1
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Van Raden JM, Deng JR, Gotfredsen H, Hergenhahn J, Clarke M, Edmondson M, Hart J, O'Shea JN, Duarte F, Saywell A, Anderson HL. Template-Directed Synthesis of Strained meso-meso-Linked Porphyrin Nanorings. Angew Chem Int Ed Engl 2024; 63:e202400103. [PMID: 38230920 DOI: 10.1002/anie.202400103] [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: 01/02/2024] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/18/2024]
Abstract
Strained macrocycles display interesting properties, such as conformational rigidity, often resulting in enhanced π-conjugation or enhanced affinity for non-covalent guest binding, yet they can be difficult to synthesize. Here we use computational modeling to design a template to direct the formation of an 18-porphyrin nanoring with direct meso-meso bonds between the porphyrin units. Coupling of a linear 18-porphyrin oligomer in the presence of this template gives the target nanoring, together with an unexpected 36-porphyrin ring by-product. Scanning tunneling microscopy (STM) revealed the elliptical conformations and flexibility of these nanorings on a Au(111) surface.
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Affiliation(s)
- Jeff M Van Raden
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Jie-Ren Deng
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Henrik Gotfredsen
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Janko Hergenhahn
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Michael Clarke
- School of Physics & Astronomy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Matthew Edmondson
- School of Physics & Astronomy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Jack Hart
- School of Physics & Astronomy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - James N O'Shea
- School of Physics & Astronomy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Fernanda Duarte
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Alex Saywell
- School of Physics & Astronomy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Harry L Anderson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
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2
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Paterson KJ, Dahiya A, Williams BD, Phipps RJ. Tertiary Amides as Directing Groups for Enantioselective C-H Amination using Ion-Paired Rhodium Complexes. Angew Chem Int Ed Engl 2024; 63:e202317489. [PMID: 38348742 DOI: 10.1002/anie.202317489] [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: 11/16/2023] [Indexed: 03/01/2024]
Abstract
Enantioselective C-H amination at a benzylic methylene is a vital disconnection towards chiral benzylamines. Here we disclose that butyric and valeric acid-derived tertiary amides can undergo highly enantioselective benzylic amination using an achiral anionic Rh complex that is ion-paired with a Cinchona alkaloid-derived chiral cation. A broad scope of compounds can be aminated encompassing numerous arene substitutions, amides, and two different chain lengths. Excellent tolerance of ortho substituents was observed, which has not been achieved before in asymmetric intermolecular C-H amination with Rh. We speculate that the tertiary amide group of the substrate engages in hydrogen bonding interactions directly with the chiral cation, enabling a high level of organisation at the transition state for C-H amination. This is in contrast with our previous work where a substrate bearing a hydrogen bond donor was required. Control experiments led to the discovery that methyl ethers also function as proficient directing groups under the optimised conditions, potentially also acting as hydrogen bond acceptors. This finding has the promise to dramatically expand the applicability of our ion-paired chiral catalysts.
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Affiliation(s)
- Kieran J Paterson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Amit Dahiya
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Benjamin D Williams
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Robert J Phipps
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
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3
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Polman EMN, Seijmonsbergen AC, Versteegh H, Kissling WD. Global geodiversity components are not equally represented in UNESCO Global Geoparks. Philos Trans A Math Phys Eng Sci 2024; 382:20230054. [PMID: 38342215 PMCID: PMC10859229 DOI: 10.1098/rsta.2023.0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/20/2023] [Indexed: 02/13/2024]
Abstract
The aim of UNESCO Global Geoparks (UGGs) is to protect globally significant geoheritage and geodiversity, but quantitative evidence on the global representativeness of geodiversity components (i.e. geology, soils, geomorphology and hydrology) in these geoparks is in short supply. Here, we provide a first assessment by deriving a global map of geodiversity to test whether the presence of geodiversity components in UGGs is representative for the global availability and distribution of geodiversity. Using openly accessible global datasets and a newly developed workflow, we have calculated metrics for each geodiversity component and a global geodiversity index; we then quantified whether UGGs represent global geodiversity and then compared their components to a randomized spatial distribution of geoparks. Our results show that lithological and topographical diversity are more represented in UGGs than outside these sites, while soil type and hydrological diversity are not significantly different. Furthermore, individual soil types and lithological classes are under-represented and unevenly distributed in Asian and European UGGs. This is probably caused by the concentration of geoparks in Asian and European mountains. To better conserve geodiversity, we suggest an initiative to consider the protection and representation of all geodiversity components in their global context. This article is part of the Theo Murphy meeting issue 'Geodiversity for science and society'.
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Affiliation(s)
- Emma M. N. Polman
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94240, 1090GE Amsterdam, The Netherlands
| | - Arie C. Seijmonsbergen
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94240, 1090GE Amsterdam, The Netherlands
| | - Hannes Versteegh
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94240, 1090GE Amsterdam, The Netherlands
| | - W. Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94240, 1090GE Amsterdam, The Netherlands
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4
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Schrodt F, Vernham G, Bailey J, Field R, Gordon JE, Gray M, Hjort J, Hoorn C, Hunter Jr. ML, Larwood J, Lausch A, Monge-Ganuzas M, Miller S, van Ree D, Seijmonsbergen AC, Zarnetske PL, Daniel Kissling W. The status and future of essential geodiversity variables. Philos Trans A Math Phys Eng Sci 2024; 382:20230052. [PMID: 38342208 PMCID: PMC10859226 DOI: 10.1098/rsta.2023.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/27/2023] [Indexed: 02/13/2024]
Abstract
Rapid environmental change, natural resource overconsumption and increasing concerns about ecological sustainability have led to the development of 'Essential Variables' (EVs). EVs are harmonized data products to inform policy and to enable effective management of natural resources by monitoring global changes. Recent years have seen the instigation of new EVs beyond those established for climate, oceans and biodiversity (ECVs, EOVs and EBVs), including Essential Geodiversity Variables (EGVs). EGVs aim to consistently quantify and monitor heterogeneity of Earth-surface and subsurface abiotic features, including geology, geomorphology, hydrology and pedology. Here we assess the status and future development of EGVs to better incorporate geodiversity into policy and sustainable management of natural resources. Getting EGVs operational requires better consensus on defining geodiversity, investments into a governance structure and open platform for curating the development of EGVs, advances in harmonizing in situ measurements and linking heterogeneous databases, and development of open and accessible computational workflows for global digital mapping using machine-learning techniques. Cross-disciplinary collaboration and partnerships with governmental and private organizations are needed to ensure the successful development and uptake of EGVs across science and policy. This article is part of the Theo Murphy meeting issue 'Geodiversity for science and society'.
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Affiliation(s)
- Franziska Schrodt
- School of Geography, University of Nottingham, Nottingham NG7 2RD, UK
| | - Grant Vernham
- School of Geography, University of Nottingham, Nottingham NG7 2RD, UK
| | - Joseph Bailey
- Department of Biology, Anglia Ruskin University - Cambridge Campus, Cambridge, Cambridgeshire CB1 1PT, UK
| | - Richard Field
- School of Geography, University of Nottingham, Nottingham NG7 2RD, UK
| | - John E. Gordon
- School of Geography and Sustainable Development, University of St Andrews, St Andrews KY169AL, UK
| | - Murray Gray
- Queen Mary University of London, London E1 4NS, UK
| | - Jan Hjort
- Geography Research Unit, University of Oulu, Oulu 90570, Finland
| | - Carina Hoorn
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam 1000 GG, The Netherlands
| | - Malcom L. Hunter Jr.
- Department of Wildlife, Fisheries, and Conservation Biology, University of Maine, Maine, USA
| | - Jonathan Larwood
- Strategy and Governance, Natural England, Peterborough, Cambridgeshire PE2 8YY, UK
| | - Angela Lausch
- Computational Landscape Ecology, Helmholtz-Centre for Environmental Research – UFZ, Leipzig, Saxony 04318, Germany
| | - Manu Monge-Ganuzas
- Geoheritage Commission, Spanish Geological Society, Busturia, Biscay 48350, Spain
| | - Stephanie Miller
- School of Biology and Ecology; Mitchell Center for Sustainability Solutions, The University of Maine, Orono, ME 04469-5751, USA
| | - Derk van Ree
- Geo-engineering, Deltares, Delft 2600 MH, The Netherlands
- Environmental Economics, Vrije Universiteit Amsterdam Faculteit der Betawetenschappen, Amsterdam, The Netherlands
| | - Arie Christoffel Seijmonsbergen
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, Noord-Holland 1090 GE, The Netherlands
| | - Phoebe L. Zarnetske
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824-1312, USA
| | - W. Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, Noord-Holland 1090 GE, The Netherlands
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5
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Wang J, Wang X, Yang K, Lu C, Fields B, Xu Y, Shen Q, Wei Z, Friman VP. Phage selection drives resistance-virulence trade-offs in Ralstonia solanacearum plant-pathogenic bacterium irrespective of the growth temperature. Evol Lett 2024; 8:253-266. [PMID: 38525025 PMCID: PMC10959482 DOI: 10.1093/evlett/qrad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 03/26/2024] Open
Abstract
While temperature has been shown to affect the survival and growth of bacteria and their phage parasites, it is unclear if trade-offs between phage resistance and other bacterial traits depend on the temperature. Here, we experimentally compared the evolution of phage resistance-virulence trade-offs and underlying molecular mechanisms in phytopathogenic Ralstonia solanacearum bacterium at 25 °C and 35 °C temperature environments. We found that while phages reduced R. solanacearum densities relatively more at 25 °C, no difference in the final level of phage resistance was observed between temperature treatments. Instead, small colony variants (SCVs) with increased growth rate and mutations in the quorum-sensing (QS) signaling receptor gene, phcS, evolved in both temperature treatments. Interestingly, SCVs were also phage-resistant and reached higher frequencies in the presence of phages. Evolving phage resistance was costly, resulting in reduced carrying capacity, biofilm formation, and virulence in planta, possibly due to loss of QS-mediated expression of key virulence genes. We also observed mucoid phage-resistant colonies that showed loss of virulence and reduced twitching motility likely due to parallel mutations in prepilin peptidase gene, pilD. Moreover, phage-resistant SCVs from 35 °C-phage treatment had parallel mutations in type II secretion system (T2SS) genes (gspE and gspF). Adsorption assays confirmed the role of pilD as a phage receptor, while no loss of adsorption was found with phcS or T2SS mutants, indicative of other downstream phage resistance mechanisms. Additional transcriptomic analysis revealed upregulation of CBASS and type I restriction-modification phage defense systems in response to phage exposure, which coincided with reduced expression of motility and virulence-associated genes, including pilD and type II and III secretion systems. Together, these results suggest that while phage resistance-virulence trade-offs are not affected by the growth temperature, they could be mediated through both pre- and postinfection phage resistance mechanisms.
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Affiliation(s)
- Jianing Wang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Xiaofang Wang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Keming Yang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Chunxia Lu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Bryden Fields
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Yangchun Xu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Zhong Wei
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Ville-Petri Friman
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Department of Biology, University of York, Wentworth Way, York , United Kingdom
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6
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Morton-Hayward AL, Anderson RP, Saupe EE, Larson G, Cosmidis JG. Human brains preserve in diverse environments for at least 12 000 years. Proc Biol Sci 2024; 291:20232606. [PMID: 38503334 PMCID: PMC10950470 DOI: 10.1098/rspb.2023.2606] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
The brain is thought to be among the first human organs to decompose after death. The discovery of brains preserved in the archaeological record is therefore regarded as unusual. Although mechanisms such as dehydration, freezing, saponification, and tanning are known to allow for the preservation of the brain on short time scales in association with other soft tissues (≲4000 years), discoveries of older brains, especially in the absence of other soft tissues, are rare. Here, we collated an archive of more than 4400 human brains preserved in the archaeological record across approximately 12 000 years, more than 1300 of which constitute the only soft tissue preserved amongst otherwise skeletonized remains. We found that brains of this type persist on time scales exceeding those preserved by other means, which suggests an unknown mechanism may be responsible for preservation particular to the central nervous system. The untapped archive of preserved ancient brains represents an opportunity for bioarchaeological studies of human evolution, health and disease.
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Affiliation(s)
- Alexandra L. Morton-Hayward
- Department of Earth Sciences, University of Oxford, Oxford, UK
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Ross P. Anderson
- Department of Earth Sciences, University of Oxford, Oxford, UK
- All Souls College, University of Oxford, Oxford, UK
| | - Erin E. Saupe
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK
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7
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Sun SJ, Chen S, Federle W, Kilner RM. Biomechanical adaptations enable phoretic mite species to occupy distinct spatial niches on host burying beetles. Proc Biol Sci 2024; 291:20240230. [PMID: 38503335 PMCID: PMC10950469 DOI: 10.1098/rspb.2024.0230] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/21/2024] [Indexed: 03/21/2024] Open
Abstract
Niche theory predicts that ecologically similar species coexist by minimizing interspecific competition through niche partitioning. Therefore, understanding the mechanisms of niche partitioning is essential for predicting interactions and coexistence between competing organisms. Here, we study two phoretic mite species, Poecilochirus carabi and Macrocheles nataliae that coexist on the same host burying beetle Nicrophorus vespilloides and use it to 'hitchhike' between reproductive sites. Field observations revealed clear spatial partitioning between species in distinct host body parts. Poecilochirus carabi preferred the ventral side of the thorax, whereas M. nataliae were exclusively found ventrally at the hairy base of the abdomen. Experimental manipulations of mite density showed that each species preferred these body parts, largely regardless of the density of the other mite species on the host beetle. Force measurements indicated that this spatial distribution is mediated by biomechanical adaptations, because each mite species required more force to be removed from their preferred location on the beetle. While P. carabi attached with large adhesive pads to the smooth thorax cuticle, M. nataliae gripped abdominal setae with their chelicerae. Our results show that specialist biomechanical adaptations for attachment can mediate spatial niche partitioning among species sharing the same host.
