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Xiao S, Xie L, Gao Y, Wang M, Geng W, Wu X, Rodriguez RD, Cheng L, Qiu L, Cheng C. Artificial Phages with Biocatalytic Spikes for Synergistically Eradicating Antibiotic-Resistant Biofilms. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2404411. [PMID: 38837809 DOI: 10.1002/adma.202404411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/01/2024] [Indexed: 06/07/2024]
Abstract
Antibiotic-resistant pathogens have become a global public health crisis, especially biofilm-induced refractory infections. Efficient, safe, and biofilm microenvironment (BME)-adaptive therapeutic strategies are urgently demanded to combat antibiotic-resistant biofilms. Here, inspired by the fascinating biological structures and functions of phages, the de novo design of a spiky Ir@Co3O4 particle is proposed to serve as an artificial phage for synergistically eradicating antibiotic-resistant Staphylococcus aureus biofilms. Benefiting from the abundant nanospikes and highly active Ir sites, the synthesized artificial phage can simultaneously achieve efficient biofilm accumulation, extracellular polymeric substance (EPS) penetration, and superior BME-adaptive reactive oxygen species (ROS) generation, thus facilitating the in situ ROS delivery and enhancing the biofilm eradication. Moreover, metabolomics found that the artificial phage obstructs the bacterial attachment to EPS, disrupts the maintenance of the BME, and fosters the dispersion and eradication of biofilms by down-regulating the associated genes for the biosynthesis and preservation of both intra- and extracellular environments. The in vivo results demonstrate that the artificial phage can treat the biofilm-induced recalcitrant infected wounds equivalent to vancomycin. It is suggested that the design of this spiky artificial phage with synergistic "penetrate and eradicate" capability to treat antibiotic-resistant biofilms offers a new pathway for bionic and nonantibiotic disinfection.
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Affiliation(s)
- Sutong Xiao
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Department of Medical Ultrasound, West China Hospital, Sichuan University, Chengdu, 610065, China
| | - Lan Xie
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Department of Medical Ultrasound, West China Hospital, Sichuan University, Chengdu, 610065, China
| | - Yang Gao
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Department of Medical Ultrasound, West China Hospital, Sichuan University, Chengdu, 610065, China
| | - Mao Wang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Department of Medical Ultrasound, West China Hospital, Sichuan University, Chengdu, 610065, China
| | - Wei Geng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Department of Medical Ultrasound, West China Hospital, Sichuan University, Chengdu, 610065, China
| | - Xizheng Wu
- Max Planck Institute for Chemical Physics of Solids, 01187, Dresden, Germany
| | - Raul D Rodriguez
- Tomsk Polytechnic University, Lenin ave. 30, Tomsk, 634050, Russia
| | - Liang Cheng
- Department of Materials Science and Engineering, The Macau University of Science and Technology, Taipa, Macau, 999078, China
| | - Li Qiu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Department of Medical Ultrasound, West China Hospital, Sichuan University, Chengdu, 610065, China
| | - Chong Cheng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Department of Medical Ultrasound, West China Hospital, Sichuan University, Chengdu, 610065, China
- Department of Endodontics, Department of Orthodontics, State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
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Babonis LS. On the evolutionary developmental biology of the cell. Trends Genet 2024:S0168-9525(24)00150-1. [PMID: 38971670 DOI: 10.1016/j.tig.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/08/2024]
Abstract
Organisms are complex assemblages of cells, cells that produce light, shoot harpoons, and secrete glue. Therefore, identifying the mechanisms that generate novelty at the level of the individual cell is essential for understanding how multicellular life evolves. For decades, the field of evolutionary developmental biology (Evo-Devo) has been developing a framework for connecting genetic variation that arises during embryonic development to the emergence of diverse adult forms. With increasing access to new single cell 'omics technologies and an array of techniques for manipulating gene expression, we can now extend these inquiries inward to the level of the individual cell. In this opinion, I argue that applying an Evo-Devo framework to single cells makes it possible to explore the natural history of cells, where this was once only possible at the organismal level.
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Affiliation(s)
- Leslie S Babonis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
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Surm JM, Landau M, Columbus-Shenkar YY, Moran Y. Sea Anemone Membrane Attack Complex/Perforin Superfamily Demonstrates an Evolutionary Transitional State between Venomous and Developmental Functions. Mol Biol Evol 2024; 41:msae082. [PMID: 38676945 PMCID: PMC11090067 DOI: 10.1093/molbev/msae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/08/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
Gene duplication is a major force driving evolutionary innovation. A classic example is generating new animal toxins via duplication of physiological protein-encoding genes and recruitment into venom. While this process drives the innovation of many animal venoms, reverse recruitment of toxins into nonvenomous cells remains unresolved. Using comparative genomics, we find members of the Membrane Attack Complex and Perforin Family (MAC) have been recruited into venom-injecting cells (cnidocytes), in soft and stony corals and sea anemones, suggesting that the ancestral MAC was a cnidocyte expressed toxin. Further investigation into the model sea anemone Nematostella vectensis reveals that three members have undergone Nematostella-specific duplications leading to their reverse recruitment into endomesodermal cells. Furthermore, simultaneous knockdown of all three endomesodermally expressed MACs leads to mis-development, supporting that these paralogs have nonvenomous function. By resolving the evolutionary history and function of MACs in Nematostella, we provide the first proof for reverse recruitment from venom to organismal development.
