paradigms and development opportunities in robotics, metamaterials, adaptive optics, flexible electronics, and microtechnology.
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Affiliation(s)
- Zhiyuan Zhang
- Acoustic Robotics Systems Lab, Institute of Robotics and Intelligent Systems, Department of Mechanical and Process Engineering, ETH Zurich, ZurichCH-8803, Switzerland
| | - Zhan Shi
- Acoustic Robotics Systems Lab, Institute of Robotics and Intelligent Systems, Department of Mechanical and Process Engineering, ETH Zurich, ZurichCH-8803, Switzerland
| | - Daniel Ahmed
- Acoustic Robotics Systems Lab, Institute of Robotics and Intelligent Systems, Department of Mechanical and Process Engineering, ETH Zurich, ZurichCH-8803, Switzerland
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19
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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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20
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Wang Y, Han B, Mayor M, Samorì P. Opto-Electrochemical Synaptic Memory in Supramolecularly Engineered Janus 2D MoS 2. Adv Mater 2024; 36:e2307359. [PMID: 37903551 DOI: 10.1002/adma.202307359] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/25/2023] [Indexed: 11/01/2023]
Abstract
Artificial synapses combining multiple yet independent signal processing strategies in a single device are key enabler to achieve high-density of integration, energy efficiency, and fast data manipulation in brain-like computing. By taming functional complexity, the use of hybrids comprising multiple materials as active components in synaptic devices represents a powerful route to encode both short-term potentiation (STP) and long-term potentiation (LTP) in synaptic circuitries. To meet such a grand challenge, herein a novel Janus 2D material is developed by dressing asymmetrically the two surfaces of 2D molybdenum disulfide (MoS2 ) with an electrochemically-switchable ferrocene (Fc)/ ferrocenium (Fc+ ) redox couple and an optically-responsive photochromic azobenzene (Azo). Upon varying the magnitude of the electrochemical stimulus, it is possible to steer the transition between STP and LTP, thereby either triggering electrochemical doping of Fc/Fc+ pair on MoS2 or controlling an adsorption/desorption process of such redox species on MoS2 . In addition, a lower magnitude LTP is recorded by activating the photoisomerization of azobenzene chemisorbed molecules and therefore modulating the dipole-induced doping of the 2D semiconductor. Significantly, the interplay of electrochemical and optical stimuli makes it possible to construct artificial synapses where LTP can be boosted to 4-bit (16 memory states) while simultaneously functioning as STP.
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Affiliation(s)
- Ye Wang
- University of Strasbourg, CNRS, ISIS UMR 7006, 8 Alleé Gaspard Monge, Strasbourg, F-67000, France
| | - Bin Han
- University of Strasbourg, CNRS, ISIS UMR 7006, 8 Alleé Gaspard Monge, Strasbourg, F-67000, France
| | - Marcel Mayor
- Department of Chemistry, University of Basel, St. Johannsring 19, Basel, 4056, Switzerland
- Karlsruhe Institute of Technology KIT, Institute for Nanotechnology, P.O. Box 3640, 76021, Karlsruhe, Germany
| | - Paolo Samorì
- University of Strasbourg, CNRS, ISIS UMR 7006, 8 Alleé Gaspard Monge, Strasbourg, F-67000, France
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21
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Simchon A, Edwards M, Lewandowsky S. The persuasive effects of political microtargeting in the age of generative artificial intelligence. PNAS Nexus 2024; 3:pgae035. [PMID: 38328785 PMCID: PMC10849795 DOI: 10.1093/pnasnexus/pgae035] [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: 08/24/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024]
Abstract
The increasing availability of microtargeted advertising and the accessibility of generative artificial intelligence (AI) tools, such as ChatGPT, have raised concerns about the potential misuse of large language models in scaling microtargeting efforts for political purposes. Recent technological advancements, involving generative AI and personality inference from consumed text, can potentially create a highly scalable "manipulation machine" that targets individuals based on their unique vulnerabilities without requiring human input. This paper presents four studies examining the effectiveness of this putative "manipulation machine." The results demonstrate that personalized political ads tailored to individuals' personalities are more effective than nonpersonalized ads (studies 1a and 1b). Additionally, we showcase the feasibility of automatically generating and validating these personalized ads on a large scale (studies 2a and 2b). These findings highlight the potential risks of utilizing AI and microtargeting to craft political messages that resonate with individuals based on their personality traits. This should be an area of concern to ethicists and policy makers.
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Affiliation(s)
- Almog Simchon
- School of Psychological Science, University of Bristol, Bristol BS8 1QU, UK
- Department of Psychology, Ben-Gurion University of the Negev, Beer Sheva 841050, Israel
| | - Matthew Edwards
- Department of Computer Science, University of Bristol, Bristol BS8 1QU,UK
| | - Stephan Lewandowsky
- School of Psychological Science, University of Bristol, Bristol BS8 1QU, UK
- School of Psychological Science, University of Western Australia, Perth 6009,Australia
- Department of Psychology, University of Potsdam, Potsdam 14476,Germany
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22
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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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23
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Blin K, Shaw S, Medema MH, Weber T. The antiSMASH database version 4: additional genomes and BGCs, new sequence-based searches and more. Nucleic Acids Res 2024; 52:D586-D589. [PMID: 37904617 PMCID: PMC10767862 DOI: 10.1093/nar/gkad984] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
Many microorganisms produce natural products that are frequently used in the development of medicines and crop protection agents. Genome mining has evolved into a prominent method to access this potential. antiSMASH is the most popular tool for this task. Here we present version 4 of the antiSMASH database, providing biosynthetic gene clusters detected by antiSMASH 7.1 in publicly available, dereplicated, high-quality microbial genomes via an interactive graphical user interface. In version 4, the database contains 231 534 high quality BGC regions from 592 archaeal, 35 726 bacterial and 236 fungal genomes and is available at https://antismash-db.secondarymetabolites.org/.
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Affiliation(s)
- Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Simon Shaw
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, 6708PB, The Netherlands
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
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24
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Suen TK, Moorlag SJCFM, Li W, de Bree LCJ, Koeken VACM, Mourits VP, Dijkstra H, Lemmers H, Bhat J, Xu CJ, Joosten LAB, Schultze JL, Li Y, Placek K, Netea MG. BCG vaccination induces innate immune memory in γδ T cells in humans. J Leukoc Biol 2024; 115:149-163. [PMID: 37672677 DOI: 10.1093/jleuko/qiad103] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023] Open
Abstract
Bacillus Calmette-Guérin vaccine is well known for inducing trained immunity in myeloid and natural killer cells, which can explain its cross-protective effect against heterologous infections. Although displaying functional characteristics of both adaptive and innate immunity, γδ T-cell memory has been only addressed in a pathogen-specific context. In this study, we aimed to determine whether human γδ T cells can mount trained immunity and therefore contribute to the cross-protective effect of the Bacillus Calmette-Guérin vaccine. We investigated in vivo induction of innate memory in γδ T cells by Bacillus Calmette-Guérin vaccination in healthy human volunteers by combining single-cell RNA sequencing technology with immune functional assays. The total number of γδ T cells and membrane markers of activation was not influenced by Bacillus Calmette-Guérin vaccination. In contrast, Bacillus Calmette-Guérin changed γδ T cells' transcriptional programs and increased their responsiveness to heterologous bacterial and fungal stimuli, including lipopolysaccharide and Candida albicans, as simultaneously characterized by higher tumor necrosis factor and interferon γ production, weeks after vaccination. Human γδ T cells in adults display the potential to develop a trained immunity phenotype after Bacillus Calmette-Guérin vaccination.
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Affiliation(s)
- Tsz K Suen
- Department of Molecular Immunology and Cell Biology, Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, Netherlands
| | - Wenchao Li
- Department of Computational Biology of Individualized Medicine, Centre for Individualized Infection Medicine (CiiM), a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Straße 7, 30625 Hannover, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Str. 7, 30625 Hannover, Germany
| | - L Charlotte J de Bree
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, Netherlands
| | - Valerie A C M Koeken
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, Netherlands
- Department of Computational Biology of Individualized Medicine, Centre for Individualized Infection Medicine (CiiM), a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Straße 7, 30625 Hannover, Germany
| | - Vera P Mourits
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, Netherlands
| | - Helga Dijkstra
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, Netherlands
| | - Heidi Lemmers
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, Netherlands
| | - Jaydeep Bhat
- Institute of Immunology, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Arnold-Heller-Straße 3, 24105 Kiel, Germany
| | - Cheng-Jian Xu
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, Netherlands
- Department of Computational Biology of Individualized Medicine, Centre for Individualized Infection Medicine (CiiM), a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Straße 7, 30625 Hannover, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Str. 7, 30625 Hannover, Germany
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, Netherlands
- Department of Medical Genetics, Iuliu Haţieganu University of Medicine and Pharmacy, Strada Victor Babeș 8, Cluj-Napoca 400347, Romania
| | - Joachim L Schultze
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases, University of Bonn, Venusberg-Campus 1/9953127, Bonn, Germany
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, Netherlands
- Department of Computational Biology of Individualized Medicine, Centre for Individualized Infection Medicine (CiiM), a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Straße 7, 30625 Hannover, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Feodor-Lynen-Str. 7, 30625 Hannover, Germany
| | - Katarzyna Placek
- Department of Molecular Immunology and Cell Biology, Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Mihai G Netea
- Department of Molecular Immunology and Cell Biology, Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, Netherlands
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25
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Hamidinejad M, Wang H, Sanders KA, De Volder M. Electrochemically Responsive 3D Nanoarchitectures. Adv Mater 2024; 36:e2304517. [PMID: 37702306 DOI: 10.1002/adma.202304517] [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: 05/13/2023] [Revised: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Responsive nanomaterials are being developed to create new unique functionalities such as switchable colors and adhesive properties or other programmable features in response to external stimuli. While many existing examples rely on changes in temperature, humidity, or pH, this study aims to explore an alternative approach relying on simple electric input signals. More specifically, 3D electrochromic architected microstructures are developed using carbon nanotube-Tin (Sn) composites that can be reconfigured by lithiating Sn with low power electric input (≈50 nanowatts). These microstructures have a continuous, regulated, and non-volatile actuation determined by the extent of the electrochemical lithiation process. In addition, this proposed fabrication process relies only on batch lithographic techniques, enabling the parallel production of thousands of 3D microstructures. Structures with a 30-97% change in open-end area upon actuation are demonstrated and the importance of geometric factors in the response and structural integrity of 3D architected microstructures during electrochemical actuation is highlighted.
