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Vigneau J, Martinho C, Godfroy O, Zheng M, Haas FB, Borg M, Coelho SM. Interactions between U and V sex chromosomes during the life cycle of Ectocarpus. Development 2024; 151:dev202677. [PMID: 38512707 DOI: 10.1242/dev.202677] [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: 01/04/2024] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
In many animals and flowering plants, sex determination occurs in the diploid phase of the life cycle with XX/XY or ZW/ZZ sex chromosomes. However, in early diverging plants and most macroalgae, sex is determined by female (U) or male (V) sex chromosomes in a haploid phase called the gametophyte. Once the U and V chromosomes unite at fertilization to produce a diploid sporophyte, sex determination no longer occurs, raising key questions about the fate of the U and V sex chromosomes in the sporophyte phase. Here, we investigate genetic and molecular interactions of the UV sex chromosomes in both the haploid and diploid phases of the brown alga Ectocarpus. We reveal extensive developmental regulation of sex chromosome genes across its life cycle and implicate the TALE-HD transcription factor OUROBOROS in suppressing sex determination in the diploid phase. Small RNAs may also play a role in the repression of a female sex-linked gene, and transition to the diploid sporophyte coincides with major reconfiguration of histone H3K79me2, suggesting a more intricate role for this histone mark in Ectocarpus development than previously appreciated.
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Affiliation(s)
| | | | - Olivier Godfroy
- Roscoff Biological Station, CNRS-Sorbonne University, Place Georges Teissier, Roscoff 29680, France
| | - Min Zheng
- Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Fabian B Haas
- Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Michael Borg
- Max Planck Institute for Biology, 72076 Tübingen, Germany
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2
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Zens B, Fäßler F, Hansen JM, Hauschild R, Datler J, Hodirnau VV, Zheden V, Alanko J, Sixt M, Schur FK. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. J Cell Biol 2024; 223:e202309125. [PMID: 38506714 PMCID: PMC10955043 DOI: 10.1083/jcb.202309125] [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: 09/26/2023] [Revised: 02/19/2024] [Accepted: 03/01/2024] [Indexed: 03/21/2024] Open
Abstract
The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly.
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Affiliation(s)
- Bettina Zens
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Florian Fäßler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jesse M. Hansen
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Robert Hauschild
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Julia Datler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | | | - Vanessa Zheden
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jonna Alanko
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Michael Sixt
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Florian K.M. Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
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3
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Chikireddy J, Lengagne L, Le Borgne R, Durieu C, Wioland H, Romet-Lemonne G, Jégou A. Fascin-induced bundling protects actin filaments from disassembly by cofilin. J Cell Biol 2024; 223:e202312106. [PMID: 38497788 PMCID: PMC10949937 DOI: 10.1083/jcb.202312106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024] Open
Abstract
Actin filament turnover plays a central role in shaping actin networks, yet the feedback mechanism between network architecture and filament assembly dynamics remains unclear. The activity of ADF/cofilin, the main protein family responsible for filament disassembly, has been mainly studied at the single filament level. This study unveils that fascin, by crosslinking filaments into bundles, strongly slows down filament disassembly by cofilin. We show that this is due to a markedly slower initiation of the first cofilin clusters, which occurs up to 100-fold slower on large bundles compared with single filaments. In contrast, severing at cofilin cluster boundaries is unaffected by fascin bundling. After the formation of an initial cofilin cluster on a filament within a bundle, we observed the local removal of fascin. Notably, the formation of cofilin clusters on adjacent filaments is highly enhanced, locally. We propose that this interfilament cooperativity arises from the local propagation of the cofilin-induced change in helicity from one filament to the other filaments of the bundle. Overall, taking into account all the above reactions, we reveal that fascin crosslinking slows down the disassembly of actin filaments by cofilin. These findings highlight the important role played by crosslinkers in tuning actin network turnover by modulating the activity of other regulatory proteins.
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Affiliation(s)
| | - Léana Lengagne
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Rémi Le Borgne
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Catherine Durieu
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Hugo Wioland
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | | | - Antoine Jégou
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
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4
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Canales-Rodríguez EJ, Pizzolato M, Zhou FL, Barakovic M, Thiran JP, Jones DK, Parker GJM, Dyrby TB. Pore size estimation in axon-mimicking microfibers with diffusion-relaxation MRI. Magn Reson Med 2024; 91:2579-2596. [PMID: 38192108 DOI: 10.1002/mrm.29991] [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: 10/17/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024]
Abstract
PURPOSE This study aims to evaluate two distinct approaches for fiber radius estimation using diffusion-relaxation MRI data acquired in biomimetic microfiber phantoms that mimic hollow axons. The methods considered are the spherical mean power-law approach and a T2-based pore size estimation technique. THEORY AND METHODS A general diffusion-relaxation theoretical model for the spherical mean signal from water molecules within a distribution of cylinders with varying radii was introduced, encompassing the evaluated models as particular cases. Additionally, a new numerical approach was presented for estimating effective radii (i.e., MRI-visible mean radii) from the ground truth radii distributions, not reliant on previous theoretical approximations and adaptable to various acquisition sequences. The ground truth radii were obtained from scanning electron microscope images. RESULTS Both methods show a linear relationship between effective radii estimated from MRI data and ground-truth radii distributions, although some discrepancies were observed. The spherical mean power-law method overestimated fiber radii. Conversely, the T2-based method exhibited higher sensitivity to smaller fiber radii, but faced limitations in accurately estimating the radius in one particular phantom, possibly because of material-specific relaxation changes. CONCLUSION The study demonstrates the feasibility of both techniques to predict pore sizes of hollow microfibers. The T2-based technique, unlike the spherical mean power-law method, does not demand ultra-high diffusion gradients, but requires calibration with known radius distributions. This research contributes to the ongoing development and evaluation of neuroimaging techniques for fiber radius estimation, highlights the advantages and limitations of both methods, and provides datasets for reproducible research.
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Affiliation(s)
- Erick J Canales-Rodríguez
- Signal Processing Laboratory 5 (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Danish Research Centre for Magnetic Resonance (DRCMR), Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
| | - Marco Pizzolato
- Danish Research Centre for Magnetic Resonance (DRCMR), Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
- Department of Applied Mathematics and Computer Science, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Feng-Lei Zhou
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London (UCL), London, UK
- MicroPhantoms Limited, Cambridge, UK
| | - Muhamed Barakovic
- Translational Imaging in Neurology (ThINk) Basel, Department of Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Jean-Philippe Thiran
- Signal Processing Laboratory 5 (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
- Centre d'Imagerie Biomédicale (CIBM), EPFL, Lausanne, Switzerland
| | - Derek K Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Cardiff, UK
| | - Geoffrey J M Parker
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London (UCL), London, UK
- Department of Neuroinflammation, Queen Square Institute of Neurology, University College London (UCL), London, UK
- Bioxydyn Limited, Manchester, UK
| | - Tim B Dyrby
- Danish Research Centre for Magnetic Resonance (DRCMR), Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
- Department of Applied Mathematics and Computer Science, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
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5
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Trejo S. Exploring the Fetal Origins Hypothesis Using Genetic Data. Soc Forces 2024; 102:1555-1581. [PMID: 38638179 PMCID: PMC11021852 DOI: 10.1093/sf/soae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/12/2023] [Accepted: 11/23/2023] [Indexed: 04/20/2024]
Abstract
Birth weight is a robust predictor of valued life course outcomes, emphasizing the importance of prenatal development. But does birth weight act as a proxy for environmental conditions in utero, or do biological processes surrounding birth weight themselves play a role in healthy development? To answer this question, we leverage variation in birth weight that is, within families, orthogonal to prenatal environmental conditions: one's genes. We construct polygenic scores in two longitudinal studies (Born in Bradford, N = 2008; Wisconsin Longitudinal Study, N = 8488) to empirically explore the molecular genetic correlates of birth weight. A 1 standard deviation increase in the polygenic score is associated with an ~100-grams increase in birth weight and a 1.4 pp (22 percent) decrease in low birth weight probability. Sibling comparisons illustrate that this association largely represents a causal effect. The polygenic score-birth weight association is increased for children who spend longer in the womb and whose mothers have higher body mass index, though we find no differences across maternal socioeconomic status. Finally, the polygenic score affects social and cognitive outcomes, suggesting that birth weight is itself related to healthy prenatal development.
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Affiliation(s)
- Sam Trejo
- Princeton University, Department of Sociology and Office of Population Research, United States
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6
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Siemers M, Lippegaus A, Papenfort K. ChimericFragments: computation, analysis and visualization of global RNA networks. NAR Genom Bioinform 2024; 6:lqae035. [PMID: 38633425 PMCID: PMC11023125 DOI: 10.1093/nargab/lqae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/08/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
RNA-RNA interactions are a key feature of post-transcriptional gene regulation in all domains of life. While ever more experimental protocols are being developed to study RNA duplex formation on a genome-wide scale, computational methods for the analysis and interpretation of the underlying data are lagging behind. Here, we present ChimericFragments, an analysis framework for RNA-seq experiments that produce chimeric RNA molecules. ChimericFragments implements a novel statistical method based on the complementarity of the base-pairing RNAs around their ligation site and provides an interactive graph-based visualization for data exploration and interpretation. ChimericFragments detects true RNA-RNA interactions with high precision and is compatible with several widely used experimental procedures such as RIL-seq, LIGR-seq or CLASH. We further demonstrate that ChimericFragments enables the systematic detection of novel RNA regulators and RNA-target pairs with crucial roles in microbial physiology and virulence. ChimericFragments is written in Julia and available at: https://github.com/maltesie/ChimericFragments.
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Affiliation(s)
- Malte Siemers
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
- Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Anne Lippegaus
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
| | - Kai Papenfort
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
- Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany
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7
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Tuomola EM, Keskinen KE, Viljanen A, Rantanen T, Portegijs E. Neighborhood Walkability, Walking Difficulties, and Participation in Leisure Activities Among Older People: A Cross-Sectional Study and 4-Year Follow-Up of a Subsample. J Aging Health 2024; 36:367-378. [PMID: 37482698 PMCID: PMC11025300 DOI: 10.1177/08982643231191444] [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: 07/25/2023]
Abstract
Objectives: To study cross-sectional and longitudinal associations between objectively assessed neighborhood walkability, walking difficulties, and participation in leisure activities among older people. Methods: Self-reported 2 km walking difficulty (intact, modifications, difficulties) at baseline and participating in organized group, outdoor recreation and cultural activities at baseline and follow-up were studied in community-dwelling persons (N = 848) aged 75-90. A walkability index, calculated using a geographic information system, was categorized into tertiles (lowest, middle, highest). Results: Residence in the highest walkability areas was associated with higher participation in cultural activities and lower participation in outdoor recreation, while the latter was most frequently reported by residents in the lowest walkability areas. Those reporting no difficulties were more likely than those reporting difficulties to participate in all studied activities. Residence in the middle or highest walkability areas predicted higher participation in cultural activities at follow-up. Discussion: Older persons activity profiles associate with neighborhood walkability and walking difficulties.
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Affiliation(s)
- Essi-Mari Tuomola
- Faculty of Sport and Health Sciences and Gerontology Research Center, University of Jyvaskyla, Jyväskylä, Finland
| | - Kirsi E. Keskinen
- Faculty of Sport and Health Sciences and Gerontology Research Center, University of Jyvaskyla, Jyväskylä, Finland
| | - Anne Viljanen
- Faculty of Sport and Health Sciences and Gerontology Research Center, University of Jyvaskyla, Jyväskylä, Finland
| | - Taina Rantanen
- Faculty of Sport and Health Sciences and Gerontology Research Center, University of Jyvaskyla, Jyväskylä, Finland
| | - Erja Portegijs
- University Medical Center Groningen, Center for Human Movement Sciences, University of Groningen, Groningen, The Netherlands
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8
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Monkley C, Reay MK, Evershed RP, Lloyd CEM. Mass spectral characterisation of cyclic oligoesters in a biodegradable mulch film. Rapid Commun Mass Spectrom 2024; 38:e9726. [PMID: 38525923 DOI: 10.1002/rcm.9726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 03/26/2024]
Abstract
RATIONALE Plastic mulch film manages weed growth and moisture loss on the surface of cropping beds. The chemical components of such plastics include polymer(s), additives and non-intentionally added substances (NIASs). The unknown chemical nature and behaviours of these constituents require investigation due to their potential to add to the anthropogenic chemical burden in the agrifood system. METHODS Solvent extracts of a commercial 15% polylactic acid (PLA)/85% poly(butylene adipate-co-terephthalate) mulch film were investigated using gas chromatography-mass spectrometry (GC-MS) with electron ionisation to characterise the additive and NIAS components. The obscurity of some of the NIASs meant their identification was not readily achieved through routine MS library comparisons. As such, the identification of several polymer-derived compounds required interpretation of the MS data and re-application of the derived fragmentation patterns with reference to the wider literature. Unknowns were confirmed using commercially available compounds. RESULTS Unknown NIASs were identified as cyclic oligoesters comprised of the monomeric building blocks of the polymer system. Cyclic structures derived from the monomers of polybutylene adipate (PBA) and polybutylene terephthalate (PBT) fragmented through a primary pathway involving 1,5- and 1,3-H transfers at ester linkages. Characteristic ions at m/z 111, 129, 183 and 201 for PBA-derived cyclic oligoesters and m/z 104, 132, 149 and 221 for PBT-derived cyclic oligoesters were assigned in the mass spectra of unknowns. Cyclic oligoesters containing sebacate moieties were also identified, indicating the presence of polybutylene sebacate as an unexpected component of the mulch. CONCLUSIONS Systematic analyses of the sort reported here are valuable for providing alternative approaches for the identification of plastic-related chemicals. Open publication of MS spectral data is required to build a greater understanding of the mulch film chemical components contributing to the environmental chemical load introduced to agroecosystems.