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Affiliation(s)
- Syuan-Jyun Sun
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- International Degree Program in Climate Change and Sustainable Development, National Taiwan University, Taipei 10617, Taiwan
| | - Simon Chen
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Walter Federle
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Rebecca M. Kilner
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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8
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Shorthouse D, Lister H, Freeman GS, Hall BA. Understanding large scale sequencing datasets through changes to protein folding. Brief Funct Genomics 2024:elae007. [PMID: 38521964 DOI: 10.1093/bfgp/elae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 02/26/2024] [Accepted: 03/01/2024] [Indexed: 03/25/2024] Open
Abstract
The expansion of high-quality, low-cost sequencing has created an enormous opportunity to understand how genetic variants alter cellular behaviour in disease. The high diversity of mutations observed has however drawn a spotlight onto the need for predictive modelling of mutational effects on phenotype from variants of uncertain significance. This is particularly important in the clinic due to the potential value in guiding clinical diagnosis and patient treatment. Recent computational modelling has highlighted the importance of mutation induced protein misfolding as a common mechanism for loss of protein or domain function, aided by developments in methods that make large computational screens tractable. Here we review recent applications of this approach to different genes, and how they have enabled and supported subsequent studies. We further discuss developments in the approach and the role for the approach in light of increasingly high throughput experimental approaches.
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Affiliation(s)
- David Shorthouse
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Harris Lister
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London WC1E 6BT, UK
| | - Gemma S Freeman
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London WC1E 6BT, UK
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London WC1E 6BT, UK
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9
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Heimeier D, Garland EC, Eichenberger F, Garrigue C, Vella A, Baker CS, Carroll EL. A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies. Mol Ecol Resour 2024:e13955. [PMID: 38520161 DOI: 10.1111/1755-0998.13955] [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: 05/19/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 03/25/2024]
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.
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Affiliation(s)
- Dorothea Heimeier
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
| | - Ellen C Garland
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Franca Eichenberger
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Claire Garrigue
- UMR ENTROPIE, (IRD, Université de La Réunion, Université de la Nouvelle-Calédonie, IFREMER, CNRS, Laboratoire d'Excellence-CORAIL), Nouméa, New Caledonia
- Opération Cétacés, Nouméa, New Caledonia
| | - Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida, Malta
| | - C Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Corvallis, Oregon, USA
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
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10
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McCorkindale W, Filep M, London N, Lee AA, King-Smith E. Deconvoluting low yield from weak potency in direct-to-biology workflows with machine learning. RSC Med Chem 2024; 15:1015-1021. [PMID: 38516605 PMCID: PMC10953487 DOI: 10.1039/d3md00719g] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
High throughput and rapid biological evaluation of small molecules is an essential factor in drug discovery and development. Direct-to-biology (D2B), whereby compound purification is foregone, has emerged as a viable technique in time efficient screening, specifically for PROTAC design and biological evaluation. However, one notable limitation is the prerequisite of high yielding reactions to ensure the desired compound is indeed the compound responsible for biological activity. Herein, we report a machine learning based yield-assay deconfounder capable of deconvoluting low yield from low potency to identify false negatives. We validated this approach by identifying promising SARS-CoV-2 main protease inhibitors with nanomolar activity that rivaled potency observed from the standard D2B workflow. Furthermore, we show how our framework can be utilized in a broad, in silico screen to produce compounds of similar potency as a D2B assay.
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Affiliation(s)
| | - Mihajlo Filep
- Department of Chemical and Structural Biology, The Weizmann Institute of Science Israel
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science Israel
| | - Alpha A Lee
- Cavendish Laboratory, University of Cambridge UK
| | - Emma King-Smith
- Yusuf Hamied Department of Chemistry, University of Cambridge UK
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11
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James KD, Cowan JE. Insm1: orchestrating cellular mimicry in the thymus medulla. Cell Mol Immunol 2024:10.1038/s41423-024-01151-z. [PMID: 38503886 DOI: 10.1038/s41423-024-01151-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024] Open
Affiliation(s)
- K D James
- UCL Institute of Immunity and Transplantation, The Pears Building, Rowland Hill Street, London, NW3 2PP, UK
| | - J E Cowan
- UCL Institute of Immunity and Transplantation, The Pears Building, Rowland Hill Street, London, NW3 2PP, UK.
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12
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Fairlamb IJS, Lynam JM. Unveiling Mechanistic Complexity in Manganese-Catalyzed C-H Bond Functionalization Using IR Spectroscopy Over 16 Orders of Magnitude in Time. Acc Chem Res 2024; 57:919-932. [PMID: 38412502 PMCID: PMC10956383 DOI: 10.1021/acs.accounts.3c00774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
ConspectusAn understanding of the mechanistic processes that underpin reactions catalyzed by 3d transition metals is vital for their development as potential replacements for scarce platinum group metals. However, this is a significant challenge because of the tendency of 3d metals to undergo mechanistically diverse pathways when compared with their heavier congeners, often as a consequence of one-electron transfer reactions and/or intrinsically weaker metal-ligand bonds. We have developed and implemented a new methodology to illuminate the pathways that underpin C-H bond functionalization pathways in reactions catalyzed by Mn-carbonyl compounds. By integrating measurements performed on catalytic reactions with in situ reaction monitoring and state-of-the-art ultrafast spectroscopic methods, unique insight into the mode of action and fate of the catalyst have been obtained.Using a combination of time-resolved spectroscopy and in situ low-temperature NMR studies, we have shown that photolysis of manganese-carbonyl precatalysts results in rapid (<5 ps) CO dissociation─the same process that occurs under thermal catalytic conditions. This enabled the detection of the key states relevant to catalysis, including solvent and alkyne complexes and their resulting transformation into manganacycles, which results from a migratory insertion reaction into the Mn-C bond. By systematic variation of the substrates (many of which are real-world structurally diverse substrates and not simple benchmark systems) and quantification of the resulting rate constants for the insertion step, a universal model for this migratory insertion process has been developed. The time-resolved spectroscopic method gave insight into fundamental mechanistic pathways underpinning other aspects of modern synthetic chemistry. The most notable was the first direct experimental observation of the concerted metalation deprotonation (CMD) mechanism through which carboxylate groups are able to mediate C-H bond activation at a metal center. This step underpins a host of important synthetic applications. This study demonstrated how the time-resolved multiple probe spectroscopy (TRMPS) method enables the observation of mechanistic process occurring on time scales from several picoseconds through to μs in a single experiment, thereby allowing the sequential observation of solvation, ligand substitution, migratory insertion, and ultimate protonation of a Mn-C bond.These studies have been complemented by an investigation of the "in reaction flask" catalyst behavior, which has provided additional insight into new pathways for precatalyst activation, including evidence that alkyne C-H bond activation may occur before heterocycle activation. Crucial insight into the fate of the catalyst species showed that excess water played a key role in deactivation to give higher-order hydroxyl-bridged manganese carbonyl clusters, which were independently found to be inactive. Traditional in situ IR and NMR spectroscopic analysis on the second time scale bridges the gap to the analysis of real catalytic reaction systems. As a whole, this work has provided unprecedented insight into the processes underpinning manganese-catalyzed reactions spanning 16 orders of magnitude in time.
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Affiliation(s)
- Ian J. S. Fairlamb
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Jason M. Lynam
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
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13
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Mwanga EP, Siria DJ, Mshani IH, Mwinyi SH, Abbasi S, Jimenez MG, Wynne K, Baldini F, Babayan SA, Okumu FO. Rapid classification of epidemiologically relevant age categories of the malaria vector, Anopheles funestus. Parasit Vectors 2024; 17:143. [PMID: 38500231 PMCID: PMC10949582 DOI: 10.1186/s13071-024-06209-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Accurately determining the age and survival probabilities of adult mosquitoes is crucial for understanding parasite transmission, evaluating the effectiveness of control interventions and assessing disease risk in communities. This study was aimed at demonstrating the rapid identification of epidemiologically relevant age categories of Anopheles funestus, a major Afro-tropical malaria vector, through the innovative combination of infrared spectroscopy and machine learning, instead of the cumbersome practice of dissecting mosquito ovaries to estimate age based on parity status. METHODS Anopheles funestus larvae were collected in rural south-eastern Tanzania and reared in an insectary. Emerging adult females were sorted by age (1-16 days old) and preserved using silica gel. Polymerase chain reaction (PCR) confirmation was conducted using DNA extracted from mosquito legs to verify the presence of An. funestus and to eliminate undesired mosquitoes. Mid-infrared spectra were obtained by scanning the heads and thoraces of the mosquitoes using an attenuated total reflection-Fourier transform infrared (ATR-FT-IR) spectrometer. The spectra (N = 2084) were divided into two epidemiologically relevant age groups: 1-9 days (young, non-infectious) and 10-16 days (old, potentially infectious). The dimensionality of the spectra was reduced using principal component analysis, and then a set of machine learning and multi-layer perceptron (MLP) models were trained using the spectra to predict the mosquito age categories. RESULTS The best-performing model, XGBoost, achieved overall accuracy of 87%, with classification accuracy of 89% for young and 84% for old An. funestus. When the most important spectral features influencing the model performance were selected to train a new model, the overall accuracy increased slightly to 89%. The MLP model, utilizing the significant spectral features, achieved higher classification accuracy of 95% and 94% for the young and old An. funestus, respectively. After dimensionality reduction, the MLP achieved 93% accuracy for both age categories. CONCLUSIONS This study shows how machine learning can quickly classify epidemiologically relevant age groups of An. funestus based on their mid-infrared spectra. Having been previously applied to An. gambiae, An. arabiensis and An. coluzzii, this demonstration on An. funestus underscores the potential of this low-cost, reagent-free technique for widespread use on all the major Afro-tropical malaria vectors. Future research should demonstrate how such machine-derived age classifications in field-collected mosquitoes correlate with malaria in human populations.
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Affiliation(s)
- Emmanuel P Mwanga
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P.O. Box 53, Morogoro, Tanzania.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Doreen J Siria
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P.O. Box 53, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Issa H Mshani
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P.O. Box 53, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Sophia H Mwinyi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P.O. Box 53, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Said Abbasi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P.O. Box 53, Morogoro, Tanzania
| | - Mario Gonzalez Jimenez
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francesco Baldini
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Simon A Babayan
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fredros O Okumu
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, P.O. Box 53, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Life Science and Bioengineering, The Nelson Mandela African Institution of Science and Technology, P. O. Box 447, Arusha, Tanzania
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Zhao LS, Wang N, Li K, Li CY, Guo JP, He FY, Liu GM, Chen XL, Gao J, Liu LN, Zhang YZ. Architecture of symbiotic dinoflagellate photosystem I-light-harvesting supercomplex in Symbiodinium. Nat Commun 2024; 15:2392. [PMID: 38493166 PMCID: PMC10944487 DOI: 10.1038/s41467-024-46791-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Symbiodinium are the photosynthetic endosymbionts for corals and play a vital role in supplying their coral hosts with photosynthetic products, forming the nutritional foundation for high-yield coral reef ecosystems. Here, we determine the cryo-electron microscopy structure of Symbiodinium photosystem I (PSI) supercomplex with a PSI core composed of 13 subunits including 2 previously unidentified subunits, PsaT and PsaU, as well as 13 peridinin-Chl a/c-binding light-harvesting antenna proteins (AcpPCIs). The PSI-AcpPCI supercomplex exhibits distinctive structural features compared to their red lineage counterparts, including extended termini of PsaD/E/I/J/L/M/R and AcpPCI-1/3/5/7/8/11 subunits, conformational changes in the surface loops of PsaA and PsaB subunits, facilitating the association between the PSI core and peripheral antennae. Structural analysis and computational calculation of excitation energy transfer rates unravel specific pigment networks in Symbiodinium PSI-AcpPCI for efficient excitation energy transfer. Overall, this study provides a structural basis for deciphering the mechanisms governing light harvesting and energy transfer in Symbiodinium PSI-AcpPCI supercomplexes adapted to their symbiotic ecosystem, as well as insights into the evolutionary diversity of PSI-LHCI among various photosynthetic organisms.
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Affiliation(s)
- Long-Sheng Zhao
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237, China
| | - Ning Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Kang Li
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237, China
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237, China
| | - Jian-Ping Guo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei-Yu He
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Gui-Ming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lu-Ning Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237, China.