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Affiliation(s)
- Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Morani Landau
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yaara Y Columbus-Shenkar
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
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Foster B, Hugosson F, Scucchia F, Enjolras C, Babonis LS, Hoaen W, Martindale MQ. A novel in vivo system to study coral biomineralization in the starlet sea anemone, Nematostella vectensis. iScience 2024; 27:109131. [PMID: 38384856 PMCID: PMC10879693 DOI: 10.1016/j.isci.2024.109131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/18/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
Coral conservation requires a mechanistic understanding of how environmental stresses disrupt biomineralization, but progress has been slow, primarily because corals are not easily amenable to laboratory research. Here, we highlight how the starlet sea anemone, Nematostella vectensis, can serve as a model to interrogate the cellular mechanisms of coral biomineralization. We have developed transgenic constructs using biomineralizing genes that can be injected into Nematostella zygotes and designed such that translated proteins may be purified for physicochemical characterization. Using fluorescent tags, we confirm the ectopic expression of the coral biomineralizing protein, SpCARP1, in Nematostella. We demonstrate via calcein staining that SpCARP1 concentrates calcium ions in Nematostella, likely initiating the formation of mineral precursors, consistent with its suspected role in corals. These results lay a fundamental groundwork for establishing Nematostella as an in vivo system to explore the evolutionary and cellular mechanisms of coral biomineralization, improve coral conservation efforts, and even develop novel biomaterials.
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Affiliation(s)
- Brent Foster
- The Whitney Laboratory for Marine Bioscience, Department of Biology, University of Florida, Gainesville, FL 32080, USA
| | - Fredrik Hugosson
- The Whitney Laboratory for Marine Bioscience, Department of Biology, University of Florida, Gainesville, FL 32080, USA
| | - Federica Scucchia
- The Whitney Laboratory for Marine Bioscience, Department of Biology, University of Florida, Gainesville, FL 32080, USA
| | - Camille Enjolras
- The Whitney Laboratory for Marine Bioscience, Department of Biology, University of Florida, Gainesville, FL 32080, USA
- Institute of Human Genetics, CNRS, Montpellier 34090, France
| | - Leslie S. Babonis
- The Whitney Laboratory for Marine Bioscience, Department of Biology, University of Florida, Gainesville, FL 32080, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - William Hoaen
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Mark Q. Martindale
- The Whitney Laboratory for Marine Bioscience, Department of Biology, University of Florida, Gainesville, FL 32080, USA
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Warner JF, Besemer R, Schickle A, Borbee E, Changsut IV, Sharp K, Babonis LS. Microinjection, gene knockdown, and CRISPR-mediated gene knock-in in the hard coral, Astrangia poculata. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567385. [PMID: 38948709 PMCID: PMC11213136 DOI: 10.1101/2023.11.16.567385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Cnidarians have become valuable models for understanding many aspects of developmental biology including the evolution of body plan diversity, novel cell type specification, and regeneration. Most of our understanding of gene function during early development in cnidarians comes from a small number of experimental systems including the sea anemone, Nematostella vectensis. Few molecular tools have been developed for use in hard corals, limiting our understanding of this diverse and ecologically important clade. Here, we report the development of a suite of tools for manipulating and analyzing gene expression during early development in the northern star coral, Astrangia poculata. We present methods for gene knockdown using short hairpin RNAs, gene overexpression using exogenous mRNAs, and endogenous gene tagging using CRISPR-mediated gene knock-in. Combined with our ability to control spawning in the laboratory, these tools make A. poculata a tractable experimental system for investigative studies of coral development. Further application of these tools will enable functional analyses of embryonic patterning and morphogenesis across Anthozoa and open new frontiers in coral biology research.
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Affiliation(s)
- Jacob F. Warner
- Department of Biology and Marine Biology, UNC Wilmington, Wilmington, NC, 28409
| | - Ryan Besemer
- Department of Biology and Marine Biology, UNC Wilmington, Wilmington, NC, 28409
| | - Alicia Schickle
- Feinstein School of Social and Natural Sciences, Roger Williams University, Bristol, RI 02871
| | - Erin Borbee
- Department of Biology, Texas State University, San Marcos, TX, 78666
| | | | - Koty Sharp
- Feinstein School of Social and Natural Sciences, Roger Williams University, Bristol, RI 02871
| | - Leslie S. Babonis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
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