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Affiliation(s)
- Charlie Monkley
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
| | - Michaela K Reay
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
| | - Charlotte E M Lloyd
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
- School of Geographical Sciences, University of Bristol, Bristol, UK
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9
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Liu C, Van Meerbeek K. Predicting the responses of European grassland communities to climate and land cover change. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230335. [PMID: 38583469 PMCID: PMC10999271 DOI: 10.1098/rstb.2023.0335] [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: 09/14/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024] Open
Abstract
European grasslands are among the most species-rich ecosystems on small spatial scales. However, human-induced activities like land use and climate change pose significant threats to this diversity. To explore how climate and land cover change will affect biodiversity and community composition in grassland ecosystems, we conducted joint species distribution models (SDMs) on the extensive vegetation-plot database sPlotOpen to project distributions of 1178 grassland species across Europe under current conditions and three future scenarios. We further compared model accuracy and computational efficiency between joint SDMs (JSDMs) and stacked SDMs, especially for rare species. Our results show that: (i) grassland communities in the mountain ranges are expected to suffer high rates of species loss, while those in western, northern and eastern Europe will experience substantial turnover; (ii) scaling anomalies were observed in the predicted species richness, reflecting regional differences in the dominant drivers of assembly processes; (iii) JSDMs did not outperform stacked SDMs in predictive power but demonstrated superior efficiency in model fitting and predicting; and (iv) incorporating co-occurrence datasets improved the model performance in predicting the distribution of rare species. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.
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Affiliation(s)
- Chang Liu
- Department of Earth and Environmental Sciences, KU Leuven, Leuven, Flanders 3001, Belgium
| | - Koenraad Van Meerbeek
- Department of Earth and Environmental Sciences, KU Leuven, Leuven, Flanders 3001, Belgium
- KU Leuven Plant Institute, Leuven, Flanders, Belgium
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10
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Ordonez A, Riede F, Normand S, Svenning JC. Towards a novel biosphere in 2300: rapid and extensive global and biome-wide climatic novelty in the Anthropocene. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230022. [PMID: 38583475 PMCID: PMC10999272 DOI: 10.1098/rstb.2023.0022] [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: 07/23/2023] [Accepted: 11/10/2023] [Indexed: 04/09/2024] Open
Abstract
Recent climate change has effectively rewound the climate clock by approximately 120 000 years and is expected to reverse this clock a further 50 Myr by 2100. We aimed to answer two essential questions to better understand the changes in ecosystems worldwide owing to predicted climate change. Firstly, we identify the locations and time frames where novel ecosystems could emerge owing to climate change. Secondly, we aim to determine the extent to which biomes, in their current distribution, will experience an increase in climate-driven ecological novelty. To answer these questions, we analysed three perspectives on how climate changes could result in novel ecosystems in the near term (2100), medium (2200) and long term (2300). These perspectives included identifying areas where climate change could result in new climatic combinations, climate isoclines moving faster than species migration capacity and current environmental patterns being disaggregated. Using these metrics, we determined when and where novel ecosystems could emerge. Our analysis shows that unless rapid mitigation measures are taken, the coverage of novel ecosystems could be over 50% of the land surface by 2100 under all change scenarios. By 2300, the coverage of novel ecosystems could be above 80% of the land surface. At the biome scale, these changes could mean that over 50% of locations could shift towards novel ecosystems, with the majority seeing these changes in the next few decades. Our research shows that the impact of climate change on ecosystems is complex and varied, requiring global action to mitigate and adapt to these changes. This article is part of the theme issue 'Biodiversity dynamics and stewardship in a transforming biosphere'. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.
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Affiliation(s)
- Alejandro Ordonez
- Centre for Biodiversity Dynamics in a Changing World, Section of Ecoinformatics and Biodiversity, and Department of Biology, Aarhus University, Ny Munkegade 116, 8000 Aarhus C, Denmark
| | - Felix Riede
- Centre for Biodiversity Dynamics in a Changing World, School of Culture and Society, and Department of Archeology and Heritage Studies, Aarhus University, Moesgård Allé, 208270 Højbjerg, Denmark
| | - Signe Normand
- Centre for Biodiversity Dynamics in a Changing World, Section of Ecoinformatics and Biodiversity, and Department of Biology, Aarhus University, Ny Munkegade 116, 8000 Aarhus C, Denmark
| | - Jens-Christian Svenning
- Centre for Biodiversity Dynamics in a Changing World, Section of Ecoinformatics and Biodiversity, and Department of Biology, Aarhus University, Ny Munkegade 116, 8000 Aarhus C, Denmark
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11
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Ibrahim MTI, Alatoom D, Furtenbacher T, Császár AG, Yurchenko SN, Azzam AAA, Tennyson J. MARVEL analysis of high-resolution rovibrational spectra of 13 C 16 O 2 . J Comput Chem 2024; 45:969-984. [PMID: 38189163 DOI: 10.1002/jcc.27266] [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: 09/17/2023] [Revised: 11/02/2023] [Accepted: 11/11/2023] [Indexed: 01/09/2024]
Abstract
A set of empirical rovibrational energy levels, obtained through the MARVEL (measured active rotational-vibrational energy levels) procedure, is presented for the 13 C 16 O 2 isotopologue of carbon dioxide. This procedure begins with the collection and analysis of experimental rovibrational transitions from the literature, allowing for a comprehensive review of the literature on the high-resolution spectroscopy of 13 C 16 O 2 , which is also presented. A total of 60 sources out of more than 750 checked provided 14,101 uniquely measured and assigned rovibrational transitions in the wavenumber range of 579-13,735 cm - 1 . This is followed by a weighted least-squares refinement yielding the energy levels of the states involved in the measured transitions. Altogether 6318 empirical rovibrational energies have been determined for 13 C 16 O 2 . Finally, estimates have been given for the uncertainties of the empirical energies, based on the experimental uncertainties of the transitions. The detailed analysis of the lines and the spectroscopic network built from them, as well as the uncertainty estimates, all serve to pinpoint possible errors in the experimental data, such as typos, misassignment of quantum numbers, and misidentifications. Errors found in the literature data were corrected before including them in the final MARVEL dataset and analysis.
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Affiliation(s)
- Mohammad Taha I Ibrahim
- AstroJo Institute, Amman, Jordan
- Department of Physics and Astronomy, University College London, London, UK
| | - Dunia Alatoom
- AstroJo Institute, Amman, Jordan
- Department of Physics and Astronomy, University College London, London, UK
| | | | - Attila G Császár
- ELTE Eötvös Loránd University, Institute of Chemistry, Budapest and HUN-REN-ELTE Complex Chemical Systems Research Group, Budapest, Hungary
| | - Sergei N Yurchenko
- Department of Physics and Astronomy, University College London, London, UK
| | - Ala'a A A Azzam
- AstroJo Institute, Amman, Jordan
- Department of Physics, The University of Jordan, Amman, Jordan
| | - Jonathan Tennyson
- Department of Physics and Astronomy, University College London, London, UK
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12
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Li JD, Gao YY, Stevens EJ, King KC. Dual stressors of infection and warming can destabilize host microbiomes. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230069. [PMID: 38497264 PMCID: PMC10945407 DOI: 10.1098/rstb.2023.0069] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/02/2024] [Indexed: 03/19/2024] Open
Abstract
Climate change is causing extreme heating events and intensifying infectious disease outbreaks. Animals harbour microbial communities, which are vital for their survival and fitness under stressful conditions. Understanding how microbiome structures change in response to infection and warming may be important for forecasting host performance under global change. Here, we evaluated alterations in the microbiomes of several wild Caenorhabditis elegans isolates spanning a range of latitudes, upon warming temperatures and infection by the parasite Leucobacter musarum. Using 16S rRNA sequencing, we found that microbiome diversity decreased, and dispersion increased over time, with the former being more prominent in uninfected adults and the latter aggravated by infection. Infection reduced dominance of specific microbial taxa, and increased microbiome dispersion, indicating destabilizing effects on host microbial communities. Exposing infected hosts to warming did not have an additive destabilizing effect on their microbiomes. Moreover, warming during pre-adult development alleviated the destabilizing effects of infection on host microbiomes. These results revealed an opposing interaction between biotic and abiotic factors on microbiome structure. Lastly, we showed that increased microbiome dispersion might be associated with decreased variability in microbial species interaction strength. Overall, these findings improve our understanding of animal microbiome dynamics amidst concurrent climate change and epidemics. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- J. D. Li
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
| | - Y. Y. Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, People's Republic of China
- School of Ecology and Nature Conservation, Beijing Forestry University, 35 Tsinghua East Road, Beijing 100083, People's Republic of China
| | - E. J. Stevens
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
| | - K. C. King
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
- Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
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13
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Cosson C, Riou R, Patoli D, Niu T, Rey A, Groslambert M, De Rosny C, Chatre E, Allatif O, Henry T, Venet F, Milhavet F, Boursier G, Belot A, Jamilloux Y, Merlin E, Duquesne A, Grateau G, Savey L, Jacques Maria AT, Pagnier A, Poutrel S, Lambotte O, Mallebranche C, Ardois S, Richer O, Lemelle I, Rieux-Laucat F, Bader-Meunier B, Amoura Z, Melki I, Cuisset L, Touitou I, Geyer M, Georgin-Lavialle S, Py BF. Functional diversity of NLRP3 gain-of-function mutants associated with CAPS autoinflammation. J Exp Med 2024; 221:e20231200. [PMID: 38530241 DOI: 10.1084/jem.20231200] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/22/2023] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
NLRP3-associated autoinflammatory disease is a heterogenous group of monogenic conditions caused by NLRP3 gain-of-function mutations. The poor functional characterization of most NLRP3 variants hinders diagnosis despite efficient anti-IL-1 treatments. Additionally, while NLRP3 is controlled by priming and activation signals, gain-of-functions have only been investigated in response to priming. Here, we characterize 34 NLRP3 variants in vitro, evaluating their activity upon induction, priming, and/or activation signals, and their sensitivity to four inhibitors. We highlight the functional diversity of the gain-of-function mutants and describe four groups based on the signals governing their activation, correlating partly with the symptom severity. We identify a new group of NLRP3 mutants responding to the activation signal without priming, associated with frequent misdiagnoses. Our results identify key NLRP3 residues controlling inflammasome activity and sensitivity to inhibitors, and antagonistic mechanisms with broader efficacy for therapeutic strategies. They provide new insights into NLRP3 activation, an explanatory mechanism for NLRP3-AID heterogeneity, and original tools for NLRP3-AID diagnosis and drug development.