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15
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Lin GL, Drysdale SB, Snape MD, O'Connor D, Brown A, MacIntyre-Cockett G, Mellado-Gomez E, de Cesare M, Ansari MA, Bonsall D, Bray JE, Jolley KA, Bowden R, Aerssens J, Bont L, Openshaw PJM, Martinon-Torres F, Nair H, Golubchik T, Pollard AJ. Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus. Nat Commun 2024; 15:2379. [PMID: 38493135 PMCID: PMC10944482 DOI: 10.1038/s41467-024-46648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 02/23/2024] [Indexed: 03/18/2024] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of hospitalisation for respiratory infection in young children. RSV disease severity is known to be age-dependent and highest in young infants, but other correlates of severity, particularly the presence of additional respiratory pathogens, are less well understood. In this study, nasopharyngeal swabs were collected from two cohorts of RSV-positive infants <12 months in Spain, the UK, and the Netherlands during 2017-20. We show, using targeted metagenomic sequencing of >100 pathogens, including all common respiratory viruses and bacteria, from samples collected from 433 infants, that burden of additional viruses is common (111/433, 26%) but only modestly correlates with RSV disease severity. In contrast, there is strong evidence in both cohorts and across age groups that presence of Haemophilus bacteria (194/433, 45%) is associated with higher severity, including much higher rates of hospitalisation (odds ratio 4.25, 95% CI 2.03-9.31). There is no evidence for association between higher severity and other detected bacteria, and no difference in severity between RSV genotypes. Our findings reveal the genomic diversity of additional pathogens during RSV infection in infants, and provide an evidence base for future causal investigations of the impact of co-infection on RSV disease severity.
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Affiliation(s)
- Gu-Lung Lin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Simon B Drysdale
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Centre for Neonatal and Paediatric Infection, Institute for Infection and Immunity, St George's, University of London, London, UK
| | - Matthew D Snape
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | | | - Esther Mellado-Gomez
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Human Technopole, Milan, Italy
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Bonsall
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James E Bray
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jeroen Aerssens
- Translational Biomarkers, Infectious Diseases Therapeutic Area, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Louis Bont
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands
- ReSViNET Foundation, Zeist, Netherlands
| | | | - Federico Martinon-Torres
- Translational Pediatrics and Infectious Diseases, Pediatrics Department, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, University of Santiago de Compostela, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Harish Nair
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Sydney Infectious Diseases Institute, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia.
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
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16
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Boddy A, Sahay AK, Rivers EL, White AJP, Spivey AC, Bull JA. Enantioselective Phase-Transfer-Catalyzed Synthesis of Spirocyclic Azetidine Oxindoles. Org Lett 2024; 26:2079-2084. [PMID: 38447584 PMCID: PMC10949229 DOI: 10.1021/acs.orglett.4c00358] [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: 01/29/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Spiro-3,2'-azetidine oxindoles combine two independently important pharmacophores in an understudied spirocyclic motif that is attractive for medicinal chemistry. Here, the enantioselective synthesis of these structures is achieved in up to 2:98 er through intramolecular C-C bond formation, involving activation of the substrate with a novel SF5-containing chiral cation phase-transfer (PT) catalyst. The products are readily elaborated/deprotected to afford medicinally relevant enantioenriched compounds. Control experiments suggest an interfacial PT mechanism, whereby catalytic asymmetric induction is achieved through the activation of the chloride leaving group.
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Affiliation(s)
- Alexander
J. Boddy
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K.
| | - Aditya K. Sahay
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K.
| | - Emma L. Rivers
- Hit
Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, U.K.
| | - Andrew J. P. White
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K.
| | - Alan C. Spivey
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K.
| | - James A. Bull
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K.
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17
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Williams-Noonan BJ, Kulkarni K, Todorova N, Franceschi M, Wilde C, Borgo MPD, Serpell LC, Aguilar MI, Yarovsky I. Atomic Scale Structure of Self-Assembled Lipidated Peptide Nanomaterials. Adv Mater 2024:e2311103. [PMID: 38489817 DOI: 10.1002/adma.202311103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/12/2024] [Indexed: 03/17/2024]
Abstract
β-Peptides have great potential as novel biomaterials and therapeutic agents, due to their unique ability to self-assemble into low dimensional nanostructures, and their resistance to enzymatic degradation in vivo. However, the self-assembly mechanisms of β-peptides, which possess increased flexibility due to the extra backbone methylene groups present within the constituent β-amino acids, are not well understood due to inherent difficulties of observing their bottom-up growth pathway experimentally. A computational approach is presented for the bottom-up modelling of the self-assembled lipidated β3-peptides, from monomers, to oligomers, to supramolecular low-dimensional nanostructures, in all-atom detail. The approach is applied to elucidate the self-assembly mechanisms of recently discovered, distinct structural morphologies of low dimensional nanomaterials, assembled from lipidated β3-peptide monomers. The resultant structures of the nanobelts and the twisted fibrils are stable throughout subsequent unrestrained all-atom molecular dynamics simulations, and these assemblies display good agreement with the structural features obtained from X-ray fiber diffraction and atomic force microscopy data. This is the first reported, fully-atomistic model of a lipidated β3-peptide-based nanomaterial, and the computational approach developed here, in combination with experimental fiber diffraction analysis and atomic force microscopy, will be useful in elucidating the atomic scale structure of self-assembled peptide-based and other supramolecular nanomaterials.
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Affiliation(s)
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Nevena Todorova
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Matteo Franceschi
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Christopher Wilde
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Mark P Del Borgo
- Department of Pharmacology, Monash University, Clayton, Victoria, 3800, Australia
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex, BN1 9QG, UK
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
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18
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Brand MC, Trowell HG, Fuchter MJ, Greenaway RL. Incorporating Photoresponses into Porous Liquids. Chemistry 2024; 30:e202303593. [PMID: 38095875 DOI: 10.1002/chem.202303593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Indexed: 01/13/2024]
Abstract
Porous liquids combine the properties of a porous solid with those of a liquid, creating a porous flowable media. Since their discovery, these materials have gathered widespread interest within the scientific community, with substantial numbers of new systems being discovered, often with a focus on increasing the pore volume and gas capacity. Which begs the question, what does the future hold for porous liquids? Recently, the first examples of photoresponsive porous liquids have emerged, allowing changes in porosity to be observed under UV irradiation. Here, we expand on our previous report of photoresponsive porous liquids and explore the conceptualisation of responsive porous liquids and how these materials could be developed with the ability to respond to light, thereby offering a potential mechanism of controllable uptake and release in these systems. This concept article summarises different approaches that could be used to incorporate a photoresponse in a porous liquid before discussing recently reported systems, alongside important factors to consider in their design. Finally, by taking inspiration from the methods used to translate porous solids into the liquid state, combined with the field of photoresponsive materials, we discuss potential strategies that could be employed to realise further examples of photoresponsive porous liquids.
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Affiliation(s)
- Michael C Brand
- Department of Chemistry, Materials Innovation Factory and Leverhulme Research Centre for Functional Materials Design, University of Liverpool, 51 Oxford Street, Liverpool, L7 3NY, UK
| | - Hamish G Trowell
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London, W12 0BZ, UK
| | - Matthew J Fuchter
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London, W12 0BZ, UK
| | - Rebecca L Greenaway
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London, W12 0BZ, UK
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19
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Harvey Sky N, Britnell J, Antwis R, Kartzinel T, Rubenstein D, Toye P, Karani B, Njeru R, Gaymer J, Mutisya S, Shultz S. Linking diet switching to reproductive performance across populations of two critically endangered mammalian herbivores. Commun Biol 2024; 7:333. [PMID: 38491117 PMCID: PMC10943211 DOI: 10.1038/s42003-024-05983-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
Optimal foraging theory predicts that animals maximise energy intake by consuming the most valuable foods available. When resources are limited, they may include lower-quality fallback foods in their diets. As seasonal herbivore diet switching is understudied, we evaluate its extent and effects across three Kenyan reserves each for Critically Endangered eastern black rhino (Diceros bicornis michaeli) and Grevy's zebra (Equus grevyi), and its associations with habitat quality, microbiome variation, and reproductive performance. Black rhino diet breadth increases with vegetation productivity (NDVI), whereas zebra diet breadth peaks at intermediate NDVI. Black rhino diets associated with higher vegetation productivity have less acacia (Fabaceae: Vachellia and Senegalia spp.) and more grass suggesting that acacia are fallback foods, upending conventional assumptions. Larger dietary shifts are associated with longer calving intervals. Grevy's zebra diets in high rainfall areas are consistently grass-dominated, whereas in arid areas they primarily consume legumes during low vegetation productivity periods. Whilst microbiome composition between individuals is affected by the environment, and diet composition in black rhino, seasonal dietary shifts do not drive commensurate microbiome shifts. Documenting diet shifts across ecological gradients can increase the effectiveness of conservation by informing habitat suitability models and improving understanding of responses to resource limitation.
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Affiliation(s)
- Nick Harvey Sky
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9NT, UK.
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, CH2 1LH, UK.
| | - Jake Britnell
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9NT, UK
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, CH2 1LH, UK
| | - Rachael Antwis
- School of Environment and Life Sciences, University of Salford, Salford, M5 4WX, UK
| | - Tyler Kartzinel
- Department of Ecology, Evolution, and Organismal Biology, Brown University, 85 Waterman Street, Providence, RI, 02912, USA
- Institute at Brown for Environment and Society, Brown University, 85 Waterman Street, Providence, RI, 02912, USA
| | - Daniel Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544-2016, USA
| | - Phil Toye
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, P.O. Box 30709-00100, Kenya
| | - Benedict Karani
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, P.O. Box 30709-00100, Kenya
| | - Regina Njeru
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, P.O. Box 30709-00100, Kenya
| | | | | | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9NT, UK
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20
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Aura CM, Humphrey OS, Marriott AL, Watts MJ, Ongore CO, Mwamburi JM, Osano O, Coffey TJ. Assessing the spatial distribution of elemental concentrations in surface sediments of Lake Victoria, Kenya: implications for ecological health and management. Environ Geochem Health 2024; 46:137. [PMID: 38483759 DOI: 10.1007/s10653-024-01930-7] [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] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/19/2024]
Abstract
Lacustrine sediment quality indicates the effects of both natural and anthropogenic activities on the ecosystem and communities. Despite its ecological importance, myriad complexities, and potential contaminant sources, the spatial distribution of surficial sediments in Lake Victoria's Winam Gulf has never been comprehensively documented. The purpose of this study was to assess the spatial distribution, pathways, and ecological risk of metal elements in the lake using a sediment matrix. Sediment samples were collected throughout the gulf in November 2022. The concentrations of Al, As, Cd, Co, Cr, Cu, Fe, K, Mn, Mo, Ni, P, Pb, Sb, Sn, Ti, Tl, U, and Zn were compared to different contamination metrics and ecological risk assessment indices. The average concentrations were in the following decreasing order: Zn > > > Cr > > Cu > Ni > Pb > Co > As > Cd with mean (± SD) of 185 ± 45 mg kg-1, 56 ± 15 mg kg-1, 45 ± 16 mg kg-1, 37 ± 11 mg kg-1, 24 ± 5 mg kg-1, 20 ± 7 mg kg-1, 3.9 ± 1.3 mg kg-1, 0.30 ± 0.09 mg kg-1, respectively, with strong indications of anthropogenic sources. Average concentrations were in the following decreasing order: Zn > > > Cr, Cu, Ni, Pb, Co, As, and Cd levels (mean ± SD) were 185 ± 45 mg kg-1, 56 ± 15 mg kg-1, 45 ± 16 mg kg-1, 37 ± 11 mg kg-1, 24 ± 5 mg kg-1, 20 ± 7 mg kg-1, 3.9 ± 1.3 mg kg-1 and 0.30 ± 0.09 mg kg-1 with strong indications of anthropogenic sources. The geo-accumulation index (Igeo) and enrichment factor categorisation schemes, respectively, classified these as uncontaminated (level 0) and depletion to minimal enrichment (level 1), while the ecological risk analysis classified them as "low risk". The mouth of the Nyando River, as well as Kisumu, Kendu, and Homa bays, were the most element-enriched and should be prioritised for focused monitoring and remediation. As a result, targeted land management of urban, industrial, transportation, and agricultural areas offers the opportunity to reduce sediment inputs into the lake ecosystem.