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Affiliation(s)
- Mahdi Hamidinejad
- Department of Engineering, University of Cambridge, Cambridge, CB3 0FS, UK
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, T6G1H9, Canada
| | - Heng Wang
- Department of Engineering, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Kate A Sanders
- Department of Engineering, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Michael De Volder
- Department of Engineering, University of Cambridge, Cambridge, CB3 0FS, UK
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26
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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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Pri-Tal O, Sun Y, Dadras A, Fürst-Jansen JMR, Zimran G, Michaeli D, Wijerathna-Yapa A, Shpilman M, Merilo E, Yarmolinsky D, Efroni I, de Vries J, Kollist H, Mosquna A. Constitutive activation of ABA receptors in Arabidopsis reveals unique regulatory circuitries. New Phytol 2024; 241:703-714. [PMID: 37915144 DOI: 10.1111/nph.19363] [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: 08/20/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023]
Abstract
Abscisic acid (ABA) is best known for regulating the responses to abiotic stressors. Thus, applications of ABA signaling pathways are considered promising targets for securing yield under stress. ABA levels rise in response to abiotic stress, mounting physiological and metabolic responses that promote plant survival under unfavorable conditions. ABA elicits its effects by binding to a family of soluble receptors found in monomeric and dimeric states, differing in their affinity to ABA and co-receptors. However, the in vivo significance of the biochemical differences between these receptors remains unclear. We took a gain-of-function approach to study receptor-specific functionality. First, we introduced activating mutations that enforce active ABA-bound receptor conformation. We then transformed Arabidopsis ABA-deficient mutants with the constitutive receptors and monitored suppression of the ABA deficiency phenotype. Our findings suggest that PYL4 and PYL5, monomeric ABA receptors, have differential activity in regulating transpiration and transcription of ABA biosynthesis and stress response genes. Through genetic and metabolic data, we demonstrate that PYR1, but not PYL5, is sufficient to activate the ABA positive feedback mechanism. We propose that ABA signaling - from perception to response - flows differently when triggered by different PYLs, due to tissue and transcription barriers, thus resulting in distinct circuitries.
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Affiliation(s)
- Oded Pri-Tal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Yufei Sun
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Armin Dadras
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany
| | - Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany
| | - Gil Zimran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Daphna Michaeli
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Akila Wijerathna-Yapa
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Michal Shpilman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Ebe Merilo
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | | | - Idan Efroni
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goldschmidtsr. 1, 37077, Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077, Goettingen, Germany
| | - Hannes Kollist
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
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28
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Linares-Moreau M, Brandner LA, Velásquez-Hernández MDJ, Fonseca J, Benseghir Y, Chin JM, Maspoch D, Doonan C, Falcaro P. Fabrication of Oriented Polycrystalline MOF Superstructures. Adv Mater 2024; 36:e2309645. [PMID: 38018327 DOI: 10.1002/adma.202309645] [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: 09/18/2023] [Revised: 10/19/2023] [Indexed: 11/30/2023]
Abstract
The field of metal-organic frameworks (MOFs) has progressed beyond the design and exploration of powdery and single-crystalline materials. A current challenge is the fabrication of organized superstructures that can harness the directional properties of the individual constituent MOF crystals. To date, the progress in the fabrication methods of polycrystalline MOF superstructures has led to close-packed structures with defined crystalline orientation. By controlling the crystalline orientation, the MOF pore channels of the constituent crystals can be aligned along specific directions: these systems possess anisotropic properties including enhanced diffusion along specific directions, preferential orientation of guest species, and protection of functional guests. In this perspective, we discuss the current status of MOF research in the fabrication of oriented polycrystalline superstructures focusing on the specific crystalline directions of orientation. Three methods are examined in detail: the assembly from colloidal MOF solutions, the use of external fields for the alignment of MOF particles, and the heteroepitaxial ceramic-to-MOF growth. This perspective aims at promoting the progress of this field of research and inspiring the development of new protocols for the preparation of MOF systems with oriented pore channels, to enable advanced MOF-based devices with anisotropic properties.
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Affiliation(s)
- Mercedes Linares-Moreau
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Graz, 8010, Austria
| | - Lea A Brandner
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Graz, 8010, Austria
| | | | - Javier Fonseca
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Youven Benseghir
- Faculty of Chemistry, Institute of Functional Materials and Catalysis, University of Vienna, Währingerstr. 42, Vienna, A-1090, Austria
| | - Jia Min Chin
- Faculty of Chemistry, Institute of Functional Materials and Catalysis, University of Vienna, Währingerstr. 42, Vienna, A-1090, Austria
| | - Daniel Maspoch
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Barcelona, 08193, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain
| | - Christian Doonan
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Paolo Falcaro
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Graz, 8010, Austria
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29
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Wang C, Cusin L, Ma C, Unsal E, Wang H, Consolaro VG, Montes-García V, Han B, Vitale S, Dianat A, Croy A, Zhang H, Gutierrez R, Cuniberti G, Liu Z, Chi L, Ciesielski A, Samorì P. Enhancing the Carrier Transport in Monolayer MoS 2 through Interlayer Coupling with 2D Covalent Organic Frameworks. Adv Mater 2024; 36:e2305882. [PMID: 37690084 DOI: 10.1002/adma.202305882] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/23/2023] [Indexed: 09/12/2023]
Abstract
The coupling of different 2D materials (2DMs) to form van der Waals heterostructures (vdWHs) is a powerful strategy for adjusting the electronic properties of 2D semiconductors, for applications in opto-electronics and quantum computing. 2D molybdenum disulfide (MoS2 ) represents an archetypical semiconducting, monolayer thick versatile platform for the generation of hybrid vdWH with tunable charge transport characteristics through its interfacing with molecules and assemblies thereof. However, the physisorption of (macro)molecules on 2D MoS2 yields hybrids possessing a limited thermal stability, thereby jeopardizing their technological applications. Herein, the rational design and optimized synthesis of 2D covalent organic frameworks (2D-COFs) for the generation of MoS2 /2D-COF vdWHs exhibiting strong interlayer coupling effects are reported. The high crystallinity of the 2D-COF films makes it possible to engineer an ultrastable periodic doping effect on MoS2 , boosting devices' field-effect mobility at room temperature. Such a performance increase can be attributed to the synergistic effect of the efficient interfacial electron transfer process and the pronounced suppression of MoS2 's lattice vibration. This proof-of-concept work validates an unprecedented approach for the efficient modulation of the electronic properties of 2D transition metal dichalcogenides toward high-performance (opto)electronics for CMOS digital circuits.