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Affiliation(s)
- Camille Cosson
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
| | - Romane Riou
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
| | - Danish Patoli
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
| | - Tingting Niu
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University , Shanghai, China
| | - Amaury Rey
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
| | - Marine Groslambert
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
| | - Charlotte De Rosny
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
| | - Elodie Chatre
- Univ Lyon, ENS de Lyon, Inserm, CNRS SFR Biosciences US8 UAR3444, Université Claude Bernard Lyon 1 , Lyon, France
| | - Omran Allatif
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
| | - Thomas Henry
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
| | - Fabienne Venet
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
| | - Florian Milhavet
- Institute for Regenerative Medicine and Biotherapy, Inserm, U1183, University of Montpellier , Montpellier, France
- Department of Molecular Genetics, Medical Genetics of Rare and Autoinflammatory Disease Unit, Montpellier University Hospital, Montpellier, France
- Centre de Référence des Maladies Autoinflammatoires et des Amyloses Inflammatoires, CEREMAIA , France
| | - Guilaine Boursier
- Institute for Regenerative Medicine and Biotherapy, Inserm, U1183, University of Montpellier , Montpellier, France
- Department of Molecular Genetics, Medical Genetics of Rare and Autoinflammatory Disease Unit, Montpellier University Hospital, Montpellier, France
- Centre de Référence des Maladies Autoinflammatoires et des Amyloses Inflammatoires, CEREMAIA , France
| | - Alexandre Belot
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
- Centre de Référence des Maladies Autoinflammatoires et des Amyloses Inflammatoires, CEREMAIA , France
- Pediatric Nephrology, Rheumatology, Dermatology Department, National Referee Centre for Rheumatic and Autoimmune Diseases in Children (RAISE), Hôpital Femme-Mère-Enfant, Hospices Civils de Lyon, Bron, France
- Lyon Immunopathology Federation (LIFE), Université Claude Bernard Lyon 1 , Lyon, France
| | - Yvan Jamilloux
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
- Centre de Référence des Maladies Autoinflammatoires et des Amyloses Inflammatoires, CEREMAIA , France
- Lyon Immunopathology Federation (LIFE), Université Claude Bernard Lyon 1 , Lyon, France
- Service de Médecine Interne, Hôpital de la Croix-Rousse, Hospices Civils de Lyon , Lyon, France
| | - Etienne Merlin
- Department of Pediatrics, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Agnès Duquesne
- Centre de Référence des Maladies Autoinflammatoires et des Amyloses Inflammatoires, CEREMAIA , France
- Pediatric Nephrology, Rheumatology, Dermatology Department, National Referee Centre for Rheumatic and Autoimmune Diseases in Children (RAISE), Hôpital Femme-Mère-Enfant, Hospices Civils de Lyon, Bron, France
| | - Gilles Grateau
- Centre de Référence des Maladies Autoinflammatoires et des Amyloses Inflammatoires, CEREMAIA , France
- Sorbonne Université, Department of Internal Medicine, National Reference Center for Autoinflammatory Diseases and AA Amyloidosis, Tenon Hospital, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Léa Savey
- Centre de Référence des Maladies Autoinflammatoires et des Amyloses Inflammatoires, CEREMAIA , France
- Sorbonne Université, Department of Internal Medicine, National Reference Center for Autoinflammatory Diseases and AA Amyloidosis, Tenon Hospital, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Alexandre Thibault Jacques Maria
- Internal Medicine and Onco-Immunology (MedI2O), Institute for Regenerative Medicine and Biotherapy (IRMB), Saint Eloi Hospital, Montpellier University , Montpellier, France
| | - Anne Pagnier
- Centre Hospitalier Universitaire Grenoble Alpes, Immunologie Clinique, Immuno-Hémato-Oncologie (IHO), Hôpital Couple-Enfant , Grenoble, France
| | - Solène Poutrel
- Service de Médecine Interne, Hospices Civils de Lyon, Edouard Herriot Hospital , Lyon, France
| | - Olivier Lambotte
- Assistance Publique-Hôpitaux de Paris, Service de Médecine Interne et Immunologie Clinique, Groupe Hospitalier Universitaire Paris Saclay, Hôpital Bicêtre , Le Kremlin-Bicêtre, France
- Université Paris Saclay, Inserm UMR, 1184, CEA , Le Kremlin-Bicêtre, France
| | - Coralie Mallebranche
- Université d'Angers, Université de Nantes, Inserm, CNRS, CRCI2NA, SFR ICAT, Angers, France
- Centre Hospitalier Universitaire d'Angers, Pediatric Immuno-Hemato-Oncology Unit, France
| | - Samuel Ardois
- Médecine Interne et Immunologie Clinique , Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Olivier Richer
- Paediatric, Rheumatology and Paediatric Internal Medicine, Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Children's Hospital , Bordeaux, France
| | - Irène Lemelle
- Department of Pediatric Onco-hematology, Children Hospital, University Hospital of Nancy, Lorraine University, Vandoeuvre-lès-Nancy, France
| | - Frédéric Rieux-Laucat
- Université Paris Cité, Institut Imagine, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Inserm UMR 1163 , Paris, France
| | - Brigitte Bader-Meunier
- Université Paris Cité, Institut Imagine, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Inserm UMR 1163 , Paris, France
- Pediatric Immunology, Hematology and Rheumatology Department, Hôpital Necker, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Zahir Amoura
- Assistance Publique-Hôpitaux de Paris (AP-HP)-Sorbonne Université, Hopital Pitié-Salpétrière, Institut E3M, Service de Médecine Interne 2, Centre National de Référence Lupus et Syndrome des Anticorps Antiphospholipides, Centre d'Immunologie et des Maladies Infectieuses (CIMI), Paris, France
| | - Isabelle Melki
- Paediatric, Rheumatology and Paediatric Internal Medicine, Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Children's Hospital , Bordeaux, France
- General Pediatrics, Infectious Disease and Internal Medicine Department, Hôpital Robert Debre, Assistance Publique-Hôpitaux de Paris (AP-HP), Reference Center for Rheumatic, AutoImmune and Systemic Diseases in Children (RAISE), Paris, France
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute , Paris, France
| | - Laurence Cuisset
- Université Paris Cité, Service de Médecine Génomique des Maladies de Système et D'Organe, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Isabelle Touitou
- Institute for Regenerative Medicine and Biotherapy, Inserm, U1183, University of Montpellier , Montpellier, France
- Department of Molecular Genetics, Medical Genetics of Rare and Autoinflammatory Disease Unit, Montpellier University Hospital, Montpellier, France
- Centre de Référence des Maladies Autoinflammatoires et des Amyloses Inflammatoires, CEREMAIA , France
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn , Bonn, Germany
| | - Sophie Georgin-Lavialle
- Centre de Référence des Maladies Autoinflammatoires et des Amyloses Inflammatoires, CEREMAIA , France
- Sorbonne Université, Department of Internal Medicine, National Reference Center for Autoinflammatory Diseases and AA Amyloidosis, Tenon Hospital, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Bénédicte F Py
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308 , ENS de Lyon, Lyon, France
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14
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Vitali DG, Fonseca D, Carvalho P. The derlin Dfm1 couples retrotranslocation of a folded protein domain to its proteasomal degradation. J Cell Biol 2024; 223:e202308074. [PMID: 38448163 DOI: 10.1083/jcb.202308074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/05/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Endoplasmic reticulum (ER) proteins are degraded by proteasomes in the cytosol through ER-associated degradation (ERAD). This process involves the retrotranslocation of substrates across the ER membrane, their ubiquitination, and membrane extraction by the Cdc48/Npl4/Ufd1 ATPase complex prior to delivery to proteasomes for degradation. How the presence of a folded luminal domain affects substrate retrotranslocation and this event is coordinated with subsequent ERAD steps remains unknown. Here, using a model substrate with a folded luminal domain, we showed that Cdc48 ATPase activity is sufficient to drive substrate retrotranslocation independently of ERAD membrane components. However, the complete degradation of the folded luminal domain required substrate-tight coupling of retrotranslocation and proteasomal degradation, which was ensured by the derlin Dfm1. Mutations in Dfm1 intramembrane rhomboid-like or cytosolic Cdc48-binding regions resulted in partial degradation of the substrate with accumulation of its folded domain. Our study revealed Dfm1 as a critical regulator of Cdc48-driven retrotranslocation and highlights the importance of coordinating substrate retrotranslocation and degradation during ERAD.
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Affiliation(s)
- Daniela G Vitali
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Daniel Fonseca
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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15
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Ingelman-Sundberg M, Pirmohamed M. Precision medicine in cardiovascular therapeutics: Evaluating the role of pharmacogenetic analysis prior to drug treatment. J Intern Med 2024; 295:583-598. [PMID: 38343077 DOI: 10.1111/joim.13772] [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] [Indexed: 04/09/2024]
Abstract
Pharmacogenomics is the examination of how genetic variation influences drug metabolism and response, in terms of both efficacy and safety. In cardiovascular disease, patient-specific diplotypes determine phenotypes, thereby influencing the efficacy and safety of drug treatments, including statins, antiarrhythmics, anticoagulants and antiplatelets. Notably, polymorphisms in key genes, such as CYP2C9, CYP2C19, VKORC1 and SLCO1B1, significantly impact the outcomes of treatment with clopidogrel, warfarin and simvastatin. Furthermore, the CYP2C19 polymorphism influences the pharmacokinetics and safety of the novel hypertrophic cardiomyopathy inhibitor, mavacamten. In this review, we critically assess the clinical application of pharmacogenomics in cardiovascular disease and delineate present and future utilization of pharmacogenomics. This includes insights into identifying missing heritability, the integration of whole genome sequencing and the application of polygenic risk scores to enhance the precision of personalized drug therapy. Our discussion encompasses health economic analyses that underscore the cost benefits associated with pre-emptive genotyping for warfarin and clopidogrel treatments, albeit acknowledging the need for further research in this area. In summary, we contend that cardiovascular pharmacogenomic analyses are underpinned by a wealth of evidence, and implementation is already occurring for some of these gene-drug pairs, but as with any area of medicine, we need to continually gather more information to optimize the use of pharmacogenomics in clinical practice.
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Affiliation(s)
- Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Biomedicum 5B, Karolinska Institutet, Stockholm, Sweden
| | - Munir Pirmohamed
- Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
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16
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Ding Y, Postle BR, van Ede F. Neural Signatures of Competition between Voluntary and Involuntary Influences over the Focus of Attention in Visual Working Memory. J Cogn Neurosci 2024; 36:815-827. [PMID: 38319683 DOI: 10.1162/jocn_a_02123] [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] [Indexed: 02/07/2024]
Abstract
Adaptive behavior relies on the selection and prioritization of relevant sensory inputs from the external environment as well as from among internal sensory representations held in working memory. Recent behavioral evidence suggests that the classic distinction between voluntary (goal-driven) and involuntary (stimulus-driven) influences over attentional allocation also applies to the selection of internal representations held in working memory. In the current EEG study, we set out to investigate the neural dynamics associated with the competition between voluntary and involuntary control over the focus of attention in visual working memory. We show that when voluntary and involuntary factors compete for the internal focus of attention, prioritization of the appropriate item is delayed-as reflected both in delayed gaze biases that track internal selection and in delayed neural beta (15-25 Hz) dynamics that track the planning for the upcoming memory-guided manual action. We further show how this competition is paralleled-possibly resolved-by an increase in frontal midline theta (4-8 Hz) activity that, moreover, predicts the speed of ensuing memory-guided behavior. Finally, because theta increased following retrocues that effectively reduced working-memory load, our data unveil how frontal theta activity during internal attentional focusing tracks demands on cognitive control over and above working-memory load. Together, these data yield new insight into the neural dynamics that govern the focus of attention in visual working memory, and disentangle the contributions of frontal midline theta activity to the processes of control versus retention in working memory.
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17
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Biancari L, Aguiar MR, Saiz H, Gross N, Le Bagousse-Pinguet Y, Eldridge DJ, Maestre FT. Upper boundary on tree cover at global drylands. New Phytol 2024; 242:836-840. [PMID: 38362948 DOI: 10.1111/nph.19598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/28/2024] [Indexed: 02/17/2024]
Affiliation(s)
- Lucio Biancari
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, CONICET, Buenos Aires, C1417DSE, Argentina
- Cátedra de Ecología, Departamento de Recursos Naturales y Ambiente, Facultad de Agronomía, UBA, Buenos Aires, C1417DSE, Argentina
| | - Martín R Aguiar
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, CONICET, Buenos Aires, C1417DSE, Argentina
- Cátedra de Ecología, Departamento de Recursos Naturales y Ambiente, Facultad de Agronomía, UBA, Buenos Aires, C1417DSE, Argentina
| | - Hugo Saiz
- Departamento de Ciencias Agrarias y Medio Natural, Escuela Politécnica Superior, Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA), Universidad de Zaragoza, Huesca, 50009, Spain
- Institute of Plant Sciences, University of Bern, Bern, 3013, Switzerland
| | - Nicolas Gross
- Université Clermont Auvergne, l'Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, VetAgro Sup, Unité Mixte de Recherche 212 Ecosystème Prairial, Clermont-Ferrand, F-63000, France
| | | | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramon Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, Alicante, 03690, Spain
- Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, Alicante, 03690, Spain
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18
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Hewett AM, Johnston SE, Morris A, Morris S, Pemberton JM. Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer. Mol Ecol 2024; 33:e17335. [PMID: 38549143 DOI: 10.1111/mec.17335] [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: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024]
Abstract
Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH, we use chromosome-specific inbreeding coefficients (FROHChr) to explore whether the effect of inbreeding varies between chromosomes. Under the assumption that within an individual the probability of being identical-by-descent is equal across all chromosomes, we used a multi-membership model to estimate the deviation of FROHChr from the average inbreeding effect. This novel approach ensures effect sizes are not overestimated whilst maximising the power of our available dataset of >3000 individuals genotyped on >35,000 autosomal SNPs. We find that most chromosomes confer a minor reduction in fitness-related traits, which when these effects are summed, results in the observed inbreeding depression in birth weight, survival and lifetime breeding success. However, no chromosomes had a significant detrimental effect compared to the overall effect of inbreeding, indicating no major effect loci. We conclude that in this population, inbreeding depression is likely the result of multiple mildly or moderately deleterious mutations spread across all chromosomes, which are difficult to detect with statistical confidence. Such mutations will be inefficiently purged, which may explain the persistence of inbreeding depression in this population.
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Affiliation(s)
- Anna M Hewett
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Department of Ecology and Evolution, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alison Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Sean Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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19
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Sun W, Maseyk K, Lett C, Seibt U. Restricted internal diffusion weakens transpiration-photosynthesis coupling during heatwaves: Evidence from leaf carbonyl sulphide exchange. Plant Cell Environ 2024; 47:1813-1833. [PMID: 38321806 DOI: 10.1111/pce.14840] [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: 04/19/2023] [Revised: 11/13/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
Increasingly frequent and intense heatwaves threaten ecosystem health in a warming climate. However, plant responses to heatwaves are poorly understood. A key uncertainty concerns the intensification of transpiration when heatwaves suppress photosynthesis, known as transpiration-photosynthesis decoupling. Field observations of such decoupling are scarce, and the underlying physiological mechanisms remain elusive. Here, we use carbonyl sulphide (COS) as a leaf gas exchange tracer to examine potential mechanisms leading to transpiration-photosynthesis decoupling on a coast live oak in a southern California woodland in spring 2013. We found that heatwaves suppressed both photosynthesis and leaf COS uptake but increased transpiration or sustained it at non-heatwave levels throughout the day. Despite statistically significant decoupling between transpiration and photosynthesis, stomatal sensitivity to environmental factors did not change during heatwaves. Instead, midday photosynthesis during heatwaves was restricted by internal diffusion, as indicated by the lower internal conductance to COS. Thus, increased evaporative demand and nonstomatal limitation to photosynthesis act jointly to decouple transpiration from photosynthesis without altering stomatal sensitivity. Decoupling offered limited potential cooling benefits, questioning its effectiveness for leaf thermoregulation in xeric ecosystems. We suggest that adding COS to leaf and ecosystem flux measurements helps elucidate diverse physiological mechanisms underlying transpiration-photosynthesis decoupling.
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Affiliation(s)
- Wu Sun
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
| | - Kadmiel Maseyk
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK
| | - Céline Lett
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Ulli Seibt
- Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, California, USA
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20
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Cornet A, Ronca A, Shen J, Zontone F, Chushkin Y, Cammarata M, Garbarino G, Sprung M, Westermeier F, Deschamps T, Ruta B. High-pressure X-ray photon correlation spectroscopy at fourth-generation synchrotron sources. J Synchrotron Radiat 2024; 31:S1600577524001784. [PMID: 38597746 DOI: 10.1107/s1600577524001784] [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: 11/15/2023] [Accepted: 02/23/2024] [Indexed: 04/11/2024]
Abstract
A new experimental setup combining X-ray photon correlation spectroscopy (XPCS) in the hard X-ray regime and a high-pressure sample environment has been developed to monitor the pressure dependence of the internal motion of complex systems down to the atomic scale in the multi-gigapascal range, from room temperature to 600 K. The high flux of coherent high-energy X-rays at fourth-generation synchrotron sources solves the problems caused by the absorption of diamond anvil cells used to generate high pressure, enabling the measurement of the intermediate scattering function over six orders of magnitude in time, from 10-3 s to 103 s. The constraints posed by the high-pressure generation such as the preservation of X-ray coherence, as well as the sample, pressure and temperature stability, are discussed, and the feasibility of high-pressure XPCS is demonstrated through results obtained on metallic glasses.