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Affiliation(s)
- C M Aura
- Kenya Marine Fisheries Research Institution (KMFRI), P.O. Box 1881-40100, Kisumu, Kenya.
| | - O S Humphrey
- Inorganic Geochemistry, Centre for Environmental Geochemistry, British Geological Survey, Nottingham, UK
| | - A L Marriott
- Inorganic Geochemistry, Centre for Environmental Geochemistry, British Geological Survey, Nottingham, UK
| | - M J Watts
- Inorganic Geochemistry, Centre for Environmental Geochemistry, British Geological Survey, Nottingham, UK
| | - C O Ongore
- Kenya Marine Fisheries Research Institution (KMFRI), P.O. Box 1881-40100, Kisumu, Kenya
- Pelagic Ecology Research Group, Gatty Marine Laboratory, Scottish Oceans Institute, University of St. Andrews, Fife, KY16 8LB, Scotland, UK
| | - J M Mwamburi
- Kenya Marine Fisheries Research Institution (KMFRI), P.O. Box 1881-40100, Kisumu, Kenya
| | - O Osano
- School of Environmental Sciences, University of Eldoret, Eldoret, Kenya
| | - T J Coffey
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
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21
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Banerjee A, Leeson P. Scoring systems developed by machine learning: intelligent but simple to use? Eur Heart J 2024; 45:937-939. [PMID: 38320252 DOI: 10.1093/eurheartj/ehae053] [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: 02/08/2024] Open
Affiliation(s)
- Abhirup Banerjee
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Paul Leeson
- Oxford Cardiovascular Clinical Research Facility, RDM Division of Cardiovascular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
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22
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Huang J, Sokolikova M, Ruiz-Gonzalez A, Kong Y, Wang Y, Liu Y, Xu L, Wang M, Mattevi C, Davenport A, Lee TC, Li B. Ultrasensitive colorimetric detection of creatinine via its dual binding affinity for silver nanoparticles and silver ions. RSC Adv 2024; 14:9114-9121. [PMID: 38500617 PMCID: PMC10946247 DOI: 10.1039/d3ra08736k] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/12/2024] [Indexed: 03/20/2024] Open
Abstract
Creatinine is an important biomarker for the diagnosis of chronic kidney disease (CKD). Recently, it has been reported that the concentration of salivary creatinine correlates well with the concentration of serum creatinine, which makes the former useful for the development of non-invasive and point-of-care (POC) detection for CKD diagnosis. However, there exists a technical challenge in the rapid detection of salivary creatinine at low concentrations of 3-18 μM when using the current kidney function test strips as well as the traditional methods employed in hospitals. Herein, we demonstrate a simple, sensitive colorimetric assay for the detection of creatinine with a limit-of-detection (LOD) down to the nanomolar level. Our approach utilises the dual binding affinity of creatinine for citrate-capped silver nanoparticles (Ag NPs) and Ag(i) ions, which can trigger the aggregation of Ag NPs and thus lead to the colour change of a sample. The quantitative detection of creatinine was achieved using UV-Vis spectroscopy with a LOD of 6.9 nM in artificial saliva and a linear dynamic range of 0.01-0.06 μM. This method holds promise to be further developed into a POC platform for the CKD diagnosis.
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Affiliation(s)
- Jingle Huang
- Institute for Materials Discovery, University College London London WC1H 0AJ UK
| | - Maria Sokolikova
- Department of Materials, Imperial College London London SW7 2AZ UK
| | | | - Yingqi Kong
- Institute for Materials Discovery, University College London London WC1H 0AJ UK
| | - Yuxuan Wang
- Department of Materials, Imperial College London London SW7 2AZ UK
| | - Yingjia Liu
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Centre Hangzhou 311200 China
| | - Lizhou Xu
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Centre Hangzhou 311200 China
- College of Biosystems Engineering and Food Science, Zhejiang University Hangzhou 310058 China
| | - Mingqing Wang
- Institute for Materials Discovery, University College London London WC1H 0AJ UK
| | - Cecilia Mattevi
- Department of Materials, Imperial College London London SW7 2AZ UK
| | - Andrew Davenport
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Centre Hangzhou 311200 China
- Department of Renal Medicine, Royal Free Hospital, University College London NW3 2PF UK
| | - Tung-Chun Lee
- Institute for Materials Discovery, University College London London WC1H 0AJ UK
| | - Bing Li
- Institute for Materials Discovery, University College London London WC1H 0AJ UK
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23
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Oluwole A, Hernández-Rocamora VM, Cao Y, Li X, Vollmer W, Robinson CV, Bolla JR. Real-Time Biosynthetic Reaction Monitoring Informs the Mechanism of Action of Antibiotics. J Am Chem Soc 2024; 146:7007-7017. [PMID: 38428018 PMCID: PMC10941186 DOI: 10.1021/jacs.4c00081] [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: 01/05/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
The rapid spread of drug-resistant pathogens and the declining discovery of new antibiotics have created a global health crisis and heightened interest in the search for novel antibiotics. Beyond their discovery, elucidating mechanisms of action has necessitated new approaches, especially for antibiotics that interact with lipidic substrates and membrane proteins. Here, we develop a methodology for real-time reaction monitoring of the activities of two bacterial membrane phosphatases, UppP and PgpB. We then show how we can inhibit their activities using existing and newly discovered antibiotics such as bacitracin and teixobactin. Additionally, we found that the UppP dimer is stabilized by phosphatidylethanolamine, which, unexpectedly, enhanced the speed of substrate processing. Overall, our results demonstrate the potential of native mass spectrometry for real-time biosynthetic reaction monitoring of membrane enzymes, as well as their in situ inhibition and cofactor binding, to inform the mode of action of emerging antibiotics.
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Affiliation(s)
- Abraham
O. Oluwole
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Víctor M. Hernández-Rocamora
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K.
| | - Yihui Cao
- Department
of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Xuechen Li
- Department
of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Waldemar Vollmer
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K.
- Institute
for Molecular Bioscience, University of
Queensland, Carmody Road, Brisbane, Queensland 4072, Australia
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Jani R. Bolla
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
- Department
of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K.
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24
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Mücke D, Cooley I, Liang B, Wang Z, Park S, Dong R, Feng X, Qi H, Besley E, Kaiser U. Understanding the Electron Beam Resilience of Two-Dimensional Conjugated Metal-Organic Frameworks. Nano Lett 2024; 24:3014-3020. [PMID: 38427697 PMCID: PMC10941249 DOI: 10.1021/acs.nanolett.3c04125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/03/2024]
Abstract
Knowledge of the atomic structure of layer-stacked two-dimensional conjugated metal-organic frameworks (2D c-MOFs) is an essential prerequisite for establishing their structure-property correlation. For this, atomic resolution imaging is often the method of choice. In this paper, we gain a better understanding of the main properties contributing to the electron beam resilience and the achievable resolution in the high-resolution TEM images of 2D c-MOFs, which include chemical composition, density, and conductivity of the c-MOF structures. As a result, sub-angstrom resolution of 0.95 Å has been achieved for the most stable 2D c-MOF of the considered structures, Cu3(BHT) (BHT = benzenehexathiol), at an accelerating voltage of 80 kV in a spherical and chromatic aberration-corrected TEM. Complex damage mechanisms induced in Cu3(BHT) by the elastic interactions with the e-beam have been explained using detailed ab initio molecular dynamics calculations. Experimental and calculated knock-on damage thresholds are in good agreement.
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Affiliation(s)
- David Mücke
- Central
Facility for Materials Science Electron Microscopy, Universität Ulm, 89081 Ulm, Germany
| | - Isabel Cooley
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Baokun Liang
- Central
Facility for Materials Science Electron Microscopy, Universität Ulm, 89081 Ulm, Germany
| | - Zhiyong Wang
- Max
Planck Institute of Microstructure Physics, 06120 Halle (Saale), Germany
- Faculty
of Chemistry and Food Chemistry & Center for Advancing Electronics
Dresden, Technische Universität Dresden, 01062 Dresden, Germany
| | - SangWook Park
- Faculty
of Chemistry and Food Chemistry & Center for Advancing Electronics
Dresden, Technische Universität Dresden, 01062 Dresden, Germany
| | - Renhao Dong
- Faculty
of Chemistry and Food Chemistry & Center for Advancing Electronics
Dresden, Technische Universität Dresden, 01062 Dresden, Germany
- Key
Laboratory of Colloid and Interface Chemistry of the Ministry of Education,
School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, China
| | - Xinliang Feng
- Max
Planck Institute of Microstructure Physics, 06120 Halle (Saale), Germany
- Faculty
of Chemistry and Food Chemistry & Center for Advancing Electronics
Dresden, Technische Universität Dresden, 01062 Dresden, Germany
| | - Haoyuan Qi
- Central
Facility for Materials Science Electron Microscopy, Universität Ulm, 89081 Ulm, Germany
- Faculty
of Chemistry and Food Chemistry & Center for Advancing Electronics
Dresden, Technische Universität Dresden, 01062 Dresden, Germany
| | - Elena Besley
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Ute Kaiser
- Central
Facility for Materials Science Electron Microscopy, Universität Ulm, 89081 Ulm, Germany
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25
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Li T, Chang P, Chen W, Shi Z, Xue C, Dykes GF, Huang F, Wang Q, Liu LN. Nanoengineering Carboxysome Shells for Protein Cages with Programmable Cargo Targeting. ACS Nano 2024; 18:7473-7484. [PMID: 38326220 PMCID: PMC10938918 DOI: 10.1021/acsnano.3c11559] [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: 11/20/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Protein nanocages have emerged as promising candidates for enzyme immobilization and cargo delivery in biotechnology and nanotechnology. Carboxysomes are natural proteinaceous organelles in cyanobacteria and proteobacteria and have exhibited great potential in creating versatile nanocages for a wide range of applications given their intrinsic characteristics of self-assembly, cargo encapsulation, permeability, and modularity. However, how to program intact carboxysome shells with specific docking sites for tunable and efficient cargo loading is a key question in the rational design and engineering of carboxysome-based nanostructures. Here, we generate a range of synthetically engineered nanocages with site-directed cargo loading based on an α-carboxysome shell in conjunction with SpyTag/SpyCatcher and Coiled-coil protein coupling systems. The systematic analysis demonstrates that the cargo-docking sites and capacities of the carboxysome shell-based protein nanocages could be precisely modulated by selecting specific anchoring systems and shell protein domains. Our study provides insights into the encapsulation principles of the α-carboxysome and establishes a solid foundation for the bioengineering and manipulation of nanostructures capable of capturing cargos and molecules with exceptional efficiency and programmability, thereby enabling applications in catalysis, delivery, and medicine.
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Affiliation(s)
- Tianpei Li
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Ping Chang
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Weixian Chen
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Zhaoyang Shi
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Chunling Xue
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Gregory F. Dykes
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Fang Huang
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Qiang Wang
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Lu-Ning Liu
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
- MOE
Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science
Center for Deep Ocean Multispheres and Earth System & College
of Marine Life Sciences, Ocean University
of China, Qingdao 266003, China
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26
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Shatabayeva E, Kaldybekov DB, Ulmanova L, Zhaisanbayeva BA, Mun EA, Kenessova ZA, Kudaibergenov SE, Khutoryanskiy VV. Enhancing Mucoadhesive Properties of Gelatin through Chemical Modification with Unsaturated Anhydrides. Biomacromolecules 2024; 25:1612-1628. [PMID: 38319691 PMCID: PMC10934270 DOI: 10.1021/acs.biomac.3c01183] [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: 10/31/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
Gelatin is a water-soluble natural polyampholyte with poor mucoadhesive properties. It has traditionally been used as a major ingredient in many pharmaceuticals, including soft and hard capsules, suppositories, tissue engineering, and regenerative medicine. The mucoadhesive properties of gelatin can be improved by modifying it through conjugation with specific adhesive unsaturated groups. In this study, gelatin was modified by reacting with crotonic, itaconic, and methacrylic anhydrides in varying molar ratios to yield crotonoylated-, itaconoylated-, and methacryloylated gelatins (abbreviated as Gel-CA, Gel-IA, and Gel-MA, respectively). The successful synthesis was confirmed using 1H NMR, FTIR spectroscopies, and colorimetric TNBSA assay. The effect of chemical modification on the isoelectric point was studied through viscosity and electrophoretic mobility measurements. The evolution of the storage (G') and loss (G'') moduli was employed to determine thermoreversible gelation points of modified and unmodified gelatins. The safety of modified gelatin derivatives was assessed with an in vivo slug mucosal irritation test (SMIT) and an in vitro MTT assay utilizing human pulmonary fibroblasts cell line. Two different model dosage forms, such as physical gels and spray-dried microparticles, were prepared and their mucoadhesive properties were evaluated using a flow-through technique with fluorescent detection and a tensile test with ex vivo porcine vaginal tissues and sheep nasal mucosa. Gelatins modified with unsaturated groups exhibited superior mucoadhesive properties compared to native gelatin. The enhanced ability of gelatin modified with these unsaturated functional groups is due to the formation of covalent bonds with cysteine-rich subdomains present in the mucin via thiol-ene click Michael-type addition reactions occurring under physiologically relevant conditions.