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Affiliation(s)
- Can Wang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, P. R. China
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS, 8 allée Gaspard Monge, Strasbourg, 67000, France
| | - Luca Cusin
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS, 8 allée Gaspard Monge, Strasbourg, 67000, France
| | - Chun Ma
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS, 8 allée Gaspard Monge, Strasbourg, 67000, France
| | - Elif Unsal
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062, Dresden, Germany
| | - Hanlin Wang
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS, 8 allée Gaspard Monge, Strasbourg, 67000, France
| | | | - Verónica Montes-García
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS, 8 allée Gaspard Monge, Strasbourg, 67000, France
| | - Bin Han
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS, 8 allée Gaspard Monge, Strasbourg, 67000, France
| | - Stefania Vitale
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS, 8 allée Gaspard Monge, Strasbourg, 67000, France
| | - Arezoo Dianat
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062, Dresden, Germany
| | - Alexander Croy
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07737, Jena, Germany
| | - Haiming Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon Based Functional Materials & Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Rafael Gutierrez
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062, Dresden, Germany
| | - Gianaurelio Cuniberti
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062, Dresden, Germany
- Dresden Center for Computational Materials Science (DCMS), TU Dresden, 01062, Dresden, Germany
| | - Zhaoyang Liu
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, P. R. China
| | - Lifeng Chi
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon Based Functional Materials & Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Artur Ciesielski
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS, 8 allée Gaspard Monge, Strasbourg, 67000, France
| | - Paolo Samorì
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS, 8 allée Gaspard Monge, Strasbourg, 67000, France
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30
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Zhou Y, van Laar SCW, Meggiolaro D, Gregori L, Martani S, Heng JY, Datta K, Jiménez-López J, Wang F, Wong EL, Poli I, Treglia A, Cortecchia D, Prato M, Kobera L, Gao F, Zhao N, Janssen RAJ, De Angelis F, Petrozza A. How Photogenerated I 2 Induces I-Rich Phase Formation in Lead Mixed Halide Perovskites. Adv Mater 2024; 36:e2305567. [PMID: 37722700 DOI: 10.1002/adma.202305567] [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: 06/10/2023] [Revised: 08/27/2023] [Indexed: 09/20/2023]
Abstract
Bandgap tunability of lead mixed halide perovskites (LMHPs) is a crucial characteristic for versatile optoelectronic applications. Nevertheless, LMHPs show the formation of iodide-rich (I-rich) phase under illumination, which destabilizes the semiconductor bandgap and impedes their exploitation. Here, it is shown that how I2 , photogenerated upon charge carrier trapping at iodine interstitials in LMHPs, can promote the formation of I-rich phase. I2 can react with bromide (Br- ) in the perovskite to form a trihalide ion I2 Br- (Iδ- -Iδ+ -Brδ- ), whose negatively charged iodide (Iδ- ) can further exchange with another lattice Br- to form the I-rich phase. Importantly, it is observed that the effectiveness of the process is dependent on the overall stability of the crystalline perovskite structure. Therefore, the bandgap instability in LMHPs is governed by two factors, i.e., the density of native defects leading to I2 production and the Br- binding strength within the crystalline unit. Eventually, this study provides rules for the design of chemical composition in LMHPs to reach their full potential for optoelectronic devices.
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Affiliation(s)
- Yang Zhou
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, via Rubattino 81, Milano, 20134, Italy
| | - Simone C W van Laar
- Molecular Materials and Nanosystems, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - Daniele Meggiolaro
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Chimiche "'Giulio Natta"' (CNR-SCITEC), Via Elce di Sotto 8, Perugia, 06123, Italy
| | - Luca Gregori
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Chimiche "'Giulio Natta"' (CNR-SCITEC), Via Elce di Sotto 8, Perugia, 06123, Italy
- Department of Chemistry, Biology and Biotechnology, University of Perugia and INSTM, Via Elce di Sotto 8, Perugia, 06123, Italy
| | - Samuele Martani
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, via Rubattino 81, Milano, 20134, Italy
| | - Jia-Yong Heng
- Electronic Engineering Department, The Chinese University of Hong Kong, Shatin, NT, 999077, Hong Kong
| | - Kunal Datta
- Molecular Materials and Nanosystems, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - Jesús Jiménez-López
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, via Rubattino 81, Milano, 20134, Italy
| | - Feng Wang
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, SE-581 83, Sweden
| | - E Laine Wong
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, via Rubattino 81, Milano, 20134, Italy
| | - Isabella Poli
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, via Rubattino 81, Milano, 20134, Italy
| | - Antonella Treglia
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, via Rubattino 81, Milano, 20134, Italy
| | - Daniele Cortecchia
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, via Rubattino 81, Milano, 20134, Italy
| | - Mirko Prato
- Materials Characterization Facility, Istituto Italiano di Tecnologia, Via Morego, Genova, 16163, Italy
| | - Libor Kobera
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Sq. 2, Prague 6, 162 06, Czech Republic
| | - Feng Gao
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, SE-581 83, Sweden
| | - Ni Zhao
- Electronic Engineering Department, The Chinese University of Hong Kong, Shatin, NT, 999077, Hong Kong
| | - René A J Janssen
- Molecular Materials and Nanosystems, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - Filippo De Angelis
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Chimiche "'Giulio Natta"' (CNR-SCITEC), Via Elce di Sotto 8, Perugia, 06123, Italy
- Department of Chemistry, Biology and Biotechnology, University of Perugia and INSTM, Via Elce di Sotto 8, Perugia, 06123, Italy
- SKKU Institute of Energy Science and Technology (SIEST) Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Annamaria Petrozza
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, via Rubattino 81, Milano, 20134, Italy
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31
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More YD, Mollick S, Saurabh S, Fajal S, Tricarico M, Dutta S, Shirolkar MM, Mandal W, Tan JC, Ghosh SK. Nanotrap Grafted Anionic MOF for Superior Uranium Extraction from Seawater. Small 2024; 20:e2302014. [PMID: 37698252 DOI: 10.1002/smll.202302014] [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: 03/08/2023] [Revised: 07/28/2023] [Indexed: 09/13/2023]
Abstract
On-demand uranium extraction from seawater (UES) can mitigate growing sustainable energy needs, while high salinity and low concentration hinder its recovery. A novel anionic metal-organic framework (iMOF-1A) is demonstrated adorned with rare Lewis basic pyrazinic sites as uranyl-specific nanotrap serving as robust ion exchange material for selective uranium extraction, rendering its intrinsic ionic characteristics to minimize leaching. Ionic adsorbents sequestrate 99.8% of the uranium in 120 mins (from 20,000 ppb to 24 ppb) and adsorb large amounts of 1336.8 mg g-1 and 625.6 mg g-1 from uranium-spiked deionized water and artificial seawater, respectively, with high distribution coefficient, Kd U ≥ 0.97 × 106 mL g-1 . The material offers a very high enrichment index of ≈5754 and it achieves the UES standard of 6.0 mg g-1 in 16 days, and harvests 9.42 mg g-1 in 30 days from natural seawater. Isothermal titration calorimetry (ITC) studies quantify thermodynamic parameters, previously uncharted in uranium sorption experiments. Infrared nearfield nanospectroscopy (nano-FTIR) and tip-force microscopy (TFM) enable chemical and mechanical elucidation of host-guest interaction at atomic level in sub-micron crystals revealing extant capture events throughout the crystal rather than surface solely. Comprehensive experimentally guided computational studies reveal ultrahigh-selectivity for uranium from seawater, marking mechanistic insight.
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Affiliation(s)
- Yogeshwar D More
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Samraj Mollick
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
- Multifunctional Materials & Composites (MMC) Laboratory, Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Satyam Saurabh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Sahel Fajal
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Michele Tricarico
- Multifunctional Materials & Composites (MMC) Laboratory, Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Subhajit Dutta
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Mandar M Shirolkar
- Symbiosis Center for Nanoscience and Nanotechnology (SCNN), Symbiosis International (Deemed University) (SIU), Lavale, Pune, 412115, India
| | - Writakshi Mandal
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Jin-Chong Tan
- Multifunctional Materials & Composites (MMC) Laboratory, Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Sujit K Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
- Centre for Water Research (CWR), Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
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32
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Leso M, Kokla A, Feng M, Melnyk CW. Pectin modifications promote haustoria development in the parasitic plant Phtheirospermum japonicum. Plant Physiol 2023; 194:229-242. [PMID: 37311199 PMCID: PMC10762509 DOI: 10.1093/plphys/kiad343] [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] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 06/15/2023]
Abstract
Parasitic plants are globally prevalent pathogens with important ecological functions but also potentially devastating agricultural consequences. Common to all parasites is the formation of the haustorium which requires parasite organ development and tissue invasion into the host. Both processes involve cell wall modifications. Here, we investigated a role for pectins during haustorium development in the facultative parasitic plant Phtheirospermum japonicum. Using transcriptomics data from infected Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), we identified genes for multiple P. japonicum pectin methylesterases (PMEs) and their inhibitors (PMEIs) whose expression was upregulated by haustoria formation. Changes in PME and PMEI expression were associated with tissue-specific modifications in pectin methylesterification. While de-methylesterified pectins were present in outer haustorial cells, highly methylesterified pectins were present in inner vascular tissues, including the xylem bridge that connects parasite to host. Specifically blocking xylem bridge formation in the haustoria inhibited several PME and PMEI genes from activating. Similarly, inhibiting PME activity using chemicals or by overexpressing PMEI genes delayed haustoria development. Our results suggest a dynamic and tissue-specific regulation of pectin contributes to haustoria initiation and to the establishment of xylem connections between parasite and host.
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Affiliation(s)
- Martina Leso
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Anna Kokla
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Ming Feng
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
| | - Charles W Melnyk
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas allé 5, 756 51 Uppsala, Sweden
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33
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Woods EV, Singh MP, Kim SH, Schwarz TM, Douglas JO, El-Zoka AA, Giulani F, Gault B. A Versatile and Reproducible Cryo-sample Preparation Methodology for Atom Probe Studies. Microsc Microanal 2023; 29:1992-2003. [PMID: 37856778 DOI: 10.1093/micmic/ozad120] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/14/2023] [Accepted: 10/01/2023] [Indexed: 10/21/2023]
Abstract
Repeatable and reliable site-specific preparation of specimens for atom probe tomography (APT) at cryogenic temperatures has proven challenging. A generalized workflow is required for cryogenic specimen preparation including lift-out via focused ion beam and in situ deposition of capping layers, to strengthen specimens that will be exposed to high electric field and stresses during field evaporation in APT and protect them from environment during transfer into the atom probe. Here, we build on existing protocols and showcase preparation and analysis of a variety of metals, oxides, and supported frozen liquids and battery materials. We demonstrate reliable in situ deposition of a metallic capping layer that significantly improves the atom probe data quality for challenging material systems, particularly battery cathode materials which are subjected to delithiation during the atom probe analysis itself. Our workflow design is versatile and transferable widely to other instruments.