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Affiliation(s)
- Antoine Cornet
- Institut Néel, Université Grenoble Alpes and Centre National de la Recherche Scientifique, 25 rue des Martyrs - BP 166, 38042 Grenoble, France
| | - Alberto Ronca
- Institut Néel, Université Grenoble Alpes and Centre National de la Recherche Scientifique, 25 rue des Martyrs - BP 166, 38042 Grenoble, France
| | - Jie Shen
- Institut Néel, Université Grenoble Alpes and Centre National de la Recherche Scientifique, 25 rue des Martyrs - BP 166, 38042 Grenoble, France
| | - Federico Zontone
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Yuriy Chushkin
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Marco Cammarata
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Gaston Garbarino
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | | | | | - Thierry Deschamps
- University of Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-6922 Villeurbanne, France
| | - Beatrice Ruta
- Institut Néel, Université Grenoble Alpes and Centre National de la Recherche Scientifique, 25 rue des Martyrs - BP 166, 38042 Grenoble, France
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21
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van de Weijer MP, Demange PA, Pelt DHM, Bartels M, Nivard MG. Disentangling potential causal effects of educational duration on well-being, and mental and physical health outcomes. Psychol Med 2024; 54:1403-1418. [PMID: 37964430 DOI: 10.1017/s003329172300329x] [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] [Indexed: 11/16/2023]
Abstract
BACKGROUND Extensive research has focused on the potential benefits of education on various mental and physical health outcomes. However, whether the associations reflect a causal effect is harder to establish. METHODS To examine associations between educational duration and specific aspects of well-being, anxiety and mood disorders, and cardiovascular health in a sample of European Ancestry UK Biobank participants born in England and Wales, we apply four different causal inference methods (a natural policy experiment leveraging the minimum school-leaving age, a sibling-control design, Mendelian randomization [MR], and within-family MR), and assess if the methods converge on the same conclusion. RESULTS A comparison of results across the four methods reveals that associations between educational duration and these outcomes appears predominantly to be the result of confounding or bias rather than a true causal effect of education on well-being and health outcomes. Although we do consistently find no associations between educational duration and happiness, family satisfaction, work satisfaction, meaning in life, anxiety, and bipolar disorder, we do not find consistent significant associations across all methods for the other phenotypes (health satisfaction, depression, financial satisfaction, friendship satisfaction, neuroticism, and cardiovascular outcomes). CONCLUSIONS We discuss inconsistencies in results across methods considering their respective limitations and biases, and additionally discuss the generalizability of our findings in light of the sample and phenotype limitations. Overall, this study strengthens the idea that triangulation across different methods is necessary to enhance our understanding of the causal consequences of educational duration.
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Affiliation(s)
- Margot P van de Weijer
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, The Netherlands
- Genetic Epidemiology, Department of Psychiatry, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Perline A Demange
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Dirk H M Pelt
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Michel G Nivard
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, The Netherlands
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22
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Mulder RH, Kraaij R, Schuurmans IK, Frances-Cuesta C, Sanz Y, Medina-Gomez C, Duijts L, Rivadeneira F, Tiemeier H, Jaddoe VWV, Felix JF, Cecil CAM. Early-life stress and the gut microbiome: A comprehensive population-based investigation. Brain Behav Immun 2024; 118:117-127. [PMID: 38402916 PMCID: PMC7615798 DOI: 10.1016/j.bbi.2024.02.024] [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: 10/27/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024] Open
Abstract
Early-life stress (ELS) has been robustly associated with a range of poor mental and physical health outcomes. Recent studies implicate the gut microbiome in stress-related mental, cardio-metabolic and immune health problems, but research on humans is scarce and thus far often based on small, selected samples, often using retrospective reports of ELS. We examined associations between ELS and the human gut microbiome in a large, population-based study of children. ELS was measured prospectively from birth to 10 years of age in 2,004 children from the Generation R Study. We studied overall ELS, as well as unique effects of five different ELS domains, including life events, contextual risk, parental risk, interpersonal risk, and direct victimization. Stool microbiome was assessed using 16S rRNA sequencing at age 10 years and data were analyzed at multiple levels (i.e. α- and β-diversity indices, individual genera and predicted functional pathways). In addition, we explored potential mediators of ELS-microbiome associations, including diet at age 8 and body mass index at 10 years. While no associations were observed between overall ELS (composite score of five domains) and the microbiome after multiple testing correction, contextual risk - a specific ELS domain related to socio-economic stress, including risk factors such as financial difficulties and low maternal education - was significantly associated with microbiome variability. This ELS domain was associated with lower α-diversity, with β-diversity, and with predicted functional pathways involved, amongst others, in tryptophan biosynthesis. These associations were in part mediated by overall diet quality, a pro-inflammatory diet, fiber intake, and body mass index (BMI). These results suggest that stress related to socio-economic adversity - but not overall early life stress - is associated with a less diverse microbiome in the general population, and that this association may in part be explained by poorer diet and higher BMI. Future research is needed to test causality and to establish whether modifiable factors such as diet could be used to mitigate the negative effects of socio-economic adversity on the microbiome and related health consequences.
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Affiliation(s)
- Rosa H Mulder
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Isabel K Schuurmans
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Carlos Frances-Cuesta
- Microbiome, Nutrition & Health Research Unit. Institute of Agrochemistry and Food Technology, Severo Ochoa Centre of Excellence, National Research Council (IATA-CSIC), Valencia, Spain.
| | - Yolanda Sanz
- Microbiome, Nutrition & Health Research Unit. Institute of Agrochemistry and Food Technology, Severo Ochoa Centre of Excellence, National Research Council (IATA-CSIC), Valencia, Spain.
| | - Carolina Medina-Gomez
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Neonatal and Pediatric Intensive Care, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Social and Behavioral Sciences, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
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23
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Bilgic B, Costagli M, Chan KS, Duyn J, Langkammer C, Lee J, Li X, Liu C, Marques JP, Milovic C, Robinson SD, Schweser F, Shmueli K, Spincemaille P, Straub S, van Zijl P, Wang Y. Recommended implementation of quantitative susceptibility mapping for clinical research in the brain: A consensus of the ISMRM electro-magnetic tissue properties study group. Magn Reson Med 2024; 91:1834-1862. [PMID: 38247051 PMCID: PMC10950544 DOI: 10.1002/mrm.30006] [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: 07/11/2023] [Revised: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
This article provides recommendations for implementing QSM for clinical brain research. It is a consensus of the International Society of Magnetic Resonance in Medicine, Electro-Magnetic Tissue Properties Study Group. While QSM technical development continues to advance rapidly, the current QSM methods have been demonstrated to be repeatable and reproducible for generating quantitative tissue magnetic susceptibility maps in the brain. However, the many QSM approaches available have generated a need in the neuroimaging community for guidelines on implementation. This article outlines considerations and implementation recommendations for QSM data acquisition, processing, analysis, and publication. We recommend that data be acquired using a monopolar 3D multi-echo gradient echo (GRE) sequence and that phase images be saved and exported in Digital Imaging and Communications in Medicine (DICOM) format and unwrapped using an exact unwrapping approach. Multi-echo images should be combined before background field removal, and a brain mask created using a brain extraction tool with the incorporation of phase-quality-based masking. Background fields within the brain mask should be removed using a technique based on SHARP or PDF, and the optimization approach to dipole inversion should be employed with a sparsity-based regularization. Susceptibility values should be measured relative to a specified reference, including the common reference region of the whole brain as a region of interest in the analysis. The minimum acquisition and processing details required when reporting QSM results are also provided. These recommendations should facilitate clinical QSM research and promote harmonized data acquisition, analysis, and reporting.
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Affiliation(s)
- Berkin Bilgic
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Mauro Costagli
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Sciences (DINOGMI), University of Genoa, Genoa, Italy
- Laboratory of Medical Physics and Magnetic Resonance, IRCCS Stella Maris, Pisa, Italy
| | - Kwok-Shing Chan
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Jeff Duyn
- Advanced MRI Section, NINDS, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Jongho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Xu Li
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Chunlei Liu
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA
| | - José P Marques
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Carlos Milovic
- School of Electrical Engineering (EIE), Pontificia Universidad Catolica de Valparaiso, Valparaiso, Chile
| | - Simon Daniel Robinson
- High Field MR Centre, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
- Centre of Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Ferdinand Schweser
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences at the University at Buffalo, Buffalo, New York, USA
- Center for Biomedical Imaging, Clinical and Translational Science Institute at the University at Buffalo, Buffalo, New York, USA
| | - Karin Shmueli
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Pascal Spincemaille
- MRI Research Institute, Department of Radiology, Weill Cornell Medicine, New York, New York, USA
| | - Sina Straub
- Department of Radiology, Mayo Clinic, Jacksonville, Florida, USA
| | - Peter van Zijl
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Yi Wang
- MRI Research Institute, Departments of Radiology and Biomedical Engineering, Cornell University, New York, New York, USA
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24
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Young JJ, Zywiel MG, Skou ST, Chandran V, Davey JR, Gandhi R, Mahomed NN, Syed K, Veillette CJH, Rampersaud YR, Perruccio AV. Total Knee Arthroplasty Versus Education and Exercise for Knee Osteoarthritis: A Propensity-Matched Analysis. Arthritis Care Res (Hoboken) 2024; 76:682-690. [PMID: 38191793 DOI: 10.1002/acr.25293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/10/2024]
Abstract
OBJECTIVE We estimate the treatment effect of total knee arthroplasty (TKA) versus an education and exercise (Edu+Ex) program on pain, function, and quality of life outcomes 3 and 12 months after treatment initiation for knee osteoarthritis (OA). METHODS Patients with knee OA who had undergone TKA were matched on a 1:1 ratio with participants in an Edu+Ex program based on a propensity score fitted to a range of pretreatment covariates. After matching, between-group differences in improvement (the treatment effect) in Knee Injury and Osteoarthritis Outcome Score 12-item version (0, worst to 100, best) pain, function, and quality of life from baseline to 3 and 12 months were estimated using linear mixed models, adjusting for unbalanced covariates, if any, after matching. RESULTS The matched sample consisted of 522 patients (Edu+Ex, n = 261; TKA, n = 261) who were balanced on all pretreatment characteristics. At 12-month follow-up, TKA resulted in significantly greater improvements in pain (mean difference [MD] 22.8; 95% confidence interval [95% CI] 19.7-25.8), function (MD 21.2; 95% CI 17.7-24.4), and quality of life (MD 18.3; 15.0-21.6). Even so, at least one-third of patients receiving Edu+Ex had a clinically meaningful improvement in outcomes at 12 months compared with 75% of patients with TKA. CONCLUSION TKA is associated with greater improvements in pain, function, and quality of life, but these findings also suggest that Edu+Ex may be a viable alternative to TKA in a meaningful proportion of patients, which may reduce overall TKA need. Confirmatory trials are needed.
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Affiliation(s)
- James J Young
- University Health Network, Toronto, Ontario, Canada, and University of Southern Denmark, Odense, Denmark
| | - Michael G Zywiel
- University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Søren T Skou
- University of Southern Denmark, Odense, Denmark, and Næstved-Slagelse-Ringsted Hospitals, Slagelse, Denmark
| | - Vinod Chandran
- University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - J Rod Davey
- University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Rajiv Gandhi
- University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Nizar N Mahomed
- University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Khalid Syed
- University Health Network, Toronto, Ontario, Canada
| | | | - Y Raja Rampersaud
- University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Anthony V Perruccio
- University Health Network and University of Toronto, Toronto, Ontario, Canada
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25
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Hall A, Barbera M, Lehtisalo J, Antikainen R, Huque H, Laatikainen T, Ngandu T, Soininen H, Stephen R, Strandberg T, Kivipelto M, Anstey KJ, Solomon A. The Australian National University Alzheimer's Disease Risk Index (ANU-ADRI) score as a predictor for cognitive decline and potential surrogate outcome in the FINGER lifestyle randomized controlled trial. Eur J Neurol 2024; 31:e16238. [PMID: 38323508 DOI: 10.1111/ene.16238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND AND PURPOSE The complex aetiology of Alzheimer's disease suggests prevention potential. Risk scores have potential as risk stratification tools and surrogate outcomes in multimodal interventions targeting specific at-risk populations. The Australian National University Alzheimer's Disease Risk Index (ANU-ADRI) was tested in relation to cognition and its suitability as a surrogate outcome in a multidomain lifestyle randomized controlled trial, in older adults at risk of dementia. METHODS In this post hoc analysis of the Finnish Intervention Study to Prevent Cognitive Impairment and Disability (FINGER), ANU-ADRI was calculated at baseline, 12, and 24 months (n = 1174). The association between ANU-ADRI and cognition (at baseline and over time), the intervention effect on changes in ANU-ADRI, and the potential impact of baseline ANU-ADRI on the intervention effect on changes in cognition were assessed using linear mixed models with maximum likelihood estimation. RESULTS A higher ANU-ADRI was significantly related to worse cognition, at baseline (e.g., estimate for global cognition [95% confidence interval] was -0.028 [-0.032 to -0.025]) and over the 2-year study (e.g., estimate for 2-year changes in ANU-ADRI and per-year changes in global cognition [95% confidence interval] was -0.068 [-0.026 to -0.108]). No significant beneficial intervention effect was reported for ANU-ADRI, and baseline ANU-ADRI did not significantly affect the response to the intervention on changes in cognition. CONCLUSIONS The ANU-ADRI was effective for the risk prediction of cognitive decline. Risk scores may be crucial for the success of novel dementia prevention strategies, but their algorithm, the target population, and the intervention design should be carefully considered when choosing the appropriate tool for each context.