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Affiliation(s)
- Elvira
O. Shatabayeva
- Reading
School of Pharmacy, University of Reading, Whiteknights, RG6 6DX Reading, United Kingdom
- Department
of Chemistry and Chemical Technology, Al-Farabi
Kazakh National University, 050040 Almaty, Kazakhstan
| | - Daulet B. Kaldybekov
- Reading
School of Pharmacy, University of Reading, Whiteknights, RG6 6DX Reading, United Kingdom
- Department
of Chemistry and Chemical Technology, Al-Farabi
Kazakh National University, 050040 Almaty, Kazakhstan
- Institute
of Polymer Materials and Technology, 050019 Almaty, Kazakhstan
| | - Leila Ulmanova
- School
of Sciences and Humanities, Nazarbayev University, 010000 Astana, Kazakhstan
| | - Balnur A. Zhaisanbayeva
- School
of Engineering and Digital Sciences, Nazarbayev
University, 010000 Astana, Kazakhstan
| | - Ellina A. Mun
- School
of Sciences and Humanities, Nazarbayev University, 010000 Astana, Kazakhstan
| | - Zarina A. Kenessova
- Department
of Chemistry and Chemical Technology, Al-Farabi
Kazakh National University, 050040 Almaty, Kazakhstan
| | | | - Vitaliy V. Khutoryanskiy
- Reading
School of Pharmacy, University of Reading, Whiteknights, RG6 6DX Reading, United Kingdom
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27
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Tapia-Rojo R, Mora M, Garcia-Manyes S. Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales. Nat Protoc 2024:10.1038/s41596-024-00965-5. [PMID: 38467905 DOI: 10.1038/s41596-024-00965-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 12/18/2023] [Indexed: 03/13/2024]
Abstract
The reversible unfolding and refolding of proteins is a regulatory mechanism of tissue elasticity and signalling used by cells to sense and adapt to extracellular and intracellular mechanical forces. However, most of these proteins exhibit low mechanical stability, posing technical challenges to the characterization of their conformational dynamics under force. Here, we detail step-by-step instructions for conducting single-protein nanomechanical experiments using ultra-stable magnetic tweezers, which enable the measurement of the equilibrium conformational dynamics of single proteins under physiologically relevant low forces applied over biologically relevant timescales. We report the basic principles determining the functioning of the magnetic tweezer instrument, review the protein design strategy and the fluid chamber preparation and detail the procedure to acquire and analyze the unfolding and refolding trajectories of individual proteins under force. This technique adds to the toolbox of single-molecule nanomechanical techniques and will be of particular interest to those interested in proteins involved in mechanosensing and mechanotransduction. The procedure takes 4 d to complete, plus an additional 6 d for protein cloning and production, requiring basic expertise in molecular biology, surface chemistry and data analysis.
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Affiliation(s)
- Rafael Tapia-Rojo
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK.
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK.
| | - Marc Mora
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK.
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK.
| | - Sergi Garcia-Manyes
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK.
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK.
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28
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Liu Z, Haque MA, Savory CN, Liu T, Matsuishi S, Fenwick O, Scanlon DO, Zwijnenburg MA, Baran D, Schroeder BC. Controlling the thermoelectric properties of organo-metallic coordination polymers through backbone geometry. Faraday Discuss 2024; 250:377-389. [PMID: 37965928 PMCID: PMC10926974 DOI: 10.1039/d3fd00139c] [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: 07/13/2023] [Accepted: 09/06/2023] [Indexed: 11/16/2023]
Abstract
Poly(nickel-benzene-1,2,4,5-tetrakis(thiolate)) (Ni-btt), an organometallic coordination polymer (OMCP) characterized by the coordination between benzene-1,2,4,5-tetrakis(thiolate) (btt) and Ni2+ ions, has been recognized as a promising p-type thermoelectric material. In this study, we employed a constitutional isomer based on benzene-1,2,3,4-tetrakis(thiolate) (ibtt) to generate the corresponding isomeric polymer, poly(nickel-benzene-1,2,3,4-tetrakis(thiolate)) (Ni-ibtt). Comparative analysis of Ni-ibtt and Ni-btt reveals several common infrared (IR) and Raman features attributed to their similar square-planar nickel-sulfur (Ni-S) coordination. Nevertheless, these two polymer isomers exhibit substantially different backbone geometries. Ni-btt possesses a linear backbone, whereas Ni-ibtt exhibits a more undulating, zig-zag-like structure. Consequently, Ni-ibtt demonstrates slightly higher solubility and an increased bandgap in comparison to Ni-btt. The most noteworthy dissimilarity, however, manifests in their thermoelectric properties. While Ni-btt exhibits p-type behavior, Ni-ibtt demonstrates n-type carrier characteristics. This intriguing divergence prompted further investigation into the influence of OMCP backbone geometry on the electronic structure and, particularly, the thermoelectric properties of these materials.
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Affiliation(s)
- Zilu Liu
- Department of Chemistry, University College London, London WC1H 0AJ, UK.
| | - Md Azimul Haque
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division (PSE), KAUST Solar Center (KSC), 23955, Thuwal, Saudi Arabia.
| | - Chris N Savory
- Department of Chemistry, University College London, London WC1H 0AJ, UK.
- Thomas Young Centre, University College London, London WC1E 6BT, UK
| | - Tianjun Liu
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
| | - Satoru Matsuishi
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Materials Research Center for Element Strategy, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Oliver Fenwick
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
| | - David O Scanlon
- Department of Chemistry, University College London, London WC1H 0AJ, UK.
- Thomas Young Centre, University College London, London WC1E 6BT, UK
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Martijn A Zwijnenburg
- Department of Chemistry, University College London, London WC1H 0AJ, UK.
- Thomas Young Centre, University College London, London WC1E 6BT, UK
| | - Derya Baran
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division (PSE), KAUST Solar Center (KSC), 23955, Thuwal, Saudi Arabia.
| | - Bob C Schroeder
- Department of Chemistry, University College London, London WC1H 0AJ, UK.
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29
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Bonazzola R, Ferrante E, Ravikumar N, Xia Y, Keavney B, Plein S, Syeda-Mahmood T, Frangi AF. Unsupervised ensemble-based phenotyping enhances discoverability of genes related to left-ventricular morphology. NAT MACH INTELL 2024; 6:291-306. [PMID: 38523678 PMCID: PMC10957472 DOI: 10.1038/s42256-024-00801-1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 01/25/2024] [Indexed: 03/26/2024]
Abstract
Recent genome-wide association studies have successfully identified associations between genetic variants and simple cardiac morphological parameters derived from cardiac magnetic resonance images. However, the emergence of large databases, including genetic data linked to cardiac magnetic resonance facilitates the investigation of more nuanced patterns of cardiac shape variability than those studied so far. Here we propose a framework for gene discovery coined unsupervised phenotype ensembles. The unsupervised phenotype ensemble builds a redundant yet highly expressive representation by pooling a set of phenotypes learnt in an unsupervised manner, using deep learning models trained with different hyperparameters. These phenotypes are then analysed via genome-wide association studies, retaining only highly confident and stable associations across the ensemble. We applied our approach to the UK Biobank database to extract geometric features of the left ventricle from image-derived three-dimensional meshes. We demonstrate that our approach greatly improves the discoverability of genes that influence left ventricle shape, identifying 49 loci with study-wide significance and 25 with suggestive significance. We argue that our approach would enable more extensive discovery of gene associations with image-derived phenotypes for other organs or image modalities.
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Affiliation(s)
- Rodrigo Bonazzola
- Centre for Computational Imaging and Simulation Technologies in Biomedicine, School of Computing and School of Medicine, University of Leeds, Leeds, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Enzo Ferrante
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL/CONICET, Santa Fe, Argentina
| | - Nishant Ravikumar
- Centre for Computational Imaging and Simulation Technologies in Biomedicine, School of Computing and School of Medicine, University of Leeds, Leeds, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Yan Xia
- Centre for Computational Imaging and Simulation Technologies in Biomedicine, School of Computing and School of Medicine, University of Leeds, Leeds, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Bernard Keavney
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester, UK
| | - Sven Plein
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | | | - Alejandro F. Frangi
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester, UK
- Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Department of Computer Science, School of Engineering, Faculty of Science and Engineering, University of Manchester, Manchester, UK
- Medical Imaging Research Center (MIRC), University Hospital Gasthuisberg. Cardiovascular Sciences and Electrical Engineering Departments, KU Leuven, Leuven, Belgium
- Alan Turing Institute, London, UK
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30
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Worsley CA, Dunlop TO, Potts SJ, Garcia-Rodriguez R, Bolton RS, Davies ML, Jewell E, Watson TM. Quantifying Infiltration for Quality Control in Printed Mesoscopic Perovskite Solar Cells: A Microscopic Perspective. ACS Appl Energy Mater 2024; 7:1938-1948. [PMID: 38487267 PMCID: PMC10934285 DOI: 10.1021/acsaem.3c03056] [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: 12/08/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/17/2024]
Abstract
Mesoscopic carbon-based perovskite solar cells (CPSCs) are often cited as a potential frontrunner to perovskite commercialization. Infiltration, the extent to which perovskite fills the mesoporous scaffold, is critical for optimum performance and stability. However, infiltration data are usually presented as qualitative photographic comparisons of samples with extreme infiltration variation. This work examines how small infiltration defects impact performance using an optical microscopy examination of the base TiO2 layer to identify issues and develop targeted techniques for infiltration enhancement. Critically, the uninfiltrated area at the base of the stack was found to correlate well with PCE across multiple batches of varied print quality and ZrO2 thickness. Through reduction of mesh mark defects and improvement of print quality in the ZrO2 and carbon layers, a champion PCE of 15.01% is attained. It follows that this facile, multiscaled, nondestructive technique could enable targeted performance enhancement and quality control in future scale-up initiatives.
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Affiliation(s)
| | | | | | | | | | | | - Eifion Jewell
- Swansea University, Bay
Campus, Neath, Skewen SA18EN, Wales
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31
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Hegde S, Khanipov K, Hornett EA, Nilyanimit P, Pimenova M, Saldaña MA, de Bekker C, Golovko G, Hughes GL. Interkingdom interactions shape the fungal microbiome of mosquitoes. Anim Microbiome 2024; 6:11. [PMID: 38454530 PMCID: PMC10921588 DOI: 10.1186/s42523-024-00298-4] [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: 11/21/2023] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND The mosquito microbiome is an important modulator of vector competence and vectoral capacity. Unlike the extensively studied bacterial microbiome, fungal communities in the mosquito microbiome (the mycobiome) remain largely unexplored. To work towards getting an improved understanding of the fungi associated with mosquitoes, we sequenced the mycobiome of three field-collected and laboratory-reared mosquito species (Aedes albopictus, Aedes aegypti, and Culex quinquefasciatus). RESULTS Our analysis showed both environment and host species were contributing to the diversity of the fungal microbiome of mosquitoes. When comparing species, Ae. albopictus possessed a higher number of diverse fungal taxa than Cx. quinquefasciatus, while strikingly less than 1% of reads from Ae. aegypti samples were fungal. Fungal reads from Ae. aegypti were < 1% even after inhibiting host amplification using a PNA blocker, indicating that this species lacked a significant fungal microbiome that was amplified using this sequencing approach. Using a mono-association mosquito infection model, we confirmed that mosquito-derived fungal isolates colonize Aedes mosquitoes and support growth and development at comparable rates to their bacterial counterparts. Strikingly, native bacterial taxa isolated from mosquitoes impeded the colonization of symbiotic fungi in Ae. aegypti suggesting interkingdom interactions shape fungal microbiome communities. CONCLUSION Collectively, this study adds to our understanding of the fungal microbiome of different mosquito species, that these fungal microbes support growth and development, and highlights that microbial interactions underpin fungal colonization of these medically relevent species.
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Affiliation(s)
- Shivanand Hegde
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, UK.
- School of Life Sciences, Keele University, Newcastle, UK.
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Emily A Hornett
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
| | - Pornjarim Nilyanimit
- Center of Excellence in Clinical Virology, Faculty of Medicine , Chulalongkorn University, Bangkok, Thailand
| | - Maria Pimenova
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Miguel A Saldaña
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Charissa de Bekker
- Microbiology, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Grant L Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, UK.
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32
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Yang J, Papaderakis AA, Roh JS, Keerthi A, Adams RW, Bissett MA, Radha B, Dryfe RAW. Measuring the Capacitance of Carbon in Ionic Liquids: From Graphite to Graphene. J Phys Chem C Nanomater Interfaces 2024; 128:3674-3684. [PMID: 38476828 PMCID: PMC10926162 DOI: 10.1021/acs.jpcc.3c08269] [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: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 03/14/2024]
Abstract
The physical electrochemistry of the carbon/ionic liquids interface underpins the processes occurring in a vast range of applications spanning electrochemical energy storage, iontronic devices, and lubrication. Elucidating the charge storage mechanisms at the carbon/electrolyte interface will lead to a better understanding of the operational principles of such systems. Herein, we probe the charge stored at the electrochemical double layer formed between model carbon systems, ranging from single-layer graphene to graphite and the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EMIM-TFSI). The effect of the number of graphene layers on the overall capacitance of the interface is investigated. We demonstrate that in pure EMIM-TFSI and at moderate potential biases, the electronic properties of graphene and graphite govern the overall capacitance of the interface, while the electrolyte contribution to the latter is less significant. In mixtures of EMIM-TFSI with solvents of varying relative permittivity, the complex interplay between electrolyte ions and solvent molecules is shown to influence the charge stored at the interface, which under certain conditions overcomes the effects of relative permittivity. This work provides additional experimental insights into the continuously advancing topic of electrochemical double-layer structure at the interface between room temperature ionic liquids and carbon materials.