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Affiliation(s)
- Eric V Woods
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
| | - Mahander P Singh
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
| | - Se-Ho Kim
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
| | - Tim M Schwarz
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
| | - James O Douglas
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Ayman A El-Zoka
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Finn Giulani
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Baptiste Gault
- Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Straße 1, Düsseldorf 40237, Germany
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
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Chaguza C, Pöntinen AK, Top J, Arredondo-Alonso S, Freitas AR, Novais C, Torres C, Bentley SD, Peixe L, Coque TM, Willems RJL, Corander J. The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection. Microbiol Spectr 2023; 11:e0020123. [PMID: 37811975 PMCID: PMC10714801 DOI: 10.1128/spectrum.00201-23] [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: 01/13/2023] [Accepted: 08/29/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Enterococcus faecalis causes life-threatening invasive hospital- and community-associated infections that are usually associated with multidrug resistance globally. Although E. faecalis infections cause opportunistic infections typically associated with antibiotic use, immunocompromised immune status, and other factors, they also possess an arsenal of virulence factors crucial for their pathogenicity. Despite this, the relative contribution of these virulence factors and other genetic changes to the pathogenicity of E. faecalis strains remain poorly understood. Here, we investigated whether specific genomic changes in the genome of E. faecalis isolates influence its pathogenicity-infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection and intestinal colonization. Our findings indicate that E. faecalis genetics partially influence the infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection, possibly due to gut-to-bloodstream translocation, highlighting the potential substantial role of host and environmental factors, including gut microbiota, on the opportunistic pathogenic lifestyle of this bacterium.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Anna K. Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sergio Arredondo-Alonso
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ana R. Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Luisa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
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Costigan A, Hollville E, Martin SJ. Discriminating Between Apoptosis, Necrosis, Necroptosis, and Ferroptosis by Microscopy and Flow Cytometry. Curr Protoc 2023; 3:e951. [PMID: 38112058 DOI: 10.1002/cpz1.951] [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] [Indexed: 12/20/2023]
Abstract
Apoptosis is a mode of programmed cell death that plays important roles in tissue sculpting during development, in the maintenance of tissue homeostasis in the adult, and in the eradication of injured or infected cells during pathological processes. Numerous physiological as well as pathological stimuli trigger apoptosis, such as engagement of plasma-membrane-associated Fas, TRAIL, or TNF receptors, growth factor deprivation, hypoxia, radiation, and exposure to diverse cytotoxic drugs. Apoptosis is coordinated by members of the caspase family of cysteine proteases, which, upon activation, trigger a series of dramatic morphological and biochemical changes including retraction from the substratum, cell shrinkage, extensive and protracted plasma membrane blebbing, chromatin condensation, DNA hydrolysis, nuclear fragmentation, and proteolytic cleavage of numerous caspase substrates. These dramatic structural and biochemical alterations result not only in the controlled dismantling of the cell, but also in the rapid recognition and removal of apoptotic cells by phagocytes through the cell surface display of phagocytotic triggers such as phosphatidylserine. Necrosis, which is typically nonprogrammed or imposed upon the cell by overwhelming membrane or organelle damage, is characterized by high-amplitude cell swelling, followed by rapid plasma membrane rupture and release of cellular contents into the extracellular space. Necrosis is often provoked by infectious agents or severe departure from physiological conditions due to toxins, temperature extremes, or physical injury. However, forms of programmed necrosis (necroptosis, pyroptosis, ferroptosis) can also occur in specific circumstances. Nonprogrammed and programmed necrosis can be distinguished from apoptosis by morphological features, based on the rapid uptake of vital dyes, and through the application of specific inhibitors of key molecules associated with the latter modes of cell death. This unit describes protocols for the measurement of apoptosis and necrosis and for distinguishing apoptosis from programmed as well as conventional necrosis. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Analysis of cell morphology by phase-contrast microscopy Alternative Protocol 1: Assessment of morphological changes using eosin-methylene blue staining Alternative Protocol 2: Analysis of nuclear morphology by fluorescence microscopy Support Protocol: Preparation of cytospins Basic Protocol 2: Measurement of plasma membrane composition with annexin V and propidium iodide Basic Protocol 3: Measurement of DNA fragmentation by flow cytometry Alternative Protocol 3: Analysis of DNA fragmentation by the TUNEL assay Basic Protocol 4: Measurement of caspase activation by flow cytometry Basic Protocol 5: Discriminating between apoptosis, necrosis, necroptosis, and ferroptosis.
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Affiliation(s)
- Aoife Costigan
- Molecular Cell Biology Laboratory, Department of Genetics, Trinity College, Dublin, Ireland
| | - Emilie Hollville
- Institute of Medical Sciences, University of Aberdeen Foresterhill, Aberdeen, Scotland, United Kingdom
| | - Seamus J Martin
- Molecular Cell Biology Laboratory, Department of Genetics, Trinity College, Dublin, Ireland
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Schilling A, Sedley W, Gerum R, Metzner C, Tziridis K, Maier A, Schulze H, Zeng FG, Friston KJ, Krauss P. Predictive coding and stochastic resonance as fundamental principles of auditory phantom p erception. Brain 2023; 146:4809-4825. [PMID: 37503725 PMCID: PMC10690027 DOI: 10.1093/brain/awad255] [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: 10/26/2022] [Revised: 06/27/2023] [Accepted: 07/15/2023] [Indexed: 07/29/2023] Open
Abstract
Mechanistic insight is achieved only when experiments are employed to test formal or computational models. Furthermore, in analogy to lesion studies, phantom perception may serve as a vehicle to understand the fundamental processing principles underlying healthy auditory perception. With a special focus on tinnitus-as the prime example of auditory phantom perception-we review recent work at the intersection of artificial intelligence, psychology and neuroscience. In particular, we discuss why everyone with tinnitus suffers from (at least hidden) hearing loss, but not everyone with hearing loss suffers from tinnitus. We argue that intrinsic neural noise is generated and amplified along the auditory pathway as a compensatory mechanism to restore normal hearing based on adaptive stochastic resonance. The neural noise increase can then be misinterpreted as auditory input and perceived as tinnitus. This mechanism can be formalized in the Bayesian brain framework, where the percept (posterior) assimilates a prior prediction (brain's expectations) and likelihood (bottom-up neural signal). A higher mean and lower variance (i.e. enhanced precision) of the likelihood shifts the posterior, evincing a misinterpretation of sensory evidence, which may be further confounded by plastic changes in the brain that underwrite prior predictions. Hence, two fundamental processing principles provide the most explanatory power for the emergence of auditory phantom perceptions: predictive coding as a top-down and adaptive stochastic resonance as a complementary bottom-up mechanism. We conclude that both principles also play a crucial role in healthy auditory perception. Finally, in the context of neuroscience-inspired artificial intelligence, both processing principles may serve to improve contemporary machine learning techniques.