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Affiliation(s)
- Anette Hall
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Mariagnese Barbera
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, UK
| | - Jenni Lehtisalo
- Population Health Unit, Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Riitta Antikainen
- Center for Life Course Health Research/Geriatrics, University of Oulu, Oulu, Finland
- Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Hamidul Huque
- School of Psychology, University of New South Wales, Sydney, Sydney, New South Wales, Australia
- Neuroscience Research Australia, Randwick, New South Wales, Australia
| | - Tiina Laatikainen
- Population Health Unit, Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Tiia Ngandu
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Population Health Unit, Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Hilkka Soininen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Neurocenter Finland, Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Ruth Stephen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Population Health Unit, Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Timo Strandberg
- University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Miia Kivipelto
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, UK
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Theme Inflammation and Aging, Karolinska university hospital, Stockholm, Sweden
| | - Kaarin J Anstey
- School of Psychology, University of New South Wales, Sydney, Sydney, New South Wales, Australia
- Neuroscience Research Australia, Randwick, New South Wales, Australia
| | - Alina Solomon
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, UK
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Margiotoudi K, Fagot J, Meguerditchian A, Dautriche I. Humans (Homo sapiens) but not baboons (Papio papio) demonstrate crossmodal pitch-luminance correspondence. Am J Primatol 2024; 86:e23613. [PMID: 38475662 DOI: 10.1002/ajp.23613] [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: 06/07/2023] [Revised: 02/12/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024]
Abstract
Humans spontaneously and consistently map information coming from different sensory modalities. Surprisingly, the phylogenetic origin of such cross-modal correspondences has been under-investigated. A notable exception is the study of Ludwig et al. (Visuoauditory mappings between high luminance and high pitch are shared by chimpanzees [Pan troglodytes] and humans. Proceedings of the National Academy of Sciences, 108(51), 20661-20665) which reports that both humans and chimpanzees spontaneously map high-pitched sounds with bright objects and low-pitched sounds with dark objects. Our pre-registered study aimed to directly replicate this research on both humans and baboons (Papio papio), an old world monkey which is more phylogenetically distant from humans than chimpanzees. Following Ludwig et al. participants were presented with a visual classification task where they had to sort black and white square (low and high luminance), while background sounds (low or high-pitched tones) were playing. Whereas we replicated the finding that humans' performance on the visual task was affected by congruency between sound and luminance of the target, we did not find any of those effects on baboons' performance. These results question the presence of a shared cross-modal pitch-luminance mapping in other nonhuman primates.
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Affiliation(s)
- Konstantina Margiotoudi
- Centre de Recherche en Psychologie et Neurosciences, UMR7077, CNRS, Aix-Marseille Université, Marseille, France
- Station de Primatologie-Celphedia UAR846, CNRS, Rousset, France
| | - Joel Fagot
- Centre de Recherche en Psychologie et Neurosciences, UMR7077, CNRS, Aix-Marseille Université, Marseille, France
- Station de Primatologie-Celphedia UAR846, CNRS, Rousset, France
| | - Adrien Meguerditchian
- Centre de Recherche en Psychologie et Neurosciences, UMR7077, CNRS, Aix-Marseille Université, Marseille, France
- Station de Primatologie-Celphedia UAR846, CNRS, Rousset, France
| | - Isabelle Dautriche
- Centre de Recherche en Psychologie et Neurosciences, UMR7077, CNRS, Aix-Marseille Université, Marseille, France
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Buyukkececi Z, Leopold T. Parent-Child Relationships Following Gray Divorce: Stronger Ties With Mothers, Weaker Ties With Fathers. J Gerontol B Psychol Sci Soc Sci 2024; 79:gbae004. [PMID: 38280213 DOI: 10.1093/geronb/gbae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Indexed: 01/29/2024] Open
Abstract
OBJECTIVES With rising gray divorce rates, older individuals face heightened risk of social isolation, highlighting the significance of adult children as a vital source of solidarity in the absence of a spouse. Simultaneously, gray divorce may undermine parent-adult child relationships and weaken the core of the family safety net of older persons. This study examined the consequences of gray divorce for parent-child relationships. METHODS We used longitudinal data from the German Family Panel (Pairfam), a large-scale panel study collecting detailed information about family relationships and family structure. We focused on adult children aged 18-49 (n = 9,092) whose parents were married at first observation. During an observation period spanning up to 13 years (2008-2020), 606 individuals experienced parental divorce. Using fixed-effects models, we estimated changes in contact frequency, emotional closeness, and instrumental and emotional support provided to parents. RESULTS Consequences of gray divorce varied strongly between mothers and fathers. Adult-child solidarity intensified for mothers but eroded for fathers. This impact was strongest for changes in contact frequency, moderate for changes in emotional closeness, and smaller for changes in support. The persistence of gender role differentiation was evident, as daughters displayed closer ties and provided greater support to their mothers following a gray divorce. DISCUSSION Divorce alters relationships with adult children. A gray divorce tilts adult-child solidarity toward mothers and puts fathers at a higher risk of social isolation. Moreover, the observed gender dynamics underscore the continued influence of gender roles on family dynamics in the aftermath of gray divorce.
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Affiliation(s)
- Zafer Buyukkececi
- Institute of Sociology and Social Psychology, University of Cologne, Cologne, Germany
- Social Demography Department, Max Planck Institute for Demographic Research, Rostock, Germany
| | - Thomas Leopold
- Institute of Sociology and Social Psychology, University of Cologne, Cologne, Germany
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28
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Hoenig LC, Pliskin R, De Dreu CKW. Equality and efficiency shape cooperation in multiple-public-goods provision problems. J Exp Psychol Gen 2024; 153:1236-1256. [PMID: 38647478 DOI: 10.1037/xge0001574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The functioning of groups and societies requires that individuals cooperate on public goods such as healthcare and state defense. More often than not, individuals face multiple public goods and must choose on which to cooperate, if at all. Such decisions can be difficult when public goods are attractive on one dimension (e.g., being "efficient" in providing comparatively high returns) and unattractive on another (e.g., creating inequality by providing some group members greater returns than others). We examined how people manage such decision conflicts in five preregistered experiments (N = 900) that confronted participants with two public goods that varied in efficiency and (in)equality of returns. People cooperated more on the comparatively efficient public good and on the equal-return (vs. unequal-return) public good (Experiment 1), yet when the unequal-returns public good was also the most efficient, individuals cooperated comparatively more on this unequal-but-efficient public good when they themselves benefitted the most from inequality (Experiments 2-4). Low beneficiaries largely ignored public goods efficiency and preferentially cooperated on the equal- rather than unequal-returns public good. Expectations (Experiments 2-4), preferences for revising the multiple-public-goods provision problems' choice architecture (Experiments 3-4), and descriptive norms held by uninvolved arbitrators (Experiment 5) echoed these cooperation patterns, but uninvolved arbitrators deemed it socially appropriate to cooperate more on the equal than the unequal public good regardless of beneficiary position. We discuss implications for theory and policy on cooperation. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
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Fagernäs Z, Troché G, Olsen JV, Welker F. Digging deeper into ancient skeletal proteomes through consecutive digestion with multiple proteases. J Proteomics 2024; 298:105143. [PMID: 38423353 DOI: 10.1016/j.jprot.2024.105143] [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: 12/15/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
An increasing number of studies utilise the recovery of ancient skeletal proteomes for phylogenetic and evolutionary analysis. Although these studies manage to extract and analyse ancient peptides, the recovered proteomes are generally small in size and with low protein sequence coverage. We expand on previous observations which have shown that the parallel digestion and analysis of Pleistocene skeletal proteomes increases overall proteome size and protein sequence coverage. Furthermore, we demonstrate that the consecutive digestion of a skeletal proteome using two proteases, particularly the combination of Glu-C or chymotrypsin followed by trypsin digestion, enables the recovery of alternative proteome components not reachable through trypsin digestion alone. The proteomes preserved in Pleistocene skeletal specimens are larger than previously anticipated, but unlocking this protein sequence information requires adaptation of extraction and protein digestion protocols. The sequential utilisation of several proteases is, in this regard, a promising avenue for the study of highly degraded but unique hominin proteomes for phylogenetic purposes. SIGNIFICANCE: Palaeoproteomic analysis of archaeological materials, such as hominin skeletal elements, show great promise in studying past organisms and evolutionary relationships. However, as most proteomic methods are inherently destructive, it is essential to aim to recover as much information as possible from every sample. Currently, digestion with trypsin is the standard approach in most palaeoproteomic studies. We find that parallel or consecutive digestion with multiple proteases can improve proteome size and coverage for both Holocene and Pleistocene bone specimens. This allows for recovery of more proteomic data from a sample and maximises the chance of recovering phylogenetically relevant information.
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Affiliation(s)
- Zandra Fagernäs
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gaudry Troché
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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30
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Chen S, Katsonis N, Leigh DA, Patanapongpibul M, Ryabchun A, Zhang L. Changing Liquid Crystal Helical Pitch with a Reversible Rotaxane Switch. Angew Chem Int Ed Engl 2024; 63:e202401291. [PMID: 38445723 DOI: 10.1002/anie.202401291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/07/2024]
Abstract
The transmission of chiral information between the molecular, meso and microscopic scales is a facet of biology that remains challenging to understand mechanistically and to mimic with artificial systems. Here we demonstrate that the dynamic change in the expression of the chirality of a rotaxane can be transduced into a change in pitch of a soft matter system. Shuttling the position of the macrocycle from far-away-from to close-to a point-chiral center on the rotaxane axle changes the expression of the chiral information that is transmitted across length scales; from nanometer scale constitutional chirality that affects the conformation of the macrocycle, to the centimeter scale chirality of the liquid crystal phase, significantly changing the pitch length of the chiral nematic structure.
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Affiliation(s)
- Sujun Chen
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, P. R. China
| | - Nathalie Katsonis
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - David A Leigh
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, P. R. China
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Manee Patanapongpibul
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Alexander Ryabchun
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Liang Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, P. R. China
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31
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Gawlitt S, Collins SP, Yu Y, Blackman SA, Barquist L, Beisel CL. Expanding the flexibility of base editing for high-throughput genetic screens in bacteria. Nucleic Acids Res 2024; 52:4079-4097. [PMID: 38499498 DOI: 10.1093/nar/gkae174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/07/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide screens have become powerful tools for elucidating genotype-to-phenotype relationships in bacteria. Of the varying techniques to achieve knockout and knockdown, CRISPR base editors are emerging as promising options. However, the limited number of available, efficient target sites hampers their use for high-throughput screening. Here, we make multiple advances to enable flexible base editing as part of high-throughput genetic screening in bacteria. We first co-opt the Streptococcus canis Cas9 that exhibits more flexible protospacer-adjacent motif recognition than the traditional Streptococcus pyogenes Cas9. We then expand beyond introducing premature stop codons by mutating start codons. Next, we derive guide design rules by applying machine learning to an essentiality screen conducted in Escherichia coli. Finally, we rescue poorly edited sites by combining base editing with Cas9-induced cleavage of unedited cells, thereby enriching for intended edits. The efficiency of this dual system was validated through a conditional essentiality screen based on growth in minimal media. Overall, expanding the scope of genome-wide knockout screens with base editors could further facilitate the investigation of new gene functions and interactions in bacteria.
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Affiliation(s)
- Sandra Gawlitt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Scott P Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Samuel A Blackman
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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32
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van der Heijden O, Eggebeen JJJ, Trzesniowski H, Deka N, Golnak R, Xiao J, van Rijn M, Mom RV, Koper MTM. Li + Cations Activate NiFeOOH for Oxygen Evolution in Sodium and Potassium Hydroxide. Angew Chem Int Ed Engl 2024; 63:e202318692. [PMID: 38323697 DOI: 10.1002/anie.202318692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/08/2024]
Abstract
The efficiency of electrolysis is reduced due to the sluggish oxygen evolution reaction (OER). Besides catalyst properties, electrocatalytic activity also depends on the interaction of the electrocatalyst with the electrolyte. Here, we show that the addition of small amounts of Li+ to Fe-free NaOH or KOH electrolytes activates NiFeOOH for the OER compared to single-cation electrolytes. Moreover, the activation was maintained when the solution was returned to pure NaOH. Importantly, we show that the origin of activation by Li+ cations is primarily non-kinetic in nature, as the OER onset for the mixed electrolyte does not change and the Tafel slope at low current density is ~30 mV/dec in both electrolytes. However, the increase of the apparent Tafel slope remains lower at increasing current densities in the presence of Li+. Based on electrochemical quartz crystal microbalance and in situ X-ray absorption spectroscopy measurements, we show that this reduction of non-kinetic effects is due to enhanced intercalation of sodium, water and hydroxide. This enhanced electrolyte penetration facilitates the OER, especially at higher current densities and for increased catalyst loading. Our work shows that mixed electrolytes where distinct cations can have different roles provide a simple and promising strategy towards improved OER rates.
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Affiliation(s)
- Onno van der Heijden
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Jordy J J Eggebeen
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Hanna Trzesniowski
- Department of Atomic-Scale Dynamics in Light-Energy Conversion, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße 15, 12489, Berlin, Germany
| | - Nipon Deka
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Ronny Golnak
- Department of Highly Sensitive X-Ray Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109, Berlin, Germany
| | - Jie Xiao
- Department of Highly Sensitive X-Ray Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie, 14109, Berlin, Germany
| | - Maartje van Rijn
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Rik V Mom
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Marc T M Koper
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
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33
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Irmisch P, Mogila I, Samatanga B, Tamulaitis G, Seidel R. Retention of the RNA ends provides the molecular memory for maintaining the activation of the Csm complex. Nucleic Acids Res 2024; 52:3896-3910. [PMID: 38340341 DOI: 10.1093/nar/gkae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/23/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
The type III CRISPR-Cas effector complex Csm functions as a molecular Swiss army knife that provides multilevel defense against foreign nucleic acids. The coordinated action of three catalytic activities of the Csm complex enables simultaneous degradation of the invader's RNA transcripts, destruction of the template DNA and synthesis of signaling molecules (cyclic oligoadenylates cAn) that activate auxiliary proteins to reinforce CRISPR-Cas defense. Here, we employed single-molecule techniques to connect the kinetics of RNA binding, dissociation, and DNA hydrolysis by the Csm complex from Streptococcus thermophilus. Although single-stranded RNA is cleaved rapidly (within seconds), dual-color FCS experiments and single-molecule TIRF microscopy revealed that Csm remains bound to terminal RNA cleavage products with a half-life of over 1 hour while releasing the internal RNA fragments quickly. Using a continuous fluorescent DNA degradation assay, we observed that RNA-regulated single-stranded DNase activity decreases on a similar timescale. These findings suggest that after fast target RNA cleavage the terminal RNA cleavage products stay bound within the Csm complex, keeping the Cas10 subunit activated for DNA destruction. Additionally, we demonstrate that during Cas10 activation, the complex remains capable of RNA turnover, i.e. of ongoing degradation of target RNA.