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Affiliation(s)
- Jing Yang
- Department
of Chemistry and Henry Royce Institute, The University of Manchester, Oxford Road, M13
9PL Manchester, U.K.
| | - Athanasios A. Papaderakis
- Department
of Chemistry and Henry Royce Institute, The University of Manchester, Oxford Road, M13
9PL Manchester, U.K.
| | - Ji Soo Roh
- Department
of Materials, The University of Manchester, Oxford Road, M13 9PL Manchester, U.K.
- National
Graphene Institute, The University of Manchester, Oxford Road, M13 9PL Manchester, U.K.
| | - Ashok Keerthi
- Department
of Chemistry and Henry Royce Institute, The University of Manchester, Oxford Road, M13
9PL Manchester, U.K.
- National
Graphene Institute, The University of Manchester, Oxford Road, M13 9PL Manchester, U.K.
| | - Ralph W. Adams
- Department
of Chemistry and Henry Royce Institute, The University of Manchester, Oxford Road, M13
9PL Manchester, U.K.
| | - Mark A. Bissett
- Department
of Materials, The University of Manchester, Oxford Road, M13 9PL Manchester, U.K.
- National
Graphene Institute, The University of Manchester, Oxford Road, M13 9PL Manchester, U.K.
| | - Boya Radha
- Department
of Physics and Astronomy, The University
of Manchester, Oxford
Road, M13 9PL Manchester, U.K.
| | - Robert A. W. Dryfe
- Department
of Chemistry and Henry Royce Institute, The University of Manchester, Oxford Road, M13
9PL Manchester, U.K.
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Ermolaev GA, Voronin KV, Toksumakov AN, Grudinin DV, Fradkin IM, Mazitov A, Slavich AS, Tatmyshevskiy MK, Yakubovsky DI, Solovey VR, Kirtaev RV, Novikov SM, Zhukova ES, Kruglov I, Vyshnevyy AA, Baranov DG, Ghazaryan DA, Arsenin AV, Martin-Moreno L, Volkov VS, Novoselov KS. Wandering principal optical axes in van der Waals triclinic materials. Nat Commun 2024; 15:1552. [PMID: 38448442 PMCID: PMC10918091 DOI: 10.1038/s41467-024-45266-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/19/2024] [Indexed: 03/08/2024] Open
Abstract
Nature is abundant in material platforms with anisotropic permittivities arising from symmetry reduction that feature a variety of extraordinary optical effects. Principal optical axes are essential characteristics for these effects that define light-matter interaction. Their orientation - an orthogonal Cartesian basis that diagonalizes the permittivity tensor, is often assumed stationary. Here, we show that the low-symmetry triclinic crystalline structure of van der Waals rhenium disulfide and rhenium diselenide is characterized by wandering principal optical axes in the space-wavelength domain with above π/2 degree of rotation for in-plane components. In turn, this leads to wavelength-switchable propagation directions of their waveguide modes. The physical origin of wandering principal optical axes is explained using a multi-exciton phenomenological model and ab initio calculations. We envision that the wandering principal optical axes of the investigated low-symmetry triclinic van der Waals crystals offer a platform for unexplored anisotropic phenomena and nanophotonic applications.
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Affiliation(s)
- Georgy A Ermolaev
- Emerging Technologies Research Center, XPANCEO, Dubai Investment Park First, Dubai, United Arab Emirates
| | - Kirill V Voronin
- Donostia International Physics Center (DIPC), Donostia/San Sebastián, 20018, Spain
| | - Adilet N Toksumakov
- Moscow Center for Advanced Studies, Kulakova str. 20, Moscow, 123592, Russia
| | - Dmitriy V Grudinin
- Emerging Technologies Research Center, XPANCEO, Dubai Investment Park First, Dubai, United Arab Emirates
| | - Ilia M Fradkin
- Emerging Technologies Research Center, XPANCEO, Dubai Investment Park First, Dubai, United Arab Emirates
| | - Arslan Mazitov
- Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Aleksandr S Slavich
- Moscow Center for Advanced Studies, Kulakova str. 20, Moscow, 123592, Russia
| | | | - Dmitry I Yakubovsky
- Moscow Center for Advanced Studies, Kulakova str. 20, Moscow, 123592, Russia
| | - Valentin R Solovey
- Emerging Technologies Research Center, XPANCEO, Dubai Investment Park First, Dubai, United Arab Emirates
| | - Roman V Kirtaev
- Emerging Technologies Research Center, XPANCEO, Dubai Investment Park First, Dubai, United Arab Emirates
| | - Sergey M Novikov
- Moscow Center for Advanced Studies, Kulakova str. 20, Moscow, 123592, Russia
| | - Elena S Zhukova
- Moscow Center for Advanced Studies, Kulakova str. 20, Moscow, 123592, Russia
| | - Ivan Kruglov
- Emerging Technologies Research Center, XPANCEO, Dubai Investment Park First, Dubai, United Arab Emirates
| | - Andrey A Vyshnevyy
- Emerging Technologies Research Center, XPANCEO, Dubai Investment Park First, Dubai, United Arab Emirates
| | - Denis G Baranov
- Moscow Center for Advanced Studies, Kulakova str. 20, Moscow, 123592, Russia
| | - Davit A Ghazaryan
- Moscow Center for Advanced Studies, Kulakova str. 20, Moscow, 123592, Russia
- Laboratory of Advanced Functional Materials, Yerevan State University, Yerevan, 0025, Armenia
| | - Aleksey V Arsenin
- Emerging Technologies Research Center, XPANCEO, Dubai Investment Park First, Dubai, United Arab Emirates
- Laboratory of Advanced Functional Materials, Yerevan State University, Yerevan, 0025, Armenia
| | - Luis Martin-Moreno
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009, Zaragoza, Spain
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Valentyn S Volkov
- Emerging Technologies Research Center, XPANCEO, Dubai Investment Park First, Dubai, United Arab Emirates
- Laboratory of Advanced Functional Materials, Yerevan State University, Yerevan, 0025, Armenia
| | - Kostya S Novoselov
- National Graphene Institute (NGI), University of Manchester, Manchester, M13 9PL, UK.
- Department of Materials Science and Engineering, National University of Singapore, Singapore, 03-09, Singapore.
- Institute for Functional Intelligent Materials, National University of Singapore, 117544, Singapore, Singapore.
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34
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Du J, Cobb PJ, Ding J, Mills DP, Liddle ST. Correction: f-Element heavy pnictogen chemistry. Chem Sci 2024; 15:3767. [PMID: 38455023 PMCID: PMC10915836 DOI: 10.1039/d4sc90017k] [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: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 03/09/2024] Open
Abstract
[This corrects the article DOI: 10.1039/D3SC05056D.].
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Affiliation(s)
- Jingzhen Du
- College of Chemistry, Zhengzhou University Zhengzhou 450001 China
- Department of Chemistry and Centre for Radiochemistry Research, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Philip J Cobb
- Department of Chemistry and Centre for Radiochemistry Research, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Junru Ding
- College of Chemistry, Zhengzhou University Zhengzhou 450001 China
| | - David P Mills
- Department of Chemistry and Centre for Radiochemistry Research, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Stephen T Liddle
- Department of Chemistry and Centre for Radiochemistry Research, The University of Manchester Oxford Road Manchester M13 9PL UK
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35
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Yuan L, Avello P, Zhu Z, Lock SCL, McCarthy K, Redmond EJ, Davis AM, Song Y, Ezer D, Pitchford JW, Quint M, Xie Q, Xu X, Davis SJ, Ronald J. Complex epistatic interactions between ELF3, PRR9, and PRR7 regulate the circadian clock and plant physiology. Genetics 2024; 226:iyad217. [PMID: 38142447 PMCID: PMC10917503 DOI: 10.1093/genetics/iyad217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/07/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023] Open
Abstract
Circadian clocks are endogenous timekeeping mechanisms that coordinate internal physiological responses with the external environment. EARLY FLOWERING3 (ELF3), PSEUDO RESPONSE REGULATOR (PRR9), and PRR7 are essential components of the plant circadian clock and facilitate entrainment of the clock to internal and external stimuli. Previous studies have highlighted a critical role for ELF3 in repressing the expression of PRR9 and PRR7. However, the functional significance of activity in regulating circadian clock dynamics and plant development is unknown. To explore this regulatory dynamic further, we first employed mathematical modeling to simulate the effect of the prr9/prr7 mutation on the elf3 circadian phenotype. These simulations suggested that simultaneous mutations in prr9/prr7 could rescue the elf3 circadian arrhythmia. Following these simulations, we generated all Arabidopsis elf3/prr9/prr7 mutant combinations and investigated their circadian and developmental phenotypes. Although these assays could not replicate the results from the mathematical modeling, our results have revealed a complex epistatic relationship between ELF3 and PRR9/7 in regulating different aspects of plant development. ELF3 was essential for hypocotyl development under ambient and warm temperatures, while PRR9 was critical for root thermomorphogenesis. Finally, mutations in prr9 and prr7 rescued the photoperiod-insensitive flowering phenotype of the elf3 mutant. Together, our results highlight the importance of investigating the genetic relationship among plant circadian genes.
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Affiliation(s)
- Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Paula Avello
- Department of Mathematics, University of York, York, YO10 5DD, UK
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Zihao Zhu
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) 06108, Germany
| | - Sarah C L Lock
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Kayla McCarthy
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ethan J Redmond
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Amanda M Davis
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Yang Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Daphne Ezer
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Jonathan W Pitchford
- Department of Mathematics, University of York, York, YO10 5DD, UK
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) 06108, Germany
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Seth J Davis
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - James Ronald
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, UK
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36
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Sibug-Torres SM, Grys DB, Kang G, Niihori M, Wyatt E, Spiesshofer N, Ruane A, de Nijs B, Baumberg JJ. In situ electrochemical regeneration of nanogap hotspots for continuously reusable ultrathin SERS sensors. Nat Commun 2024; 15:2022. [PMID: 38448412 PMCID: PMC10917746 DOI: 10.1038/s41467-024-46097-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/13/2024] [Indexed: 03/08/2024] Open
Abstract
Surface-enhanced Raman spectroscopy (SERS) harnesses the confinement of light into metallic nanoscale hotspots to achieve highly sensitive label-free molecular detection that can be applied for a broad range of sensing applications. However, challenges related to irreversible analyte binding, substrate reproducibility, fouling, and degradation hinder its widespread adoption. Here we show how in-situ electrochemical regeneration can rapidly and precisely reform the nanogap hotspots to enable the continuous reuse of gold nanoparticle monolayers for SERS. Applying an oxidising potential of +1.5 V (vs Ag/AgCl) for 10 s strips a broad range of adsorbates from the nanogaps and forms a metastable oxide layer of few-monolayer thickness. Subsequent application of a reducing potential of -0.80 V for 5 s in the presence of a nanogap-stabilising molecular scaffold, cucurbit[5]uril, reproducibly regenerates the optimal plasmonic properties with SERS enhancement factors ≈106. The regeneration of the nanogap hotspots allows these SERS substrates to be reused over multiple cycles, demonstrating ≈5% relative standard deviation over at least 30 cycles of analyte detection and regeneration. Such continuous and reliable SERS-based flow analysis accesses diverse applications from environmental monitoring to medical diagnostics.
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Affiliation(s)
- Sarah May Sibug-Torres
- NanoPhotonics Centre, Cavendish Laboratory, Department of Physics, JJ Thompson Avenue, University of Cambridge, Cambridge, CB3 0HE, UK
| | - David-Benjamin Grys
- NanoPhotonics Centre, Cavendish Laboratory, Department of Physics, JJ Thompson Avenue, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Gyeongwon Kang
- NanoPhotonics Centre, Cavendish Laboratory, Department of Physics, JJ Thompson Avenue, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Chemistry, Kangwon National University, Chuncheon, 24341, South Korea
| | - Marika Niihori
- NanoPhotonics Centre, Cavendish Laboratory, Department of Physics, JJ Thompson Avenue, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Elle Wyatt
- NanoPhotonics Centre, Cavendish Laboratory, Department of Physics, JJ Thompson Avenue, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Nicolas Spiesshofer
- NanoPhotonics Centre, Cavendish Laboratory, Department of Physics, JJ Thompson Avenue, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Ashleigh Ruane
- NanoPhotonics Centre, Cavendish Laboratory, Department of Physics, JJ Thompson Avenue, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Bart de Nijs
- NanoPhotonics Centre, Cavendish Laboratory, Department of Physics, JJ Thompson Avenue, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Jeremy J Baumberg
- NanoPhotonics Centre, Cavendish Laboratory, Department of Physics, JJ Thompson Avenue, University of Cambridge, Cambridge, CB3 0HE, UK.