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Affiliation(s)
- Achim Schilling
- Neuroscience Lab, University Hospital Erlangen, 91054 Erlangen, Germany
- Cognitive Computational Neuroscience Group, University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - William Sedley
- Translational and Clinical Research Institute, Newcastle University Medical School, Newcastle upon Tyne NE2 4HH, UK
| | - Richard Gerum
- Cognitive Computational Neuroscience Group, University Erlangen-Nürnberg, 91058 Erlangen, Germany
- Department of Physics and Astronomy and Center for Vision Research, York University, Toronto, ON M3J 1P3, Canada
| | - Claus Metzner
- Neuroscience Lab, University Hospital Erlangen, 91054 Erlangen, Germany
| | | | - Andreas Maier
- Pattern Recognition Lab, University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Holger Schulze
- Neuroscience Lab, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Fan-Gang Zeng
- Center for Hearing Research, Departments of Anatomy and Neurobiology, Biomedical Engineering, Cognitive Sciences, Otolaryngology–Head and Neck Surgery, University of California Irvine, Irvine, CA 92697, USA
| | - Karl J Friston
- Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, London WC1N 3AR, UK
| | - Patrick Krauss
- Neuroscience Lab, University Hospital Erlangen, 91054 Erlangen, Germany
- Cognitive Computational Neuroscience Group, University Erlangen-Nürnberg, 91058 Erlangen, Germany
- Pattern Recognition Lab, University Erlangen-Nürnberg, 91058 Erlangen, Germany
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37
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van Borkulo CD, van Bork R, Boschloo L, Kossakowski JJ, Tio P, Schoevers RA, Borsboom D, Waldorp LJ. Comparing network structures on three aspects: A permutation test. Psychol Methods 2023; 28:1273-1285. [PMID: 35404628 DOI: 10.1037/met0000476] [Citation(s) in RCA: 194] [Impact Index Per Article: 194.0] [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] [Indexed: 01/04/2024]
Abstract
Network approaches to psychometric constructs, in which constructs are modeled in terms of interactions between their constituent factors, have rapidly gained popularity in psychology. Applications of such network approaches to various psychological constructs have recently moved from a descriptive stance, in which the goal is to estimate the network structure that pertains to a construct, to a more comparative stance, in which the goal is to compare network structures across populations. However, the statistical tools to do so are lacking. In this article, we present the network comparison test (NCT), which uses resampling-based permutation testing to compare network structures from two independent, cross-sectional data sets on invariance of (a) network structure, (b) edge (connection) strength, and (c) global strength. Performance of NCT is evaluated in simulations that show NCT to perform well in various circumstances for all three tests: The Type I error rate is close to the nominal significance level, and power proves sufficiently high if sample size and difference between networks are substantial. We illustrate NCT by comparing depression symptom networks of males and females. Possible extensions of NCT are discussed. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
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Affiliation(s)
| | - Riet van Bork
- Center for Philosophy of Science, University of Pittsburgh
| | - Lynn Boschloo
- Department of Clinical, Neuro, and Developmental Psychology, VU University Amsterdam
| | | | - Pia Tio
- Department of Psychological Methods, University of Amsterdam
| | - Robert A Schoevers
- Department of Psychiatry, Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen
| | - Denny Borsboom
- Department of Psychological Methods, University of Amsterdam
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38
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Wright DS, Manel AN, Guachamin-Rosero M, Chamba-Vaca P, Bacquet CN, Merrill RM. Quantifying visual acuity in Heliconius butterflies. Biol Lett 2023; 19:20230476. [PMID: 38087940 PMCID: PMC10716659 DOI: 10.1098/rsbl.2023.0476] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Heliconius butterflies are well-known for their colourful wing patterns, which advertise distastefulness to potential predators and are used during mate choice. However, the relative importance of different aspects of these signals will depend on the visual abilities of Heliconius and their predators. Previous studies have investigated colour sensitivity and neural anatomy, but visual acuity (the ability to perceive detail) has not been studied in these butterflies. Here, we provide the first estimate of visual acuity in Heliconius: from a behavioural optomotor assay, we found that mean visual acuity = 0.49 cycles-per-degree (cpd), with higher acuity in males than females. We also examined eye morphology and report more ommatidia in male eyes. Finally, we estimated how visual acuity affects Heliconius visual perception compared to a potential avian predator. Whereas the bird predator maintained high resolving power, Heliconius lost the ability to resolve detail at greater distances, though colours may remain salient. These results will inform future studies of Heliconius wing pattern evolution, as well as other aspects in these highly visual butterflies, which have emerged as an important system in studies of adaptation and speciation.
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Affiliation(s)
- Daniel Shane Wright
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Anupama Nayak Manel
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Michelle Guachamin-Rosero
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Universidad Regional Amazónica IKIAM, Tena, Ecuador
| | - Pamela Chamba-Vaca
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Universidad Regional Amazónica IKIAM, Tena, Ecuador
| | | | - Richard M. Merrill
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
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39
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Borba AR, Reyna-Llorens I, Dickinson PJ, Steed G, Gouveia P, Górska AM, Gomes C, Kromdijk J, Webb AAR, Saibo NJM, Hibberd JM. Compartmentation of photosynthesis gene expression in C4 maize depends on time of day. Plant Physiol 2023; 193:2306-2320. [PMID: 37555432 PMCID: PMC10663113 DOI: 10.1093/plphys/kiad447] [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] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Compared with the ancestral C3 state, C4 photosynthesis occurs at higher rates with improved water and nitrogen use efficiencies. In both C3 and C4 plants, rates of photosynthesis increase with light intensity and are maximal around midday. We determined that in the absence of light or temperature fluctuations, photosynthesis in maize (Zea mays) peaks in the middle of the subjective photoperiod. To investigate the molecular processes associated with these temporal changes, we performed RNA sequencing of maize mesophyll and bundle sheath strands over a 24-h time course. Preferential expression of C4 cycle genes in these cell types was strongest between 6 and 10 h after dawn when rates of photosynthesis were highest. For the bundle sheath, DNA motif enrichment and gene coexpression analyses suggested members of the DNA binding with one finger (DOF) and MADS (MINICHROMOSOME MAINTENANCE FACTOR 1/AGAMOUS/DEFICIENS/Serum Response Factor)-domain transcription factor families mediate diurnal fluctuations in C4 gene expression, while trans-activation assays in planta confirmed their ability to activate promoter fragments from bundle sheath expressed genes. The work thus identifies transcriptional regulators and peaks in cell-specific C4 gene expression coincident with maximum rates of photosynthesis in the maize leaf at midday.
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Affiliation(s)
- Ana Rita Borba
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras 2780-157, Portugal
| | - Ivan Reyna-Llorens
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Patrick J Dickinson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Gareth Steed
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Paulo Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras 2780-157, Portugal
| | - Alicja M Górska
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras 2780-157, Portugal
| | - Celia Gomes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras 2780-157, Portugal
| | - Johannes Kromdijk
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras 2780-157, Portugal
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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40
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Machado H, Temudo A, Niz MD. The lymphatic system favours survival of a unique T. brucei population. Biol Open 2023; 12:bio059992. [PMID: 37870927 PMCID: PMC10651106 DOI: 10.1242/bio.059992] [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: 04/28/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Trypanosoma brucei colonise and multiply in the blood vasculature, as well as in various organs of the host's body. Lymph nodes have been previously shown to harbour large numbers of parasites, and the lymphatic system has been proposed as a key site that allows T. brucei distribution through, and colonization of the mammalian body. However, visualization of host-pathogen interactions in the lymphatic system has never captured dynamic events with high spatial and temporal resolution throughout infection. In our work, we used a mixture of tools including intravital microscopy and ex vivo imaging to study T. brucei distribution in 20 sets of lymph nodes. We demonstrate that lymph node colonization by T. brucei is different across lymph node sets, with the most heavily colonised being the draining lymph nodes of main tissue reservoirs: the gonadal white adipose tissue and pancreas. Moreover, we show that the lymphatic vasculature is a pivotal site for parasite dispersal, and altering this colonization by blocking LYVE-1 is detrimental for parasite survival. Additionally, parasites within the lymphatic vasculature have unique morphological and behavioural characteristics, different to those found in the blood, demonstrating that across both types of vasculature, these environments are physically separated. Finally, we demonstrate that the lymph nodes and the lymphatic vasculature undergo significant alterations during T. brucei infection, resulting in oedema throughout the host's body.
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Affiliation(s)
- Henrique Machado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - António Temudo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
- Bioimaging Unit, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
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41
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Wang M, Wang G, Naisa C, Fu Y, Gali SM, Paasch S, Wang M, Wittkaemper H, Papp C, Brunner E, Zhou S, Beljonne D, Steinrück HP, Dong R, Feng X. Poly(benzimidazobenzophenanthroline)-Ladder-Type Two-Dimensional Conjugated Covalent Organic Framework for Fast Proton Storage. Angew Chem Int Ed Engl 2023; 62:e202310937. [PMID: 37691002 DOI: 10.1002/anie.202310937] [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: 07/30/2023] [Revised: 08/20/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Electrochemical proton storage plays an essential role in designing next-generation high-rate energy storage devices, e.g., aqueous batteries. Two-dimensional conjugated covalent organic frameworks (2D c-COFs) are promising electrode materials, but their competitive proton and metal-ion insertion mechanisms remain elusive, and proton storage in COFs is rarely explored. Here, we report a perinone-based poly(benzimidazobenzophenanthroline) (BBL)-ladder-type 2D c-COF for fast proton storage in both a mild aqueous Zn-ion electrolyte and strong acid. We unveil that the discharged C-O- groups exhibit largely reduced basicity due to the considerable π-delocalization in perinone, thus affording the 2D c-COF a unique affinity for protons with fast kinetics. As a consequence, the 2D c-COF electrode presents an outstanding rate capability of up to 200 A g-1 (over 2500 C), surpassing the state-of-the-art conjugated polymers, COFs, and metal-organic frameworks. Our work reports the first example of pure proton storage among COFs and highlights the great potential of BBL-ladder-type 2D conjugated polymers in future energy devices.