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Affiliation(s)
- Patrick Irmisch
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Irmantas Mogila
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Brighton Samatanga
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
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Svensson T, Svensson AK, Kitlinski M, Engström G, Nilsson J, Orho-Melander M, Nilsson PM, Melander O. Very short sleep duration reveals a proteomic fingerprint that is selectively associated with incident diabetes mellitus but not with incident coronary heart disease: a cohort study. BMC Med 2024; 22:173. [PMID: 38649900 DOI: 10.1186/s12916-024-03392-1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The molecular pathways linking short and long sleep duration with incident diabetes mellitus (iDM) and incident coronary heart disease (iCHD) are not known. We aimed to identify circulating protein patterns associated with sleep duration and test their impact on incident cardiometabolic disease. METHODS We assessed sleep duration and measured 78 plasma proteins among 3336 participants aged 46-68 years, free from DM and CHD at baseline, and identified cases of iDM and iCHD using national registers. Incident events occurring in the first 3 years of follow-up were excluded from analyses. Tenfold cross-fit partialing-out lasso logistic regression adjusted for age and sex was used to identify proteins that significantly predicted sleep duration quintiles when compared with the referent quintile 3 (Q3). Predictive proteins were weighted and combined into proteomic scores (PS) for sleep duration Q1, Q2, Q4, and Q5. Combinations of PS were included in a linear regression model to identify the best predictors of habitual sleep duration. Cox proportional hazards regression models with sleep duration quintiles and sleep-predictive PS as the main exposures were related to iDM and iCHD after adjustment for known covariates. RESULTS Sixteen unique proteomic markers, predominantly reflecting inflammation and apoptosis, predicted sleep duration quintiles. The combination of PSQ1 and PSQ5 best predicted sleep duration. Mean follow-up times for iDM (n = 522) and iCHD (n = 411) were 21.8 and 22.4 years, respectively. Compared with sleep duration Q3, all sleep duration quintiles were positively and significantly associated with iDM. Only sleep duration Q1 was positively and significantly associated with iCHD. Inclusion of PSQ1 and PSQ5 abrogated the association between sleep duration Q1 and iDM. Moreover, PSQ1 was significantly associated with iDM (HR = 1.27, 95% CI: 1.06-1.53). PSQ1 and PSQ5 were not associated with iCHD and did not markedly attenuate the association between sleep duration Q1 with iCHD. CONCLUSIONS We here identify plasma proteomic fingerprints of sleep duration and suggest that PSQ1 could explain the association between very short sleep duration and incident DM.
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Affiliation(s)
- Thomas Svensson
- Department of Clinical Sciences, Lund University, Skåne University Hospital, CRC, Jan Waldenströms Gata 35, 20502, Malmö, Sweden.
- Precision Health, Department of Bioengineering, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan.
- Graduate School of Health Innovation, Kanagawa University of Human Services, Kawasaki-Ku, Kawasaki-Shi, Kanagawa, Japan.
| | - Akiko Kishi Svensson
- Department of Clinical Sciences, Lund University, Skåne University Hospital, CRC, Jan Waldenströms Gata 35, 20502, Malmö, Sweden
- Precision Health, Department of Bioengineering, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
- Department of Diabetes and Metabolic Diseases, the University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | | | - Gunnar Engström
- Department of Clinical Sciences, Lund University, Skåne University Hospital, CRC, Jan Waldenströms Gata 35, 20502, Malmö, Sweden
| | - Jan Nilsson
- Department of Clinical Sciences, Lund University, Skåne University Hospital, CRC, Jan Waldenströms Gata 35, 20502, Malmö, Sweden
| | - Marju Orho-Melander
- Department of Clinical Sciences, Lund University, Skåne University Hospital, CRC, Jan Waldenströms Gata 35, 20502, Malmö, Sweden
| | - Peter M Nilsson
- Department of Clinical Sciences, Lund University, Skåne University Hospital, CRC, Jan Waldenströms Gata 35, 20502, Malmö, Sweden
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Skåne University Hospital, CRC, Jan Waldenströms Gata 35, 20502, Malmö, Sweden
- Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden
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35
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Graffunder AS, Bresser AAJ, Fernandez Vallone V, Megges M, Stachelscheid H, Kühnen P, Opitz R. Spatiotemporal expression of thyroid hormone transporter MCT8 and THRA mRNA in human cerebral organoids recapitulating first trimester cortex development. Sci Rep 2024; 14:9355. [PMID: 38654093 DOI: 10.1038/s41598-024-59533-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
Thyroid hormones (TH) play critical roles during nervous system development and patients carrying coding variants of MCT8 (monocarboxylate transporter 8) or THRA (thyroid hormone receptor alpha) present a spectrum of neurological phenotypes resulting from perturbed local TH action during early brain development. Recently, human cerebral organoids (hCOs) emerged as powerful in vitro tools for disease modelling recapitulating key aspects of early human cortex development. To begin exploring prospects of this model for thyroid research, we performed a detailed characterization of the spatiotemporal expression of MCT8 and THRA in developing hCOs. Immunostaining showed MCT8 membrane expression in neuronal progenitor cell types including early neuroepithelial cells, radial glia cells (RGCs), intermediate progenitors and outer RGCs. In addition, we detected robust MCT8 protein expression in deep layer and upper layer neurons. Spatiotemporal SLC16A2 mRNA expression, detected by fluorescent in situ hybridization (FISH), was highly concordant with MCT8 protein expression across cortical cell layers. FISH detected THRA mRNA expression already in neuroepithelium before the onset of neurogenesis. THRA mRNA expression remained low in the ventricular zone, increased in the subventricular zone whereas strong THRA expression was observed in excitatory neurons. In combination with a robust up-regulation of known T3 response genes following T3 treatment, these observations show that hCOs provide a promising and experimentally tractable model to probe local TH action during human cortical neurogenesis and eventually to model the consequences of impaired TH function for early cortex development.
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Affiliation(s)
- Adina Sophie Graffunder
- Department of Pediatric Endocrinology and Diabetology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Audrey Amber Julie Bresser
- Department of Pediatric Endocrinology and Diabetology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Valeria Fernandez Vallone
- Core Unit Pluripotent Stem Cells and Organoids (CUSCO), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Megges
- Department of Pediatric Endocrinology and Diabetology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Harald Stachelscheid
- Core Unit Pluripotent Stem Cells and Organoids (CUSCO), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Kühnen
- Department of Pediatric Endocrinology and Diabetology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Robert Opitz
- Institute of Experimental Pediatric Endocrinology, Charité Universitätsmedizin Berlin, Berlin, Germany.
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36
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Cantoni C, Salaris A, Monti A, Porciello G, Aglioti SM. Probing corporeal awareness in women through virtual reality induction of embreathment illusion. Sci Rep 2024; 14:9302. [PMID: 38654060 DOI: 10.1038/s41598-024-59766-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
We capitalized on the respiratory bodily illusion that we discovered in a previous study and called 'Embreathment' where we showed that breathing modulates corporeal awareness in men. Despite the relevance of the issue, no such studies are available in women. To bridge this gap, we tested whether the synchronization of avatar-participant respiration patterns influenced females' bodily awareness. We collected cardiac and respiratory interoceptive measures, administered body (dis)satisfaction questionnaires, and tracked participants' menstrual cycles via a mobile app. Our approach allowed us to characterize the 'Embreathment' illusion in women, and explore the relationships between menstrual cycle, interoception and body image. We found that breathing was as crucial as visual appearance in eliciting feelings of ownership and held greater significance than any other cue with respect to body agency in both women and men. Moreover, a positive correlation between menstrual cycle days and body image concerns, and a negative correlation between interoceptive sensibility and body dissatisfaction were found, confirming that women's body dissatisfaction arises during the last days of menstrual cycle and is associated with interoception. These findings have potential implications for corporeal awareness alterations in clinical conditions like eating disorders and schizophrenia.
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Affiliation(s)
- Chiara Cantoni
- Department of Psychology, Sapienza University of Rome, 00185, Rome, Italy.
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy.
| | - Andrea Salaris
- Department of Psychology, Sapienza University of Rome, 00185, Rome, Italy.
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy.
| | - Alessandro Monti
- Department of Psychology, Sapienza University of Rome, 00185, Rome, Italy
| | - Giuseppina Porciello
- Department of Psychology, Sapienza University of Rome, 00185, Rome, Italy
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy
| | - Salvatore Maria Aglioti
- Department of Psychology, Sapienza University of Rome, 00185, Rome, Italy
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy
- CLN2S@Sapienza, Istituto Italiano di Tecnologia, Sapienza University Rome, 00161, Rome, Italy
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Zhao C, Ong JH, Veic A, Patel AD, Jiang C, Fogel AR, Wang L, Hou Q, Das D, Crasto C, Chakrabarti B, Williams TI, Loutrari A, Liu F. Predictive processing of music and language in autism: Evidence from Mandarin and English speakers. Autism Res 2024. [PMID: 38651566 DOI: 10.1002/aur.3133] [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: 05/26/2023] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
Atypical predictive processing has been associated with autism across multiple domains, based mainly on artificial antecedents and consequents. As structured sequences where expectations derive from implicit learning of combinatorial principles, language and music provide naturalistic stimuli for investigating predictive processing. In this study, we matched melodic and sentence stimuli in cloze probabilities and examined musical and linguistic prediction in Mandarin- (Experiment 1) and English-speaking (Experiment 2) autistic and non-autistic individuals using both production and perception tasks. In the production tasks, participants listened to unfinished melodies/sentences and then produced the final notes/words to complete these items. In the perception tasks, participants provided expectedness ratings of the completed melodies/sentences based on the most frequent notes/words in the norms. While Experiment 1 showed intact musical prediction but atypical linguistic prediction in autism in the Mandarin sample that demonstrated imbalanced musical training experience and receptive vocabulary skills between groups, the group difference disappeared in a more closely matched sample of English speakers in Experiment 2. These findings suggest the importance of taking an individual differences approach when investigating predictive processing in music and language in autism, as the difficulty in prediction in autism may not be due to generalized problems with prediction in any type of complex sequence processing.
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Affiliation(s)
- Chen Zhao
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
| | - Jia Hoong Ong
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
| | - Anamarija Veic
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
| | - Aniruddh D Patel
- Department of Psychology, Tufts University, Medford, Massachusetts, USA
- Program in Brain, Mind, and Consciousness, Canadian Institute for Advanced Research (CIFAR), Toronto, Canada
| | - Cunmei Jiang
- Music College, Shanghai Normal University, Shanghai, China
| | - Allison R Fogel
- Department of Psychology, Tufts University, Medford, Massachusetts, USA
| | - Li Wang
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
| | - Qingqi Hou
- Department of Music and Dance, Nanjing Normal University of Special Education, Nanjing, China
| | - Dipsikha Das
- School of Psychology, Keele University, Staffordshire, UK
| | - Cara Crasto
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
| | - Bhismadev Chakrabarti
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
| | - Tim I Williams
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
| | - Ariadne Loutrari
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
| | - Fang Liu
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
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38
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Falk D, Wings O, Unitt R, Wade J, McNamara ME. Fossilized anuran soft tissues reveal a new taphonomic model for the Eocene Geiseltal Konservat-Lagerstätte, Germany. Sci Rep 2024; 14:7876. [PMID: 38654038 DOI: 10.1038/s41598-024-55822-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/28/2024] [Indexed: 04/25/2024] Open
Abstract
The Eocene Geiseltal Konservat-Lagerstätte (Germany) is famous for reports of three dimensionally preserved soft tissues with sub-cellular detail. The proposed mode of preservation, direct replication in silica, is not known in other fossils and has not been verified using modern approaches. Here, we investigated the taphonomy of the Geiseltal anurans using diverse microbeam imaging and chemical analytical techniques. Our analyses confirm the preservation of soft tissues in all body regions but fail to yield evidence for silicified soft tissues. Instead, the anuran soft tissues are preserved as two layers that differ in microstructure and composition. Layer 1 comprises sulfur-rich carbonaceous microbodies interpreted as melanosomes. Layer 2 comprises the mid-dermal Eberth-Katschenko layer, preserved in calcium phosphate. In addition, patches of original aragonite crystals define the former position of the endolymphatic sac. The primary modes of soft tissue preservation are therefore sulfurization of melanosomes and phosphatization of more labile soft tissues, i.e., skin. This is consistent with the taphonomy of vertebrates in many other Konservat-Lagerstätten. These findings emphasize an emerging model for pervasive preservation of vertebrate soft tissues via melanosome films, particularly in stagnation-type deposits, with phosphatization of more labile tissues where tissue biochemistry is favorable.
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Affiliation(s)
- Daniel Falk
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, T23 TK30, Ireland.
- Environmental Research Institute, University College Cork, Lee Rd, Cork, T23 XE10, Ireland.
| | - Oliver Wings
- Natural History Museum Bamberg, Staatliche Naturwissenschaftliche Sammlungen Bayerns, Fleischstraße 2, 96047, Bamberg, Germany
| | - Richard Unitt
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, T23 TK30, Ireland
- Environmental Research Institute, University College Cork, Lee Rd, Cork, T23 XE10, Ireland
- Copper Coast UNESCO Global Geopark, Knockmahon, Bunmahon, X42 T923, Ireland
| | - Jon Wade
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
| | - Maria E McNamara
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, T23 TK30, Ireland
- Environmental Research Institute, University College Cork, Lee Rd, Cork, T23 XE10, Ireland
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Li X, Fu YH, Wei N, Yu RJ, Bhatti H, Zhang L, Yan F, Xia F, Ewing AG, Long YT, Ying YL. Emerging Data Processing Methods for Single-Entity Electrochemistry. Angew Chem Int Ed Engl 2024; 63:e202316551. [PMID: 38411372 DOI: 10.1002/anie.202316551] [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: 11/01/2023] [Revised: 02/12/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Single-entity electrochemistry is a powerful tool that enables the study of electrochemical processes at interfaces and provides insights into the intrinsic chemical and structural heterogeneities of individual entities. Signal processing is a critical aspect of single-entity electrochemical measurements and can be used for data recognition, classification, and interpretation. In this review, we summarize the recent five-year advances in signal processing techniques for single-entity electrochemistry and highlight their importance in obtaining high-quality data and extracting effective features from electrochemical signals, which are generally applicable in single-entity electrochemistry. Moreover, we shed light on electrochemical noise analysis to obtain single-molecule frequency fingerprint spectra that can provide rich information about the ion networks at the interface. By incorporating advanced data analysis tools and artificial intelligence algorithms, single-entity electrochemical measurements would revolutionize the field of single-entity analysis, leading to new fundamental discoveries.