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37
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Hayward D, Beekman AM. Strategies for converting turn-motif and cyclic peptides to small molecules for targeting protein-protein interactions. RSC Chem Biol 2024; 5:198-208. [PMID: 38456035 PMCID: PMC10915966 DOI: 10.1039/d3cb00222e] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024] Open
Abstract
The development of small molecules that interact with protein-protein interactions is an ongoing challenge. Peptides offer a starting point in the drug discovery process for targeting protein-interactions due to their larger, more flexible structure and the structurally diverse properties that allow for a greater interaction with the protein. The techniques for rapidly identifying potent cyclic peptides and turn-motif peptides are highly effective, but this potential has not yet transferred to approved drug candidates. By applying the properties of the peptide-protein interaction the development of small molecules for drug discovery has the potential to be more efficient. In this review, we discuss the methods that allow for the unique binding properties of peptides to proteins, and the methods deployed to transfer these qualities to potent small molecules.
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Affiliation(s)
- Deanne Hayward
- School of Pharmacy, University of East Anglia, Norwich Research Park Norwich Norfolk NR47TJ UK
| | - Andrew M Beekman
- School of Pharmacy, University of East Anglia, Norwich Research Park Norwich Norfolk NR47TJ UK
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38
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Tam B, Babacan O, Kafizas A, Nelson J. Comparing the net-energy balance of standalone photovoltaic-coupled electrolysis and photoelectrochemical hydrogen production. Energy Environ Sci 2024; 17:1677-1694. [PMID: 38449570 PMCID: PMC10913155 DOI: 10.1039/d3ee02814c] [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: 08/24/2023] [Accepted: 01/12/2024] [Indexed: 03/08/2024]
Abstract
Photovoltaic-coupled electrolysis (PV-E) and photoelectrochemical (PEC) water splitting are two options for storing solar energy as hydrogen. Understanding the requirements for achieving a positive energy balance over the lifetime of facilities using these technologies is important for ensuring sustainability. While neither technology has yet reached full commercialisation, they are also at very different technology readiness levels and scales of development. Here, we model the energy balance of standalone large-scale facilities to evaluate their energy return on energy invested (ERoEI) over time and energy payback time (EPBT). We find that for average input parameters based on present commercialised modules, a PV-E facility shows an EPBT of 6.2 years and ERoEI after 20 years of 2.1, which rises to approximately 3.7 with an EPBT of 2.7 years for favourable parameters using the best metrics amongst large-scale modules. The energy balance of PV-E facilities is influenced most strongly by the upfront embodied energy costs of the photovoltaic component. In contrast, the simulated ERoEI for a PEC facility made with earth abundant materials only peaks at 0.42 after 11 years and about 0.71 after 20 years for facilities with higher-performance active materials. Doubling the conversion efficiency to 10% and halving the degradation rate to 2% for a 10-year device lifetime can allow PEC facilities to achieve an ERoEI after 20 years of 2.1 for optimistic future parameters. We also estimate that recycling the materials used in hydrogen production technologies improves the energy balance by 28% and 14% for favourable-case PV-E and PEC water splitting facilities, respectively.
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Affiliation(s)
- Brian Tam
- Department of Physics, Imperial College London South Kensington London SW7 2AZ UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City London W12 0BZ UK
| | - Oytun Babacan
- Grantham Institute - Climate Change and the Environment, Imperial College London South Kensington London SW7 2AZ UK
| | - Andreas Kafizas
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City London W12 0BZ UK
- Grantham Institute - Climate Change and the Environment, Imperial College London South Kensington London SW7 2AZ UK
| | - Jenny Nelson
- Department of Physics, Imperial College London South Kensington London SW7 2AZ UK
- Grantham Institute - Climate Change and the Environment, Imperial College London South Kensington London SW7 2AZ UK
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39
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King ACF, Bauska TK, Brook EJ, Kalk M, Nehrbass-Ahles C, Wolff EW, Strawson I, Rhodes RH, Osman MB. Reconciling ice core CO 2 and land-use change following New World-Old World contact. Nat Commun 2024; 15:1735. [PMID: 38443398 PMCID: PMC10915154 DOI: 10.1038/s41467-024-45894-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
Ice core records of carbon dioxide (CO2) throughout the last 2000 years provide context for the unprecedented anthropogenic rise in atmospheric CO2 and insights into global carbon cycle dynamics. Yet the atmospheric history of CO2 remains uncertain in some time intervals. Here we present measurements of CO2 and methane (CH4) in the Skytrain ice core from 1450 to 1700 CE. Results suggest a sudden decrease in CO2 around 1610 CE in one widely used record may be an artefact of a small number of anomalously low values. Our analysis supports a more gradual decrease in CO2 of 0.5 ppm per decade from 1516 to 1670 CE, with an inferred land carbon sink of 2.6 PgC per decade. This corroborates modelled scenarios of large-scale reorganisation of land use in the Americas following New World-Old World contact, whereas a rapid decrease in CO2 at 1610 CE is incompatible with even the most extreme land-use change scenarios.
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Affiliation(s)
| | | | - Edward J Brook
- College of Earth, Ocean and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Mike Kalk
- College of Earth, Ocean and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Christoph Nehrbass-Ahles
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
- National Physical Laboratory, Teddington, UK
| | - Eric W Wolff
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Ivo Strawson
- British Antarctic Survey, Cambridge, UK
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Rachael H Rhodes
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Matthew B Osman
- Department of Geography, University of Cambridge, Cambridge, UK
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40
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Wang S, Kennedy N, Fujita K, Uchida SI, Eisaki H, Johnson PD, Davis JCS, O'Mahony SM. Discovery of orbital ordering in Bi 2Sr 2CaCu 2O 8+x. Nat Mater 2024:10.1038/s41563-024-01817-z. [PMID: 38438620 DOI: 10.1038/s41563-024-01817-z] [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: 02/25/2023] [Accepted: 01/22/2024] [Indexed: 03/06/2024]
Abstract
The primordial ingredient of cuprate superconductivity is the CuO2 unit cell. Theories usually concentrate on the intra-atom Coulombic interactions dominating the 3d9 and 3d10 configurations of each copper ion. However, if Coulombic interactions also occur between electrons of the 2p6 orbitals of each planar oxygen atom, spontaneous orbital ordering may split their energy levels. This long-predicted intra-unit-cell symmetry breaking should generate an orbitally ordered phase, for which the charge transfer energy ε separating the 2p6 and 3d10 orbitals is distinct for the two oxygen atoms. Here we introduce sublattice-resolved ε(r) imaging to CuO2 studies and discover intra-unit-cell rotational symmetry breaking of ε(r). Spatially, this state is arranged in disordered Ising domains of orthogonally oriented orbital order bounded by dopant ions, and within whose domain walls low-energy electronic quadrupolar two-level systems occur. Overall, these data reveal a Q = 0 orbitally ordered state that splits the oxygen energy levels by ~50 meV, in underdoped CuO2.
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Affiliation(s)
- Shuqiu Wang
- Clarendon Laboratory, University of Oxford, Oxford, UK.
- Department of Physics, Cornell University, Ithaca, NY, USA.
- H. H. Wills Physics Laboratory, University of Bristol, Bristol, UK.
| | - Niall Kennedy
- Clarendon Laboratory, University of Oxford, Oxford, UK
- School of Physics, University College Cork, Cork, Ireland
| | - Kazuhiro Fujita
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA
| | | | - Hiroshi Eisaki
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Peter D Johnson
- Clarendon Laboratory, University of Oxford, Oxford, UK
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA
| | - J C Séamus Davis
- Clarendon Laboratory, University of Oxford, Oxford, UK.
- Department of Physics, Cornell University, Ithaca, NY, USA.
- School of Physics, University College Cork, Cork, Ireland.
- Max Planck Institute for Chemical Physics of Solids, Dresden, Germany.
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41
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Abstract
When he first introduced the notion of a conformal boundary into the study of asymptotically empty space-times, Penrose noted that the boundary would be null, space-like or time-like according as the cosmological constant [Formula: see text] was zero, positive or negative. While most applications of the idea of a conformal boundary have been to the zero-[Formula: see text], asymptotically Minkowskian case, there also has been work on the non-zero cases. Here, we review work with a positive [Formula: see text], which is the appropriate case for cosmology of the universe in which we live. This article is part of a discussion meeting issue 'At the interface of asymptotics, conformal methods and analysis in general relativity'.
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Affiliation(s)
- Paul Tod
- Mathematical Institute, Oxford University, Woodstock Road, Oxford OX2 6GG, UK
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42
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Skinner MF, Delezene LK, Skinner MM, Mahoney P. Linear enamel hypoplasia in Homo naledi reappraised in light of new Retzius periodicities. Am J Biol Anthropol 2024:e24927. [PMID: 38433613 DOI: 10.1002/ajpa.24927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 03/05/2024]
Abstract
OBJECTIVES Among low-latitude apes, developmental defects of enamel often recur twice yearly, linkable to environmental cycles. Surprisingly, teeth of Homo naledi from Rising Star in South Africa (241-335 kya), a higher latitude site with today a single rainy season, also exhibit bimodally distributed hypoplastic enamel defects, but with uncertain timing and etiology. Newly determined Retzius periodicities for enamel formation in this taxon enable a reconstruction of the temporal patterning of childhood stress. METHODS Using high resolution casts of 31 isolated anterior teeth from H. naledi, 82 enamel defects (linear enamel hypoplasia [LEH]) were identified. Seventeen teeth are assigned to three individuals. Perikymata in the occlusal wall of enamel furrows and between the onsets of successive LEH were visualized with scanning electron microscopy and counted. Defects were measured with an optical scanner. Conversion of perikymata counts to estimates of LEH duration and inter-LEH interval draws upon Retzius periodicities of 9 and 11 days. RESULTS Anterior teeth record more than a year of developmental distress, expressed as two asymmetric intervals centered on 4.5 and 7.5 months bounded by three LEH. Durations, also, show bimodal distributions, lasting 3 or 12 weeks. Short duration LEH are more severe than long duration. Relative incisor/canine rates of formation are indistinguishable from modern humans. DISCUSSION We invoke a disease and dearth model, with short episodes of distress reflecting onset of disease in young infants, lasting about 3 weeks, followed by a season of undernutrition, possibly intensified by secondary plant compounds, spanning about 12 weeks, inferably coincident with austral winter.
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Affiliation(s)
- Mark Fretson Skinner
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Lucas Kyle Delezene
- Department of Anthropology, University of Arkansas, Fayetteville, Arkansas, USA
- Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Johannesburg, South Africa
| | - Matthew M Skinner
- Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Johannesburg, South Africa
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Patrick Mahoney
- Skeletal Biology Research Centre, School of Anthropology and Conservation, University of Kent, Canterbury, UK
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43
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Dorrat JC, Taylor CGP, Young RJ, Solea AB, Turner DR, Dennison GH, Ward MD, Tuck KL. A Study on Auto-Catalysis and Product Inhibition: A Nucleophilic Aromatic Substitution Reaction Catalysed within the Cavity of an Octanuclear Coordination Cage. Chemistry 2024:e202400501. [PMID: 38433109 DOI: 10.1002/chem.202400501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/05/2024]
Abstract
The ability of an octanuclear cubic coordination cage to catalyse a nucleophilic aromatic substitution reaction on a cavity-bound guest was studied with 2,4-dinitrofluorobenzene (DNFB) as the guest/substrate. It was found that DNFB undergoes a catalysed reaction with hydroxide ions within the cavity of the cubic cage (in aqueous buffer solution, pH 8.6). The rate enhancement of kcat/kuncat was determined to be 22, with cavity binding of the guest being required for catalysis to occur. The product, 2,4-dinitrophenolate (DNP), remained bound within the cavity due to electrostatic stabilisation and exerts two apparently contradictory effects: it initially auto-catalyses the reaction when present at low concentrations, but at higher concentrations inhibits catalysis when a pair of DNP guests block the cavity. When encapsulated, the UV/Vis absorption spectrum of DNP is red-shifted when compared to the spectrum of free DNP in aqueous solution. Further investigations using other aromatic guests determined that a similar red-shift on cavity binding also occurred for 4-nitrophenolate (4NP) at pH 8.6. The red-shift was used to determine the stoichiometry of guest binding of DNP and 4NP within the cage cavity, which was confirmed by structural analysis with X-ray crystallography; and was also used to perform catalytic kinetic studies in the solution-state.
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Affiliation(s)
- Jack C Dorrat
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | | | - Rosemary J Young
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Atena B Solea
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - David R Turner
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Genevieve H Dennison
- CBRN Defence, Sensors and Effectors Division, Defence Science and Technology Group, Fishermans Bend, VIC, 3207, Australia
- Electro Optics Sensing and Electromagnetic Warfare, Sensors and Effectors Division, Defence Science and Technology Group, Edinburgh, SA, 5111, Australia
| | - Michael D Ward
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Kellie L Tuck
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
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44
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Tian M, Zhong S, Al Ghassani MAM, Johanning L, Sucala VI. Simulation and feasibility assessment of a green hydrogen supply chain: a case study in Oman. Environ Sci Pollut Res Int 2024:10.1007/s11356-024-32563-z. [PMID: 38429594 DOI: 10.1007/s11356-024-32563-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 02/17/2024] [Indexed: 03/03/2024]
Abstract
The transition to sustainable energy is crucial for mitigating climate change impacts. This study addresses this imperative by simulating a green hydrogen supply chain tailored for residential cooking in Oman. The supply chain encompasses solar energy production, underground storage, pipeline transportation, and residential application, aiming to curtail greenhouse gas emissions and reduce the levelized cost of hydrogen (LCOH). The simulation results suggest leveraging a robust 7 GW solar plant. Oman achieves an impressive annual production of 9.78 TWh of green hydrogen, equivalent to 147,808 tonnes of H2, perfectly aligning with the ambitious goals of Oman Vision 2040. The overall LCOH for the green hydrogen supply chain is estimated at a highly competitive 6.826 USD/kg, demonstrating cost competitiveness when benchmarked against analogous studies. A sensitivity analysis highlights Oman's potential for cost-effective investments in green hydrogen infrastructure, propelling the nation towards a sustainable energy future. This study not only addresses the pressing issue of reducing carbon emissions in the residential sector but also serves as a model for other regions pursuing sustainable energy transitions. The developed simulation models are publicly accessible at https://hychain.co.uk , providing a valuable resource for further research and development in the field of green hydrogen supply chains.