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Affiliation(s)
- Mingchao Wang
- Center for Advancing Electronics Dresden (cfaed) and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstrasse 4, 01062, Dresden, Germany
| | - Gang Wang
- Center for Advancing Electronics Dresden (cfaed) and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstrasse 4, 01062, Dresden, Germany
- Key Laboratory of Advanced Fuel Cells and Electrolyzers Technology of Zhejiang Province, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chandrasekhar Naisa
- Center for Advancing Electronics Dresden (cfaed) and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstrasse 4, 01062, Dresden, Germany
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120, Halle, Germany
| | - Yubin Fu
- Center for Advancing Electronics Dresden (cfaed) and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstrasse 4, 01062, Dresden, Germany
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120, Halle, Germany
| | - Sai Manoj Gali
- Laboratory for Chemistry of Novel Materials, University of Mons, Place du Parc 20, 7000, Mons, Belgium
| | - Silvia Paasch
- Center for Advancing Electronics Dresden (cfaed) and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstrasse 4, 01062, Dresden, Germany
| | - Mao Wang
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328, Dresden, Germany
- Laboratory of Micro-Nano Optics, College of Physics and Electronic Engineering, Sichuan Normal University, Chengdu, 610101, China
| | - Haiko Wittkaemper
- Institute of Physical Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstr. 3, 91058, Erlangen, Germany
| | - Christian Papp
- Institute of Physical Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstr. 3, 91058, Erlangen, Germany
- Physical Chemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Eike Brunner
- Center for Advancing Electronics Dresden (cfaed) and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstrasse 4, 01062, Dresden, Germany
| | - Shengqiang Zhou
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328, Dresden, Germany
| | - David Beljonne
- Laboratory for Chemistry of Novel Materials, University of Mons, Place du Parc 20, 7000, Mons, Belgium
| | - Hans-Peter Steinrück
- Institute of Physical Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstr. 3, 91058, Erlangen, Germany
| | - Renhao Dong
- Center for Advancing Electronics Dresden (cfaed) and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstrasse 4, 01062, Dresden, Germany
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, China
| | - Xinliang Feng
- Center for Advancing Electronics Dresden (cfaed) and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstrasse 4, 01062, Dresden, Germany
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120, Halle, Germany
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Ingham CS, Engl T, Kaltenpoth M. Protection of a defensive symbiont does not constrain the composition of the multifunctional hydrocarbon profile in digger wasps. Biol Lett 2023; 19:20230301. [PMID: 37909057 PMCID: PMC10618855 DOI: 10.1098/rsbl.2023.0301] [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: 06/27/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023] Open
Abstract
Hydrocarbons (HCs) fulfil indispensable functions in insects, protecting against desiccation and serving chemical communication. However, the link between composition and function, and the selection pressures shaping HC profiles remain poorly understood. Beewolf digger wasps (Hymenoptera: Crabronidae) use an antennal gland secretion rich in linear unsaturated HCs to form a hydrophobic barrier around their defensive bacterial symbiont, protecting it from brood cell fumigation by toxic egg-produced nitric oxide (NO). Virtually identical HC compositions mediate desiccation protection and prey preservation from moulding in underground beewolf brood cells. It is unknown whether this composition presents an optimized adaptation to all functions, or a compromise due to conflicting selection pressures. Here, we reconstitute the NO barrier with single and binary combinations of synthetic linear saturated and unsaturated HCs, corresponding to HCs found in beewolves. The results show that pure alkanes as well as 3 : 1 mixtures of alkanes and alkenes resembling the composition of beewolf HCs form efficient protective barriers against NO, indicating that protection can be achieved by different mixtures of HCs. Since in vitro assays with symbiont cultures from different beewolf hosts indicate widespread NO sensitivity, HC-mediated protection from NO is likely important across Philanthini wasps. We conclude that HC-mediated protection of the symbiont from NO does not exert a conflicting selection pressure on the multifunctional HC profile of beewolves.
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Affiliation(s)
- Chantal Selina Ingham
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Tobias Engl
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
- Department of Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
- Department of Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
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Zur Y, Noah A, Boix-Constant C, Mañas-Valero S, Fridman N, Rama-Eiroa R, Huber ME, Santos EJG, Coronado E, Anahory Y. Magnetic Imaging and Domain Nucleation in CrSBr Down to the 2D Limit. Adv Mater 2023; 35:e2307195. [PMID: 37702506 DOI: 10.1002/adma.202307195] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/31/2023] [Indexed: 09/14/2023]
Abstract
Recent advancements in 2D materials have revealed the potential of van der Waals magnets, and specifically of their magnetic anisotropy that allows applications down to the 2D limit. Among these materials, CrSBr has emerged as a promising candidate, because its intriguing magnetic and electronic properties have appeal for both fundamental and applied research in spintronics or magnonics. In this work, nano-SQUID-on-tip (SOT) microscopy is used to obtain direct magnetic imaging of CrSBr flakes with thicknesses ranging from monolayer (N = 1) to few-layer (N = 5). The ferromagnetic order is preserved down to the monolayer, while the antiferromagnetic coupling of the layers starts from the bilayer case. For odd layers, at zero applied magnetic field, the stray field resulting from the uncompensated layer is directly imaged. The progressive spin reorientation along the out-of-plane direction (hard axis) is also measured with a finite applied magnetic field, allowing evaluation of the anisotropy constant, which remains stable down to the monolayer and is close to the bulk value. Finally, by selecting the applied magnetic field protocol, the formation of Néel magnetic domain walls is observed down to the single-layer limit.
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Affiliation(s)
- Yishay Zur
- The Racah Institute of Physics, The Hebrew University, Jerusalem, 9190401, Israel
- Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Avia Noah
- The Racah Institute of Physics, The Hebrew University, Jerusalem, 9190401, Israel
- Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Carla Boix-Constant
- Instituto de Ciencia Molecular (ICMol), Universitat de València, Catedrático José Beltrán 2, Paterna, 46980, Spain
| | - Samuel Mañas-Valero
- Instituto de Ciencia Molecular (ICMol), Universitat de València, Catedrático José Beltrán 2, Paterna, 46980, Spain
| | - Nofar Fridman
- The Racah Institute of Physics, The Hebrew University, Jerusalem, 9190401, Israel
- Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ricardo Rama-Eiroa
- Donostia International Physics Center (DIPC), Basque Country, Donostia-San Sebastián, 20018, Spain
- Institute for Condensed Matter Physics and Complex Systems, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH93FD, UK
| | - Martin E Huber
- Departments of Physics and Electrical Engineering, University of Colorado Denver, Denver, CO, 80217, USA
| | - Elton J G Santos
- Donostia International Physics Center (DIPC), Basque Country, Donostia-San Sebastián, 20018, Spain
- Institute for Condensed Matter Physics and Complex Systems, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH93FD, UK
- Higgs Centre for Theoretical Physics, University of Edinburgh, Edinburgh, EH93FD, UK
| | - Eugenio Coronado
- Instituto de Ciencia Molecular (ICMol), Universitat de València, Catedrático José Beltrán 2, Paterna, 46980, Spain
| | - Yonathan Anahory
- The Racah Institute of Physics, The Hebrew University, Jerusalem, 9190401, Israel
- Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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Kleizen B, de Mattos E, Papaioannou O, Monti M, Tartaglia GG, van der Sluijs P, Braakman I. Transmembrane Helices 7 and 8 Confer Aggregation Sensitivity to the Cystic Fibrosis Transmembrane Conductance Regulator. Int J Mol Sci 2023; 24:15741. [PMID: 37958724 PMCID: PMC10648718 DOI: 10.3390/ijms242115741] [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: 09/04/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a large multi-spanning membrane protein that is susceptible to misfolding and aggregation. We have identified here the region responsible for this instability. Temperature-induced aggregation of C-terminally truncated versions of CFTR demonstrated that all truncations up to the second transmembrane domain (TMD2), including the R region, largely resisted aggregation. Limited proteolysis identified a folded structure that was prone to aggregation and consisted of TMD2 and at least part of the Regulatory Region R. Only when both TM7 (TransMembrane helix 7) and TM8 were present, TMD2 fragments became as aggregation-sensitive as wild-type CFTR, in line with increased thermo-instability of late CFTR nascent chains and in silico prediction of aggregation propensity. In accord, isolated TMD2 was degraded faster in cells than isolated TMD1. We conclude that TMD2 extended at its N-terminus with part of the R region forms a protease-resistant structure that induces heat instability in CFTR and may be responsible for its limited intracellular stability.
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Affiliation(s)
- Bertrand Kleizen
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Eduardo de Mattos
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Olga Papaioannou
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Michele Monti
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy; (M.M.); (G.G.T.)
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genoa, Italy
| | - Gian Gaetano Tartaglia
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy; (M.M.); (G.G.T.)
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genoa, Italy
| | - Peter van der Sluijs
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
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Dresselhaus-Marais LE, Kozioziemski B, Holstad TS, Ræder TM, Seaberg M, Nam D, Kim S, Breckling S, Choi S, Chollet M, Cook PK, Folsom E, Galtier E, Gonzalez A, Gorkhover T, Guillet S, Haldrup K, Howard M, Katagiri K, Kim S, Kim S, Kim S, Kim H, Knudsen EB, Kuschel S, Lee HJ, Lin C, McWilliams RS, Nagler B, Nielsen MM, Ozaki N, Pal D, Pablo Pedro R, Saunders AM, Schoofs F, Sekine T, Simons H, van Driel T, Wang B, Yang W, Yildirim C, Poulsen HF, Eggert JH. Simultaneous bright- and dark-field X-ray microscopy at X-ray free electron lasers. Sci Rep 2023; 13:17573. [PMID: 37845245 PMCID: PMC10579415 DOI: 10.1038/s41598-023-35526-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 05/19/2023] [Indexed: 10/18/2023] Open
Abstract
The structures, strain fields, and defect distributions in solid materials underlie the mechanical and physical properties across numerous applications. Many modern microstructural microscopy tools characterize crystal grains, domains and defects required to map lattice distortions or deformation, but are limited to studies of the (near) surface. Generally speaking, such tools cannot probe the structural dynamics in a way that is representative of bulk behavior. Synchrotron X-ray diffraction based imaging has long mapped the deeply embedded structural elements, and with enhanced resolution, dark field X-ray microscopy (DFXM) can now map those features with the requisite nm-resolution. However, these techniques still suffer from the required integration times due to limitations from the source and optics. This work extends DFXM to X-ray free electron lasers, showing how the [Formula: see text] photons per pulse available at these sources offer structural characterization down to 100 fs resolution (orders of magnitude faster than current synchrotron images). We introduce the XFEL DFXM setup with simultaneous bright field microscopy to probe density changes within the same volume. This work presents a comprehensive guide to the multi-modal ultrafast high-resolution X-ray microscope that we constructed and tested at two XFELs, and shows initial data demonstrating two timing strategies to study associated reversible or irreversible lattice dynamics.