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Affiliation(s)
- Xinyi Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ying-Huan Fu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Nannan Wei
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ru-Jia Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, P. R. China
| | - Huma Bhatti
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Limin Zhang
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Feng Yan
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, 430034, Wuhan, P. R. China
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296, Gothenburg, Sweden
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, P. R. China
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Saadmaan G, Dalmasso MC, Ramirez A, Hiltunen M, Kemppainen N, Lehtisalo J, Mangialasche F, Ngandu T, Rinne J, Soininen H, Stephen R, Kivipelto M, Solomon A. Alzheimer's disease genetic risk score and neuroimaging in the FINGER lifestyle trial. Alzheimers Dement 2024. [PMID: 38647197 DOI: 10.1002/alz.13843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
INTRODUCTION We assessed a genetic risk score for Alzheimer's disease (AD-GRS) and apolipoprotein E (APOE4) in an exploratory neuroimaging substudy of the FINGER trial. METHODS 1260 at-risk older individuals without dementia were randomized to multidomain lifestyle intervention or health advice. N = 126 participants underwent magnetic resonance imaging (MRI), and N = 47 positron emission tomography (PET) scans (Pittsburgh Compund B [PiB], Fluorodeoxyglucose) at baseline; N = 107 and N = 38 had repeated 2-year scans. RESULTS The APOE4 allele, but not AD-GRS, was associated with baseline lower hippocampus volume (β = -0.27, p = 0.001), greater amyloid deposition (β = 0.48, p = 0.001), 2-year decline in hippocampus (β = -0.27, p = 0.01), total gray matter volume (β = -0.25, p = 0.01), and cortical thickness (β = -0.28, p = 0.003). In analyses stratified by AD-GRS (below vs above median), the PiB composite score increased less in intervention versus control in the higher AD-GRS group (β = -0.60, p = 0.03). DISCUSSION AD-GRS and APOE4 may have different impacts on potential intervention effects on amyloid, that is, less accumulation in the higher-risk group (AD-GRS) versus lower-risk group (APOE). HIGHLIGHTS First study of neuroimaging and AD genetics in a multidomain lifestyle intervention. Possible intervention effect on brain amyloid deposition may rely on genetic risk. AD-GRS and APOE4 allele may have different impacts on amyloid during intervention.
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Affiliation(s)
- Gazi Saadmaan
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Maria Carolina Dalmasso
- Studies in Neuroscience and Complex Systems Unit (ENyS), CONICET-HEC-UNAJ, Florencio Varela, Argentina
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, Cologne, Germany
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, Cologne, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases, DZNE Bonn, Bonn, Germany
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, Texas, USA
- Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Nina Kemppainen
- Turku PET Centre, University of Turku, Turku, Finland
- Division of Clinical Neurosciences, Turku University Hospital, Turku, Finland
| | - Jenni Lehtisalo
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Francesca Mangialasche
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Tiia Ngandu
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Juha Rinne
- Turku PET Centre, University of Turku, Turku, Finland
- Division of Clinical Neurosciences, Turku University Hospital, Turku, Finland
| | - Hilkka Soininen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Ruth Stephen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Miia Kivipelto
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, UK
| | - Alina Solomon
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, UK
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Oz S, Saar G, Olszakier S, Heinrich R, Kompanets MO, Berlin S. Revealing the MRI-Contrast in Optically Cleared Brains. Adv Sci (Weinh) 2024:e2400316. [PMID: 38647385 DOI: 10.1002/advs.202400316] [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: 01/09/2024] [Revised: 04/10/2024] [Indexed: 04/25/2024]
Abstract
The current consensus holds that optically-cleared specimens are unsuitable for Magnetic Resonance Imaging (MRI); exhibiting absence of contrast. Prior studies combined MRI with tissue-clearing techniques relying on the latter's ability to eliminate lipids, thereby fostering the assumption that lipids constitute the primary source of ex vivo MRI-contrast. Nevertheless, these findings contradict an extensive body of literature that underscores the contribution of other features to contrast. Furthermore, it remains unknown whether non-delipidating clearing methods can produce MRI-compatible specimens or whether MRI-contrast can be re-established. These limitations hinder the development of multimodal MRI-light-microscopy (LM) imaging approaches. This study assesses the relation between MRI-contrast, and delipidation in optically-cleared whole brains following different tissue-clearing approaches. It is demonstrated that uDISCO and ECi-brains are MRI-compatible upon tissue rehydration, despite both methods' substantial delipidating-nature. It is also demonstrated that, whereas Scale-clearing preserves most lipids, Scale-cleared brain lack MRI-contrast. Furthermore, MRI-contrast is restored to lipid-free CLARITY-brains without introducing lipids. Our results thereby dissociate between the essentiality of lipids to MRI-contrast. A tight association is found between tissue expansion, hyperhydration and loss of MRI-contrast. These findings then enabled us to develop a multimodal MRI-LM-imaging approach, opening new avenues to bridge between the micro- and mesoscale for biomedical research and clinical applications.
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Affiliation(s)
- Shimrit Oz
- Department of Neuroscience, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 3525433, Israel
| | - Galit Saar
- Biomedical Core Facility, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 3525433, Israel
| | - Shunit Olszakier
- Department of Neuroscience, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 3525433, Israel
| | - Ronit Heinrich
- Department of Neuroscience, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 3525433, Israel
| | - Mykhail O Kompanets
- L.M. Litvinenko Institute of Physico-Organic Chemistry and Coal Chemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Shai Berlin
- Department of Neuroscience, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 3525433, Israel
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van der Meer P, Grote Beverborg N. Intravenous iron, only for those in need. Eur Heart J 2024; 45:1427-1429. [PMID: 38471820 DOI: 10.1093/eurheartj/ehae093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/14/2024] Open
Affiliation(s)
- Peter van der Meer
- Department of Cardology, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Niels Grote Beverborg
- Department of Cardology, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
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Jackson AM, Goland S, Farhan HA, Yaseen IF, Prameswari HS, Böhm M, Jhund PS, Maggioni AP, van der Meer P, Sliwa K, Bauersachs J, Petrie MC. A novel score to predict left ventricular recovery in peripartum cardiomyopathy derived from the ESC EORP Peripartum Cardiomyopathy Registry. Eur Heart J 2024; 45:1430-1439. [PMID: 38282532 PMCID: PMC11032708 DOI: 10.1093/eurheartj/ehad888] [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: 04/18/2023] [Revised: 11/01/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND AND AIMS There are no established clinical tools to predict left ventricular (LV) recovery in women with peripartum cardiomyopathy (PPCM). Using data from women enrolled in the ESC EORP PPCM Registry, the aim was to derive a prognostic model to predict LV recovery at 6 months and develop the 'ESC EORP PPCM Recovery Score'-a tool for clinicians to estimate the probability of LV recovery. METHODS From 2012 to 2018, 752 women from 51 countries were enrolled. Eligibility included (i) a peripartum state, (ii) signs or symptoms of heart failure, (iii) LV ejection fraction (LVEF) ≤ 45%, and (iv) exclusion of alternative causes of heart failure. The model was derived using data from participants in the Registry and internally validated using bootstrap methods. The outcome was LV recovery (LVEF ≥50%) at six months. An integer score was created. RESULTS Overall, 465 women had a 6-month echocardiogram. LV recovery occurred in 216 (46.5%). The final model included baseline LVEF, baseline LV end diastolic diameter, human development index (a summary measure of a country's social and economic development), duration of symptoms, QRS duration and pre-eclampsia. The model was well-calibrated and had good discriminatory ability (C-statistic 0.79, 95% confidence interval [CI] 0.74-0.83). The model was internally validated (optimism-corrected C-statistic 0.78, 95% CI 0.73-0.82). CONCLUSIONS A model which accurately predicts LV recovery at 6 months in women with PPCM was derived. The corresponding ESC EORP PPCM Recovery Score can be easily applied in clinical practice to predict the probability of LV recovery for an individual in order to guide tailored counselling and treatment.
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Affiliation(s)
- Alice M Jackson
- BHF Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sorel Goland
- The Heart Institute, Kaplan Medical Center, Rehovot, Israel
- Hadassah Medical School, Hebrew University, Jerusalem
| | - Hasan Ali Farhan
- Iraqi Board for Medical Specializations, Scientific Council of Cardiology, Baghdad Heart Center, Medical City, Baghdad, Iraq
| | - Israa Fadhil Yaseen
- Iraqi Board for Medical Specializations, Scientific Council of Cardiology, Baghdad Heart Center, Medical City, Baghdad, Iraq
| | | | - Michael Böhm
- Klinik für Innere Medizin III, Kardiologie, Angiologie und Internistische Intensivmedizin, Universitätsklinikum des Saarlandes, Saarland University, Homburg, Germany
| | - Pardeep S Jhund
- BHF Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Aldo P Maggioni
- ANMCO Research Center, Heart Care Foundation, Firenze, Italy
| | - Peter van der Meer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Karen Sliwa
- Faculty of Health Sciences, Department of Medicine and Cardiology University of Cape Town, Cape Heart Institute, Cape Town, South Africa
| | - Johann Bauersachs
- Department of Cardiology and Angiology, Medical School Hannover, Hannover, Germany
| | - Mark C Petrie
- BHF Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
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von Preetzmann N, Zipplies D, Span R, Richter M. Utilization of a High-Pressure Vibrating Tube Densimeter for Liquids at Temperatures Down to 100 K. Int J Thermophys 2024; 45:72. [PMID: 38645609 PMCID: PMC11031472 DOI: 10.1007/s10765-024-03357-9] [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] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/16/2024] [Indexed: 04/23/2024]
Abstract
A high-pressure vibrating tube densimeter, specified by the manufacturer for temperatures from (263 to 473) K at pressures up to 140 MPa, was tested at temperatures down to 100 K and from vacuum to pressures up to 10 MPa. To verify the functionality and overall performance under these conditions, the densimeter was calibrated with measurements under vacuum as well as methane and propane as reference fluids. The calibration range is T = (120 to 200) K at pressures from (2.0 to 10.0) MPa. To evaluate the recorded data, two established calibration models were used to describe the dependence of the densimeter's oscillation period on the investigated reference fluids' temperature, pressure, and density. The experiments showed that the vibrating tube densimeter is operational even at temperatures down to 100 K, but exhibits a shift of its vacuum resonance when subjected to thermal cycling at temperatures below 180 K. Accordingly, the calibration models were modified with respect to how the vacuum resonance is considered. Then, the determined calibration parameters reproduce the densities of the reference fluids within ± 0.10 kg·m-3 for the calibration model that performed better for the present study. Measurements on pure ethane and argon validate the calibration of the densimeter. Here, the densities are within (- 0.47 to 0.16) kg·m-3 of values calculated with the respective reference equation of state. The estimated combined expanded uncertainty (k = 2) in density for the validation measurements ranges from (0.52 to 1.13) kg·m-3 or is less than 0.1 % for liquid densities. Supplementary Information The online version of this article (10.1007/s10765-024-03357-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Daniel Zipplies
- Applied Thermodynamics, Chemnitz University of Technology, 09107 Chemnitz, Germany
| | - Roland Span
- Thermodynamics, Ruhr University Bochum, 44780 Bochum, Germany
| | - Markus Richter
- Applied Thermodynamics, Chemnitz University of Technology, 09107 Chemnitz, Germany
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Krasnokutski SA, Jäger C, Henning T, Geffroy C, Remaury QB, Poinot P. Formation of extraterrestrial peptides and their derivatives. Sci Adv 2024; 10:eadj7179. [PMID: 38630826 PMCID: PMC11023503 DOI: 10.1126/sciadv.adj7179] [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: 07/12/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
The formation of protein precursors, due to the condensation of atomic carbon under the low-temperature conditions of the molecular phases of the interstellar medium, opens alternative pathways for the origin of life. We perform peptide synthesis under conditions prevailing in space and provide a comprehensive analytic characterization of its products. The application of 13C allowed us to confirm the suggested pathway of peptide formation that proceeds due to the polymerization of aminoketene molecules that are formed in the C + CO + NH3 reaction. Here, we address the question of how the efficiency of peptide production is modified by the presence of water molecules. We demonstrate that although water slightly reduces the efficiency of polymerization of aminoketene, it does not prevent the formation of peptides.
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Affiliation(s)
- Serge A. Krasnokutski
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena, Helmholtzweg 3, D-07743 Jena, Germany
| | - Cornelia Jäger
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena, Helmholtzweg 3, D-07743 Jena, Germany
| | | | - Claude Geffroy
- Institut de Chimie des Milieux et Materiaux de Poitiers, University of Poitiers, UMR CNRS 7285, France
| | - Quentin B. Remaury
- Institut de Chimie des Milieux et Materiaux de Poitiers, University of Poitiers, UMR CNRS 7285, France
| | - Pauline Poinot
- Institut de Chimie des Milieux et Materiaux de Poitiers, University of Poitiers, UMR CNRS 7285, France
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van Buuren MMA, Riedstra NS, van den Berg MA, Boel FDEM, Ahedi H, Arbabi V, Arden NK, Bierma-Zeinstra SMA, Boer CG, Cicuttini F, Cootes TF, Crossley K, Felson D, Gielis WP, Heerey J, Jones G, Kluzek S, Lane NE, Lindner C, Lynch JA, Van Meurs J, Mosler AB, Nelson AE, Nevitt M, Oei E, Runhaar J, Tang J, Weinans H, Agricola R. Cohort profile: Worldwide Collaboration on OsteoArthritis prediCtion for the Hip (World COACH) - an international consortium of prospective cohort studies with individual participant data on hip osteoarthritis. BMJ Open 2024; 14:e077907. [PMID: 38637130 PMCID: PMC11029301 DOI: 10.1136/bmjopen-2023-077907] [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: 07/18/2023] [Accepted: 02/20/2024] [Indexed: 04/20/2024] Open
Abstract
PURPOSE Hip osteoarthritis (OA) is a major cause of pain and disability worldwide. Lack of effective therapies may reflect poor knowledge on its aetiology and risk factors, and result in the management of end-stage hip OA with costly joint replacement. The Worldwide Collaboration on OsteoArthritis prediCtion for the Hip (World COACH) consortium was established to pool and harmonise individual participant data from prospective cohort studies. The consortium aims to better understand determinants and risk factors for the development and progression of hip OA, to optimise and automate methods for (imaging) analysis, and to develop a personalised prediction model for hip OA. PARTICIPANTS World COACH aimed to include participants of prospective cohort studies with ≥200 participants, that have hip imaging data available from at least 2 time points at least 4 years apart. All individual participant data, including clinical data, imaging (data), biochemical markers, questionnaires and genetic data, were collected and pooled into a single, individual-level database. FINDINGS TO DATE World COACH currently consists of 9 cohorts, with 38 021 participants aged 18-80 years at baseline. Overall, 71% of the participants were women and mean baseline age was 65.3±8.6 years. Over 34 000 participants had baseline pelvic radiographs available, and over 22 000 had an additional pelvic radiograph after 8-12 years of follow-up. Even longer radiographic follow-up (15-25 years) is available for over 6000 of these participants. FUTURE PLANS The World COACH consortium offers unique opportunities for studies on the relationship between determinants/risk factors and the development or progression of hip OA, by using harmonised data on clinical findings, imaging, biomarkers, genetics and lifestyle. This provides a unique opportunity to develop a personalised hip OA risk prediction model and to optimise methods for imaging analysis of the hip.