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Affiliation(s)
- Mi Tian
- Department of Engineering, University of Exeter, Exeter, UK.
| | - Shuya Zhong
- Department of Engineering, University of Exeter, Exeter, UK
- School of Management, University of Bath, Bath, UK
| | | | - Lars Johanning
- Department of Engineering, University of Exeter, Exeter, UK
- School of Engineering, Computing and Mathematics, University of Plymouth, Plymouth, UK
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45
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Daly S, Ferreira Fernandes J, Bruggeman E, Handa A, Peters R, Benaissa S, Zhang B, Beckwith JS, Sanders EW, Sims RR, Klenerman D, Davis SJ, O'Holleran K, Lee SF. High-density volumetric super-resolution microscopy. Nat Commun 2024; 15:1940. [PMID: 38431671 PMCID: PMC10908787 DOI: 10.1038/s41467-024-45828-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
Volumetric super-resolution microscopy typically encodes the 3D position of single-molecule fluorescence into a 2D image by changing the shape of the point spread function (PSF) as a function of depth. However, the resulting large and complex PSF spatial footprints reduce biological throughput and applicability by requiring lower labeling densities to avoid overlapping fluorescent signals. We quantitatively compare the density dependence of single-molecule light field microscopy (SMLFM) to other 3D PSFs (astigmatism, double helix and tetrapod) showing that SMLFM enables an order-of-magnitude speed improvement compared to the double helix PSF by resolving overlapping emitters through parallax. We demonstrate this optical robustness experimentally with high accuracy ( > 99.2 ± 0.1%, 0.1 locs μm-2) and sensitivity ( > 86.6 ± 0.9%, 0.1 locs μm-2) through whole-cell (scan-free) imaging and tracking of single membrane proteins in live primary B cells. We also exemplify high-density volumetric imaging (0.15 locs μm-2) in dense cytosolic tubulin datasets.
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Affiliation(s)
- Sam Daly
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - João Ferreira Fernandes
- Radcliffe Department of Medicine and MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Ezra Bruggeman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Anoushka Handa
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ruby Peters
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Sarah Benaissa
- Cambridge Advanced Imaging Centre, Downing Site, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Boya Zhang
- Cambridge Advanced Imaging Centre, Downing Site, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Joseph S Beckwith
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Edward W Sanders
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ruth R Sims
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Simon J Davis
- Radcliffe Department of Medicine and MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Kevin O'Holleran
- Cambridge Advanced Imaging Centre, Downing Site, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Steven F Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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46
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Cai D, Yang Z, Tong R, Huang H, Zhang C, Xia Y. Binder-Free MOF-Based and MOF-Derived Nanoarrays for Flexible Electrochemical Energy Storage: Progress and Perspectives. Small 2024; 20:e2305778. [PMID: 37948356 DOI: 10.1002/smll.202305778] [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: 07/10/2023] [Revised: 10/09/2023] [Indexed: 11/12/2023]
Abstract
The fast development of Internet of Things and the rapid advent of next-generation versatile wearable electronics require cost-effective and highly-efficient electroactive materials for flexible electrochemical energy storage devices. Among various electroactive materials, binder-free nanostructured arrays have attracted widespread attention. Featured with growing on a conductive and flexible substrate without using inactive and insulating binders, binder-free 3D nanoarray electrodes facilitate fast electron/ion transportation and rapid reaction kinetics with more exposed active sites, maintain structure integrity of electrodes even under bending or twisted conditions, readily release generated joule heat during charge/discharge cycles and achieve enhanced gravimetric capacity of the whole device. Binder-free metal-organic framework (MOF) nanoarrays and/or MOF-derived nanoarrays with high surface area and unique porous structure have emerged with great potential in energy storage field and been extensively exploited in recent years. In this review, common substrates used for binder-free nanoarrays are compared and discussed. Various MOF-based and MOF-derived nanoarrays, including metal oxides, sulfides, selenides, nitrides, phosphides and nitrogen-doped carbons, are surveyed and their electrochemical performance along with their applications in flexible energy storage are analyzed and overviewed. In addition, key technical issues and outlooks on future development of MOF-based and MOF-derived nanoarrays toward flexible energy storage are also offered.
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Affiliation(s)
- Dongming Cai
- Hubei Key Laboratory of Energy Storage and Power Battery, School of Mathematics, Physics and Optoelectronics Engineering, Hubei University of Automotive Technology, Shiyan, 442002, P. R. China
| | - Zhuxian Yang
- Department of Engineering, Faculty of Environment, Science and Economy, University of Exeter, Exeter, EX4 4QF, UK
| | - Rui Tong
- Hubei Key Laboratory of Energy Storage and Power Battery, School of Mathematics, Physics and Optoelectronics Engineering, Hubei University of Automotive Technology, Shiyan, 442002, P. R. China
| | - Haiming Huang
- Hubei Key Laboratory of Energy Storage and Power Battery, School of Mathematics, Physics and Optoelectronics Engineering, Hubei University of Automotive Technology, Shiyan, 442002, P. R. China
| | - Chuankun Zhang
- Hubei Key Laboratory of Energy Storage and Power Battery, School of Mathematics, Physics and Optoelectronics Engineering, Hubei University of Automotive Technology, Shiyan, 442002, P. R. China
| | - Yongde Xia
- Department of Engineering, Faculty of Environment, Science and Economy, University of Exeter, Exeter, EX4 4QF, UK
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47
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Winfrey L, Yun L, Passeri G, Suntharalingam K, Pulis AP. H 2 O ⋅ B(C 6 F 5 ) 3 -Catalyzed para-Alkylation of Anilines with Alkenes Applied to Late-Stage Functionalization of Non-Steroidal Anti-Inflammatory Drugs. Chemistry 2024; 30:e202303130. [PMID: 38224207 DOI: 10.1002/chem.202303130] [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: 09/26/2023] [Indexed: 01/16/2024]
Abstract
Anilines are core motifs in a variety of important molecules including medicines, materials and agrochemicals. We report a straightforward procedure that allows access to new chemical space of anilines via their para-C-H alkylation. The method utilizes commercially available catalytic H2 O ⋅ B(C6 F5 )3 and is highly selective for para-C-alkylation (over N-alkylation and ortho-C-alkylation) of anilines, with a wide scope in both the aniline substrates and alkene coupling partners. Readily available alkenes are used, and include new classes of alkene for the first time. The mild reaction conditions have allowed the procedure to be applied to the late-stage-functionalization of non-steroidal anti-inflammatory drugs (NSAIDs), including fenamic acids and diclofenac. The formed novel NSAID derivatives display improved anti-inflammatory properties over the parent NSAID structure.
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Affiliation(s)
- Laura Winfrey
- School of Chemistry, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Lei Yun
- School of Chemistry, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Ginevra Passeri
- School of Chemistry, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | | | - Alexander P Pulis
- School of Chemistry, University of Leicester, Leicester, LE1 7RH, United Kingdom
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48
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Moulton DE, Aubert-Kato N, Almet AA, Sato A. A multiscale computational framework for the development of spines in molluscan shells. PLoS Comput Biol 2024; 20:e1011835. [PMID: 38427695 PMCID: PMC10936779 DOI: 10.1371/journal.pcbi.1011835] [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: 04/18/2023] [Revised: 03/13/2024] [Accepted: 01/16/2024] [Indexed: 03/03/2024] Open
Abstract
From mathematical models of growth to computer simulations of pigmentation, the study of shell formation has given rise to an abundant number of models, working at various scales. Yet, attempts to combine those models have remained sparse, due to the challenge of combining categorically different approaches. In this paper, we propose a framework to streamline the process of combining the molecular and tissue scales of shell formation. We choose these levels as a proxy to link the genotype level, which is better described by molecular models, and the phenotype level, which is better described by tissue-level mechanics. We also show how to connect observations on shell populations to the approach, resulting in collections of molecular parameters that may be associated with different populations of real shell specimens. The approach is as follows: we use a Quality-Diversity algorithm, a type of black-box optimization algorithm, to explore the range of concentration profiles emerging as solutions of a molecular model, and that define growth patterns for the mechanical model. At the same time, the mechanical model is simulated over a wide range of growth patterns, resulting in a variety of spine shapes. While time-consuming, these steps only need to be performed once and then function as look-up tables. Actual pictures of shell spines can then be matched against the list of existing spine shapes, yielding a potential growth pattern which, in turn, gives us matching molecular parameters. The framework is modular, such that models can be easily swapped without changing the overall working of the method. As a demonstration of the approach, we solve specific molecular and mechanical models, adapted from available theoretical studies on molluscan shells, and apply the multiscale framework to evaluate the characteristics of spines from three distinct populations of Turbo sazae.
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Affiliation(s)
- Derek E. Moulton
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | | | - Axel A. Almet
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, United States of America
- Department of Mathematics, University of California, Irvine, California, United States of America
| | - Atsuko Sato
- Department of Biology, Ochanomizu University, Tokyo, Japan
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49
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Dodel M, Guiducci G, Dermit M, Krishnamurthy S, Alard EL, Capraro F, Rekad Z, Stojic L, Mardakheh FK. TREX reveals proteins that bind to specific RNA regions in living cells. Nat Methods 2024; 21:423-434. [PMID: 38374261 PMCID: PMC10927567 DOI: 10.1038/s41592-024-02181-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA regions in living cells and under endogenous settings. Here we introduce TREX (targeted RNase H-mediated extraction of crosslinked RBPs)-a highly sensitive approach for identifying proteins that directly bind to specific RNA regions in living cells. We demonstrate that TREX outperforms existing methods in identifying known interactors of U1 snRNA, and reveals endogenous region-specific interactors of NORAD long noncoding RNA. Using TREX, we generated a comprehensive region-by-region interactome for 45S rRNA, uncovering both established and previously unknown interactions that regulate ribosome biogenesis. With its applicability to different cell types, TREX is an RNA-centric tool for unbiased positional mapping of endogenous RNA-protein interactions in living cells.
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Affiliation(s)
- Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Giulia Guiducci
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Maria Dermit
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Sneha Krishnamurthy
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Emilie L Alard
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Federica Capraro
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Zeinab Rekad
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lovorka Stojic
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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50
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Yuan Y, Pu SD, Pérez-Osorio MA, Li Z, Zhang S, Yang S, Liu B, Gong C, Menon AS, Piper LFJ, Gao X, Bruce PG, Robertson AW. Diagnosing the Electrostatic Shielding Mechanism for Dendrite Suppression in Aqueous Zinc Batteries. Adv Mater 2024; 36:e2307708. [PMID: 37879760 DOI: 10.1002/adma.202307708] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/17/2023] [Indexed: 10/27/2023]
Abstract
Aqueous zinc electrolytes offer the potential for cheaper rechargeable batteries due to their safe compatibility with the high capacity metal anode; yet, they are stymied by irregular zinc deposition and consequent dendrite growth. Suppressing dendrite formation by tailoring the electrolyte is a proven approach from lithium batteries; yet, the underlying mechanistic understanding that guides such tailoring does not necessarily directly translate from one system to the other. Here, it is shown that the electrostatic shielding mechanism, a fundamental concept in electrolyte engineering for stable metal anodes, has different consequences for the plating morphology in aqueous zinc batteries. Operando electrochemical transmission electron microscopy is used to directly observe the zinc nucleation and growth under different electrolyte compositions and reveal that electrostatic shielding additive suppresses dendrites by inhibiting secondary zinc nucleation along the (100) edges of existing primary deposits and encouraging preferential deposition on the (002) faces, leading to a dense and block-like zinc morphology. The strong influence of the crystallography of Zn on the electrostatic shielding mechanism is further confirmed with Zn||Ti cells and density functional theory modeling. This work demonstrates the importance of considering the unique aspects of the aqueous zinc battery system when using concepts from other battery chemistries.
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Affiliation(s)
- Yi Yuan
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK
| | - Shengda D Pu
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK
| | | | - Zixuan Li
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK
| | - Shengming Zhang
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK
| | - Sixie Yang
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK
| | - Boyang Liu
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK
| | - Chen Gong
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK
| | | | | | - Xiangwen Gao
- Future Battery Research Center, Global Institute of Future Technology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Peter G Bruce
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Alex W Robertson
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
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