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Affiliation(s)
- Leora E Dresselhaus-Marais
- Department of Materials Science & Engineering, Stanford University, Stanford, CA, USA.
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
- Physics Division, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | | | - Theodor S Holstad
- Department of Physics, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Daewoong Nam
- Photon Science Center, Pohang University and Science and Technology, Pohang, Korea
- XFEL Beamline Department, Pohang Accelerator Laboratory, Pohang University and Science and Technology, Pohang, Korea
| | - Sangsoo Kim
- XFEL Beamline Department, Pohang Accelerator Laboratory, Pohang University and Science and Technology, Pohang, Korea
| | | | - Sungwook Choi
- Department of Physics, Sogang University, Seoul, Korea
| | | | - Philip K Cook
- University of Natural Resources and Life Sciences, BOKU, Vienna, Austria
- European Synchrotron Radiation Facility, Grenoble, France
| | - Eric Folsom
- Physics Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Eric Galtier
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Tais Gorkhover
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- University of Hamburg, Hamburg, Germany
| | - Serge Guillet
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | | | - Kento Katagiri
- Department of Materials Science & Engineering, Stanford University, Stanford, CA, USA
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Seonghan Kim
- XFEL Beamline Department, Pohang Accelerator Laboratory, Pohang University and Science and Technology, Pohang, Korea
| | - Sunam Kim
- XFEL Beamline Department, Pohang Accelerator Laboratory, Pohang University and Science and Technology, Pohang, Korea
| | - Sungwon Kim
- Department of Physics, Sogang University, Seoul, Korea
| | - Hyunjung Kim
- Department of Physics, Sogang University, Seoul, Korea
| | | | - Stephan Kuschel
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Institute of Nuclear Physics, Technical University of Darmstadt, Darmstadt, Germany
| | - Hae Ja Lee
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Chuanlong Lin
- Center for High Pressure Science & Technology Advanced Research, Shanghai, China
| | | | - Bob Nagler
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Norimasa Ozaki
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Dayeeta Pal
- Department of Materials Science & Engineering, Stanford University, Stanford, CA, USA
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Ricardo Pablo Pedro
- Department of Nuclear Science & Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alison M Saunders
- Physics Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Frank Schoofs
- UK Atomic Energy Authority, Culham Science Centre, Abingdon, UK
| | - Toshimori Sekine
- Center for High Pressure Science & Technology Advanced Research, Shanghai, China
| | - Hugh Simons
- Department of Physics, Technical University of Denmark, Lyngby, Denmark
| | - Tim van Driel
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Bihan Wang
- Center for High Pressure Science & Technology Advanced Research, Shanghai, China
| | - Wenge Yang
- Center for High Pressure Science & Technology Advanced Research, Shanghai, China
| | - Can Yildirim
- European Synchrotron Radiation Facility, Grenoble, France
- Université Grenoble Alpes, CEA, Grenoble, France
| | | | - Jon H Eggert
- Physics Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
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46
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Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics 2023; 225:iyad133. [PMID: 37450606 PMCID: PMC10550317 DOI: 10.1093/genetics/iyad133] [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: 11/02/2022] [Revised: 05/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023] Open
Abstract
The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents' trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the "shared" and "residual" components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M. We illustrate our results with some numerical examples.
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Affiliation(s)
- Nicholas H Barton
- Institute of Science and Technology, Am Campus I, A-3400 Klosterneuberg, Austria
| | - Alison M Etheridge
- Department of Statistics, University of Oxford, 24–29 St Giles, OX1 3LB Oxford, UK
| | - Amandine Véber
- MAP5, Université Paris Cité, CNRS, 45 rue des Saints-Pères, 75006 Paris, France
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Liu K, Réhault J, Liang B, Hambsch M, Zhang Y, Seçkin S, Zhou Y, Shivhare R, Zhang P, Polozij M, König TAF, Qi H, Zhou S, Fery A, Mannsfeld SCB, Kaiser U, Heine T, Banerji N, Dong R, Feng X. A Quasi-2D Polypyrrole Film with Band-Like Transport Behavior and High Charge-Carrier Mobility. Adv Mater 2023; 35:e2303288. [PMID: 37468165 DOI: 10.1002/adma.202303288] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/09/2023] [Accepted: 06/23/2023] [Indexed: 07/21/2023]
Abstract
Quasi-2D (q2D) conjugated polymers (CPs) are polymers that consist of linear CP chains assembled through non-covalent interactions to form a layered structure. In this work, the synthesis of a novel crystalline q2D polypyrrole (q2DPPy) film at the air/H2 SO4 (95%) interface is reported. The unique interfacial environment facilitates chain extension, prevents disorder, and results in a crystalline, layered assembly of protonated quinoidal chains with a fully extended conformation in its crystalline domains. This unique structure features highly delocalized π-electron systems within the extended chains, which is responsible for the low effective mass and narrow electronic bandgap. Thus, the temperature-dependent charge-transport properties of q2DPPy are investigated using the van der Pauw (vdP) method and terahertz time-domain spectroscopy (THz-TDS). The vdP method reveals that the q2DPPy film exhibits a semiconducting behavior with a thermally activated hopping mechanism in long-range transport between the electrodes. Conversely, THz-TDS reveals a band-like transport, indicating intrinsic charge transport up to a record short-range high THz mobility of ≈107.1 cm2 V-1 s-1 .
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Affiliation(s)
- Kejun Liu
- Faculty of Chemistry and Food Chemistry & Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - Julien Réhault
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - Baokun Liang
- Central Facility of Materials Science Electron Microscopy, Universität Ulm, 89081, Ulm, Germany
| | - Mike Hambsch
- Center for Advancing Electronics Dresden and Faculty of Electrical and Computer Engineering, Technische Universität Dresden, 01062, Dresden, Germany
| | - Yingying Zhang
- Faculty of Chemistry and Food Chemistry & Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany
| | - Sezer Seçkin
- Leibniz-Institut für Polymerforschung Dresden e.V. (IPF), 01069, Dresden, Germany
| | - Yunxia Zhou
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Ion Beam Physics and Materials Research, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Rishi Shivhare
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - Peng Zhang
- Faculty of Chemistry and Food Chemistry & Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany
- Leibniz-Institut für Polymerforschung Dresden e.V. (IPF), 01069, Dresden, Germany
| | - Miroslav Polozij
- Faculty of Chemistry and Food Chemistry & Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany
| | - Tobias A F König
- Leibniz-Institut für Polymerforschung Dresden e.V. (IPF), 01069, Dresden, Germany
| | - Haoyuan Qi
- Faculty of Chemistry and Food Chemistry & Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany
- Central Facility of Materials Science Electron Microscopy, Universität Ulm, 89081, Ulm, Germany
| | - Shengqiang Zhou
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Ion Beam Physics and Materials Research, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Andreas Fery
- Leibniz-Institut für Polymerforschung Dresden e.V. (IPF), 01069, Dresden, Germany
| | - Stefan C B Mannsfeld
- Center for Advancing Electronics Dresden and Faculty of Electrical and Computer Engineering, Technische Universität Dresden, 01062, Dresden, Germany
| | - Ute Kaiser
- Central Facility of Materials Science Electron Microscopy, Universität Ulm, 89081, Ulm, Germany
| | - Thomas Heine
- Faculty of Chemistry and Food Chemistry & Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Leipzig Research Branch, 04316, Leipzig, Germany
- Department of Chemistry, Yonsei University, Seodaemun-gu, Seoul, 120-749, South Korea
| | - Natalie Banerji
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - Renhao Dong
- Faculty of Chemistry and Food Chemistry & Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Xinliang Feng
- Faculty of Chemistry and Food Chemistry & Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany
- Max Planck Institute of Microstructure Physics, Weinberg 2, D-06120, Halle, Sachsen-Anhalt, Germany
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48
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Mathony J, Aschenbrenner S, Becker P, Niopek D. Dissecting the Determinants of Domain Insertion Tolerance and Allostery in Proteins. Adv Sci (Weinh) 2023; 10:e2303496. [PMID: 37562980 PMCID: PMC10558690 DOI: 10.1002/advs.202303496] [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: 05/30/2023] [Revised: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Domain insertion engineering is a promising approach to recombine the functions of evolutionarily unrelated proteins. Insertion of light-switchable receptor domains into a selected effector protein, for instance, can yield allosteric effectors with light-dependent activity. However, the parameters that determine domain insertion tolerance and allostery are poorly understood. Here, an unbiased screen is used to systematically assess the domain insertion permissibility of several evolutionary unrelated proteins. Training machine learning models on the resulting data allow to dissect features informative for domain insertion tolerance and revealed sequence conservation statistics as the strongest indicators of suitable insertion sites. Finally, extending the experimental pipeline toward the identification of switchable hybrids results in opto-chemogenetic derivatives of the transcription factor AraC that function as single-protein Boolean logic gates. The study reveals determinants of domain insertion tolerance and yielded multimodally switchable proteins with unique functional properties.