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Affiliation(s)
- Michiel M A van Buuren
- Department of Orthopaedics and Sports Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, Netherlands
| | - Noortje S Riedstra
- Department of Orthopaedics and Sports Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, Netherlands
| | - Myrthe A van den Berg
- Department of Orthopaedics and Sports Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, Netherlands
| | - Fleur D E M Boel
- Department of Orthopaedics and Sports Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, Netherlands
| | - Harbeer Ahedi
- Institute for Medical Research, University of Tasmania Menzies, Hobart, Tasmania, Australia
| | - Vahid Arbabi
- Department of Orthopedics, UMC Utrecht, Utrecht, Netherlands
- Orthopaedic-Biomechanics Research Group, Department of Mechanical Engineering, Faculty of Engineering, University of Birjand, Birjand, Iran
| | - Nigel K Arden
- Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford Nuffield, Oxford, Oxfordshire, UK
| | | | - Cindy G Boer
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, Netherlands
| | - Flavia Cicuttini
- Department of Epidemiology and Preventative Medicine, Monash University, Melbourne, Victoria, Australia
| | - Timothy F Cootes
- Centre for Imaging Sciences, The University of Manchester, Manchester, UK
| | - Kay Crossley
- La Trobe Sport and Exercise Medicine Research Centre, La Trobe University School of Allied Health Human Services and Sport, Melbourne, Victoria, Australia
| | - David Felson
- Boston University School of Medicine, Boston, Massachusetts, USA
| | - Willem Paul Gielis
- Department of Orthopedics, UMC Utrecht, Utrecht, Netherlands
- Department of Radiology, UMC Utrecht, Utrecht, Netherlands
| | - Joshua Heerey
- La Trobe Sport and Exercise Medicine Research Centre, La Trobe University School of Allied Health Human Services and Sport, Melbourne, Victoria, Australia
| | - Graeme Jones
- Institute for Medical Research, University of Tasmania Menzies, Hobart, Tasmania, Australia
| | - Stefan Kluzek
- Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford Nuffield, Oxford, Oxfordshire, UK
| | - Nancy E Lane
- Department of Medicine, University of California Davis School of Medicine, Sacramento, California, USA
| | - Claudia Lindner
- Centre for Imaging Sciences, The University of Manchester, Manchester, UK
| | - John A Lynch
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - J Van Meurs
- Department of Orthopaedics and Sports Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, Netherlands
| | - Andrea B Mosler
- La Trobe Sport and Exercise Medicine Research Centre, La Trobe University School of Allied Health Human Services and Sport, Melbourne, Victoria, Australia
| | - Amanda E Nelson
- Thurston Arthritis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - M Nevitt
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Edwin Oei
- Department of Radiology & Nuclear Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, Netherlands
| | - Jos Runhaar
- Department of General Practice, Erasmus Medical Center, Rotterdam, Zuid-Holland, Netherlands
| | - Jinchi Tang
- Department of Orthopaedics and Sports Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, Netherlands
| | - Harrie Weinans
- Department of Orthopedics, UMC Utrecht, Utrecht, Netherlands
- Department of Biomechanical Engineering, TU Delft, Delft, Zuid-Holland, Netherlands
| | - Rintje Agricola
- Department of Orthopaedics and Sports Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, Netherlands
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Ghosh N, Lejonberg C, Czuba T, Dekkers K, Robinson R, Ärnlöv J, Melander O, Smith ML, Evans AM, Gidlöf O, Gerszten RE, Lind L, Engström G, Fall T, Smith JG. Analysis of plasma metabolomes from 11 309 subjects in five population-based cohorts. Sci Rep 2024; 14:8933. [PMID: 38637659 PMCID: PMC11026396 DOI: 10.1038/s41598-024-59388-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Plasma metabolomics holds potential for precision medicine, but limited information is available to compare the performance of such methods across multiple cohorts. We compared plasma metabolite profiles after an overnight fast in 11,309 participants of five population-based Swedish cohorts (50-80 years, 52% women). Metabolite profiles were uniformly generated at a core laboratory (Metabolon Inc.) with untargeted liquid chromatography mass spectrometry and a comprehensive reference library. Analysis of a second sample obtained one year later was conducted in a subset. Of 1629 detected metabolites, 1074 (66%) were detected in all cohorts while only 10% were unique to one cohort, most of which were xenobiotics or uncharacterized. The major classes were lipids (28%), xenobiotics (22%), amino acids (14%), and uncharacterized (19%). The most abundant plasma metabolome components were the major dietary fatty acids and amino acids, glucose, lactate and creatinine. Most metabolites displayed a log-normal distribution. Temporal variability was generally similar to clinical chemistry analytes but more pronounced for xenobiotics. Extensive metabolite-metabolite correlations were observed but mainly restricted to within each class. Metabolites were broadly associated with clinical factors, particularly body mass index, sex and renal function. Collectively, our findings inform the conduct and interpretation of metabolite association and precision medicine studies.
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Affiliation(s)
- Nilanjana Ghosh
- The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiology, Sahlgrenska University Hospital, SE-413 45, Gothenburg, Sweden
| | - Carl Lejonberg
- Department of Cardiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Tomasz Czuba
- The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiology, Sahlgrenska University Hospital, SE-413 45, Gothenburg, Sweden
- Department of Cardiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Koen Dekkers
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | | | - Johan Ärnlöv
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
| | - Olle Melander
- Department of Internal Medicine, Clinical Sciences, Lund University, Malmö, Sweden
| | - Maya Landenhed Smith
- Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiothoracic Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Olof Gidlöf
- Department of Cardiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Gunnar Engström
- Cardiovascular Epidemiology, Clinical Sciences, Lund University, Malmö, Sweden
| | - Tove Fall
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - J Gustav Smith
- The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiology, Sahlgrenska University Hospital, SE-413 45, Gothenburg, Sweden.
- Department of Cardiology, Clinical Sciences, Lund University, Lund, Sweden.
- Department of Heart Failure and Valvular Disease, Skåne University Hospital, Lund, Sweden.
- Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, Sweden.
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48
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Gryszel M, Byun D, Burtscher B, Abrahamsson T, Brodsky J, Simon DT, Berggren M, Glowacki ED, Strakosas X, Donahue MJ. Vertical organic electrochemical transistor platforms for efficient electropolymerization of thiophene based oligomers. J Mater Chem C Mater 2024; 12:5339-5346. [PMID: 38645749 PMCID: PMC11025323 DOI: 10.1039/d3tc04730j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/23/2024] [Indexed: 04/23/2024]
Abstract
Organic electrochemical transistors (OECTs) have emerged as promising candidates for various fields, including bioelectronics, neuromorphic computing, biosensors, and wearable electronics. OECTs operate in aqueous solutions, exhibit high amplification properties, and offer ion-to-electron signal transduction. The OECT channel consists of a conducting polymer, with PEDOT:PSS receiving the most attention to date. While PEDOT:PSS is highly conductive, and benefits from optimized protocols using secondary dopants and detergents, new p-type and n-type polymers are emerging with desirable material properties. Among these, low-oxidation potential oligomers are highly enabling for bioelectronics applications, however the polymers resulting from their polymerization lag far behind in conductivity compared with the established PEDOT:PSS. In this work we show that by careful design of the OECT geometrical characteristics, we can overcome this limitation and achieve devices that are on-par with transistors employing PEDOT:PSS. We demonstrate that the vertical architecture allows for facile electropolymerization of a family of trimers that are polymerized in very low oxidation potentials, without the need for harsh chemicals or secondary dopants. Vertical and planar OECTs are compared using various characterization methods. We show that vOECTs are superior platforms in general and propose that the vertical architecture can be expanded for the realization of OECTs for various applications.
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Affiliation(s)
- Maciej Gryszel
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University 60174 Norrköping Sweden
| | - Donghak Byun
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University 60174 Norrköping Sweden
| | - Bernhard Burtscher
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University 60174 Norrköping Sweden
| | - Tobias Abrahamsson
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University 60174 Norrköping Sweden
| | - Jan Brodsky
- Bioelectronics Materials and Devices Lab, Central European Institute of Technology, Brno University of Technology Purkyňova 123 61200 Brno Czech Republic
| | - Daniel Theodore Simon
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University 60174 Norrköping Sweden
| | - Magnus Berggren
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University 60174 Norrköping Sweden
- Wallenberg Wood Science Center, Department of Science and Technology, Linköping University 60174 Norrköping Sweden
| | - Eric Daniel Glowacki
- Bioelectronics Materials and Devices Lab, Central European Institute of Technology, Brno University of Technology Purkyňova 123 61200 Brno Czech Republic
| | - Xenofon Strakosas
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University 60174 Norrköping Sweden
| | - Mary Jocelyn Donahue
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University 60174 Norrköping Sweden
- Bioelectronics Materials and Devices Lab, Central European Institute of Technology, Brno University of Technology Purkyňova 123 61200 Brno Czech Republic
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49
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Bertalan É, Rodrigues MJ, Schertler GFX, Bondar AN. Graph-based algorithms to dissect long-distance water-mediated H-bond networks for conformational couplings in GPCRs. Br J Pharmacol 2024. [PMID: 38636539 DOI: 10.1111/bph.16387] [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: 08/31/2023] [Revised: 02/03/2024] [Accepted: 03/02/2024] [Indexed: 04/20/2024] Open
Abstract
Changes in structure and dynamics elicited by agonist ligand binding at the extracellular side of G protein coupled receptors (GPCRs) must be relayed to the cytoplasmic G protein binding side of the receptors. To decipher the role of water-mediated hydrogen-bond networks in this relay mechanism, we have developed graph-based algorithms and analysis methodologies applicable to datasets of static structures of distinct GPCRs. For a reference dataset of static structures of bovine rhodopsin solved at the same resolution, we show that graph analyses capture the internal protein-water hydrogen-bond network. The extended analyses of static structures of rhodopsins and opioid receptors suggest a relay mechanism whereby inactive receptors have in place much of the internal core hydrogen-bond network required for long-distance relay of structural change, with extensive local H-bond clusters observed in structures solved at high resolution and with internal water molecules.
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Affiliation(s)
- Éva Bertalan
- Physikzentrum, RWTH-Aachen University, Aachen, Germany
| | | | | | - Ana-Nicoleta Bondar
- Forschungszentrum Jülich, Institute of Computational Biomedicine, Jülich, Germany
- Faculty of Physics, University of Bucharest, Măgurele, Romania
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50
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Gutiérrez-Llorente A, Raji A, Zhang D, Divay L, Gloter A, Gallego F, Galindo C, Bibes M, Iglesias L. Toward Reliable Synthesis of Superconducting Infinite Layer Nickelate Thin Films by Topochemical Reduction. Adv Sci (Weinh) 2024:e2309092. [PMID: 38634748 DOI: 10.1002/advs.202309092] [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: 11/24/2023] [Revised: 03/05/2024] [Indexed: 04/19/2024]
Abstract
Infinite layer (IL) nickelates provide a new route beyond copper oxides to address outstanding questions in the field of unconventional superconductivity. However, their synthesis poses considerable challenges, largely hindering experimental research on this new class of oxide superconductors. That synthesis is achieved in a two-step process that yields the most thermodynamically stable perovskite phase first, then the IL phase by topotactic reduction, the quality of the starting phase playing a crucial role. Here, a reliable synthesis of superconducting IL nickelate films is reported after successive topochemical reductions of a parent perovskite phase with nearly optimal stoichiometry. Careful analysis of the transport properties of the incompletely reduced films reveals an improvement in the strange metal behavior of their normal state resistivity over subsequent topochemical reductions, offering insight into the reduction process.
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Affiliation(s)
- Araceli Gutiérrez-Llorente
- Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Madrid, 28933, Spain
- Laboratoire Albert Fert - CNRS, Thales, Université Paris Saclay, Palaiseau, 91767, France
| | - Aravind Raji
- Laboratoire de Physique des Solides, CNRS, Université Paris Saclay, Orsay, 91405, France
- Synchrotron SOLEIL, L'Orme des Merisiers, BP 48 St Aubin, Gif sur Yvette, 91192, France
| | - Dongxin Zhang
- Laboratoire Albert Fert - CNRS, Thales, Université Paris Saclay, Palaiseau, 91767, France
| | - Laurent Divay
- Thales Research & Technology France, Palaiseau, 91767, France
| | - Alexandre Gloter
- Laboratoire de Physique des Solides, CNRS, Université Paris Saclay, Orsay, 91405, France
| | - Fernando Gallego
- Laboratoire Albert Fert - CNRS, Thales, Université Paris Saclay, Palaiseau, 91767, France
| | | | - Manuel Bibes
- Laboratoire Albert Fert - CNRS, Thales, Université Paris Saclay, Palaiseau, 91767, France
| | - Lucía Iglesias
- Laboratoire Albert Fert - CNRS, Thales, Université Paris Saclay, Palaiseau, 91767, France
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