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Affiliation(s)
- Jan Mathony
- Center for Synthetic BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
| | - Sabine Aschenbrenner
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
| | - Philipp Becker
- Center for Synthetic BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens Lyngby2800Denmark
| | - Dominik Niopek
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
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Fischer K, Tieskens JM, Luijten MAJ, Zijlmans J, van Oers HA, de Groot R, van der Doelen D, van Ewijk H, Klip H, van der Lans RM, De Meyer R, van der Mheen M, van Muilekom MM, Hyun Ruisch I, Teela L, van den Berg G, Bruining H, van der Rijken R, Buitelaar J, Hoekstra PJ, Lindauer R, Oostrom KJ, Staal W, Vermeiren R, Cornet R, Haverman L, Bartels M, Polderman TJC, Popma A. Internalizing problems before and during the COVID-19 pandemic in independent samples of Dutch children and adolescents with and without pre-existing mental health problems. Eur Child Adolesc Psychiatry 2023; 32:1873-1883. [PMID: 35616715 PMCID: PMC9133820 DOI: 10.1007/s00787-022-01991-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 04/09/2022] [Indexed: 01/25/2023]
Abstract
The aim of the study was to assess internalizing problems before and during the pandemic with data from Dutch consortium Child and adolescent mental health and wellbeing in times of the COVID-19 pandemic, consisting of two Dutch general population samples (GS) and two clinical samples (CS) referred to youth/psychiatric care. Measures of internalizing problems were obtained from ongoing data collections pre-pandemic (NGS = 35,357; NCS = 4487) and twice during the pandemic, in Apr-May 2020 (NGS = 3938; clinical: NCS = 1008) and in Nov-Dec 2020 (NGS = 1489; NCS = 1536), in children and adolescents (8-18 years) with parent (Brief Problem Monitor) and/or child reports (Patient-Reported Outcomes Measurement Information System®). Results show that, in the general population, internalizing problems were higher during the first peak of the pandemic compared to pre-pandemic based on both child and parent reports. Yet, over the course of the pandemic, on both child and parent reports, similar or lower levels of internalizing problems were observed. Children in the clinical population reported more internalizing symptoms over the course of the pandemic while parents did not report differences in internalizing symptoms from pre-pandemic to the first peak of the pandemic nor over the course of the pandemic. Overall, the findings indicate that children and adolescents of both the general and clinical population were affected negatively by the pandemic in terms of their internalizing problems. Attention is therefore warranted to investigate long-term effects and to monitor if internalizing problems return to pre-pandemic levels or if they remain elevated post-pandemic.
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Affiliation(s)
- Karen Fischer
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jacintha M Tieskens
- LUMC Curium-Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
| | - Michiel A J Luijten
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Emma Children's Hospital, Amsterdam University Medical Center, Child and Adolescent Psychiatry and Psychosocial Care, Amsterdam Reproduction and Development, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam University Medical Center, Epidemiology and Data Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Josjan Zijlmans
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry and Psychosocial Care, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Hedy A van Oers
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Emma Children's Hospital, Amsterdam University Medical Center, Child and Adolescent Psychiatry and Psychosocial Care, Amsterdam Reproduction and Development, University of Amsterdam, Amsterdam, The Netherlands
| | - Rowdy de Groot
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Medical Informatics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Daniël van der Doelen
- Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
| | - Hanneke van Ewijk
- LUMC Curium-Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
| | - Helen Klip
- Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
| | - Rikkert M van der Lans
- LUMC Curium-Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Malindi van der Mheen
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Levvel, Academic Center for Child and Adolescent Psychiatry, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Maud M van Muilekom
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Emma Children's Hospital, Amsterdam University Medical Center, Child and Adolescent Psychiatry and Psychosocial Care, Amsterdam Reproduction and Development, University of Amsterdam, Amsterdam, The Netherlands
| | - I Hyun Ruisch
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lorynn Teela
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Emma Children's Hospital, Amsterdam University Medical Center, Child and Adolescent Psychiatry and Psychosocial Care, Amsterdam Reproduction and Development, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Hilgo Bruining
- Department of Child and Adolescent Psychiatry and Psychosocial Care, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Jan Buitelaar
- Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Pieter J Hoekstra
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ramón Lindauer
- Levvel, Academic Center for Child and Adolescent Psychiatry, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Kim J Oostrom
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Emma Children's Hospital, Amsterdam University Medical Center, Child and Adolescent Psychiatry and Psychosocial Care, Amsterdam Reproduction and Development, University of Amsterdam, Amsterdam, The Netherlands
| | - Wouter Staal
- Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
| | - Robert Vermeiren
- LUMC Curium-Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
- Youz, Parnassia Psychiatric Institute, den Hague, The Netherlands
| | - Ronald Cornet
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Medical Informatics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Lotte Haverman
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Emma Children's Hospital, Amsterdam University Medical Center, Child and Adolescent Psychiatry and Psychosocial Care, Amsterdam Reproduction and Development, University of Amsterdam, Amsterdam, The Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Tinca J C Polderman
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands.
- LUMC Curium-Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, The Netherlands.
- Department of Child and Adolescent Psychiatry and Psychosocial Care, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands.
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Arne Popma
- Amsterdam University Medical Centres, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry and Psychosocial Care, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Levvel, Academic Center for Child and Adolescent Psychiatry, Amsterdam, The Netherlands
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Genco E, Modena F, Sarcina L, Björkström K, Brunetti C, Caironi M, Caputo M, Demartis VM, Di Franco C, Frusconi G, Haeberle L, Larizza P, Mancini MT, Österbacka R, Reeves W, Scamarcio G, Scandurra C, Wheeler M, Cantatore E, Esposito I, Macchia E, Torricelli F, Viola FA, Torsi L. A Single-Molecule Bioelectronic Portable Array for Early Diagnosis of Pancreatic Cancer Precursors. Adv Mater 2023; 35:e2304102. [PMID: 37452695 DOI: 10.1002/adma.202304102] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 05/03/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
A cohort of 47 patients is screened for pancreatic cancer precursors with a portable 96-well bioelectronic sensing-array for single-molecule assay in cysts fluid and blood plasma, deployable at point-of-care (POC). Pancreatic cancer precursors are mucinous cysts diagnosed with a sensitivity of at most 80% by state-of-the-art cytopathological molecular analyses (e.g., KRASmut DNA). Adding the simultaneous assay of proteins related to malignant transformation (e.g., MUC1 and CD55) is deemed essential to enhance diagnostic accuracy. The bioelectronic array proposed here, based on single-molecule-with-a-large-transistor (SiMoT) technology, can assay both nucleic acids and proteins at the single-molecule limit-of-identification (LOI) (1% of false-positives and false-negatives). It comprises an enzyme-linked immunosorbent assay (ELISA)-like 8 × 12-array organic-electronics disposable cartridge with an electrolyte-gated organic transistor sensor array, and a reusable reader, integrating a custom Si-IC chip, operating via software installed on a USB-connected smart device. The cartridge is complemented by a 3D-printed sensing gate cover plate. KRASmut , MUC1, and CD55 biomarkers either in plasma or cysts-fluid from 5 to 6 patients at a time, are multiplexed at single-molecule LOI in 1.5 h. The pancreatic cancer precursors are classified via a machine-learning analysis resulting in at least 96% diagnostic-sensitivity and 100% diagnostic-specificity. This preliminary study opens the way to POC liquid-biopsy-based early diagnosis of pancreatic-cancer precursors in plasma.
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Affiliation(s)
- Enrico Genco
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Francesco Modena
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milan, 20133, Italy
| | - Lucia Sarcina
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Kim Björkström
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
| | | | - Mario Caironi
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
| | - Mariapia Caputo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Virginia Maria Demartis
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | | | - Giulia Frusconi
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Lena Haeberle
- Institute of Pathology, Heinrich-Heine University and University Hospital of Düsseldorf, 40225, Duesseldorf, Germany
| | - Piero Larizza
- Masmec Biomed - Masmec SpA division, Modugno (BA), 70026, Italy
| | | | - Ronald Österbacka
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
| | | | - Gaetano Scamarcio
- CNR IFN, Bari, 70126, Italy
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
| | - Cecilia Scandurra
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - May Wheeler
- FlexEnable Technology Ltd, Cambridge, CB4 0FX, UK
| | - Eugenio Cantatore
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Irene Esposito
- Institute of Pathology, Heinrich-Heine University and University Hospital of Düsseldorf, 40225, Duesseldorf, Germany
| | - Eleonora Macchia
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Fabrizio Torricelli
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Fabrizio Antonio Viola
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
| | - Luisa Torsi
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
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