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Wang S, Tian Y, Bi Y, Meng F, Qiu C, Yu J, Liu L, Zhao Y. Recovery strategies and mechanisms of anammox reaction following inhibition by environmental factors: A review. ENVIRONMENTAL RESEARCH 2024; 252:118824. [PMID: 38588911 DOI: 10.1016/j.envres.2024.118824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/10/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
Anaerobic ammonium oxidation (anammox) is a promising biological method for treating nitrogen-rich, low-carbon wastewater. However, the application of anammox technology in actual engineering is easily limited by environmental factors. Considerable progress has been investigated in recent years in anammox restoration strategies, significantly addressing the challenge of poor reaction performance following inhibition. This review systematically outlines the strategies employed to recover anammox performance following inhibition by conventional environmental factors and emerging pollutants. Additionally, comprehensive summaries of strategies aimed at promoting anammox activity and enhancing nitrogen removal performance provide valuable insights into the current research landscape in this field. The review contributes to a comprehensive understanding of restoration strategies of anammox-based technologies.
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Affiliation(s)
- Shaopo Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Yu Tian
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Yanmeng Bi
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Fansheng Meng
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Chunsheng Qiu
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Jingjie Yu
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Lingjie Liu
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China.
| | - Yingxin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China.
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Toledo PL, Gianotti AR, Vazquez DS, Ermácora MR. Protein nanocondensates: the next frontier. Biophys Rev 2023; 15:515-530. [PMID: 37681092 PMCID: PMC10480383 DOI: 10.1007/s12551-023-01105-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/21/2023] [Indexed: 09/09/2023] Open
Abstract
Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.
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Affiliation(s)
- Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
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3
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Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms. THE ISME JOURNAL 2023; 17:803-812. [PMID: 36871068 DOI: 10.1038/s41396-023-01388-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
Extracellular polymeric substances (EPS) are core biofilm components, yet how they mediate interactions within and contribute to the structuring of biofilms is largely unknown, particularly for non-culturable microbial communities that predominate in environmental habitats. To address this knowledge gap, we explored the role of EPS in an anaerobic ammonium oxidation (anammox) biofilm. An extracellular glycoprotein, BROSI_A1236, from an anammox bacterium, formed envelopes around the anammox cells, supporting its identification as a surface (S-) layer protein. However, the S-layer protein also appeared at the edge of the biofilm, in close proximity to the polysaccharide-coated filamentous Chloroflexi bacteria but distal to the anammox bacterial cells. The Chloroflexi bacteria assembled into a cross-linked network at the edge of the granules and surrounding anammox cell clusters, with the S-layer protein occupying the space around the Chloroflexi. The anammox S-layer protein was also abundant at junctions between Chloroflexi cells. Thus, the S-layer protein is likely transported through the matrix as an EPS and also acts as an adhesive to facilitate the assembly of filamentous Chloroflexi into a three-dimensional biofilm lattice. The spatial distribution of the S-layer protein within the mixed species biofilm suggests that it is a "public-good" EPS, which facilitates the assembly of other bacteria into a framework for the benefit of the biofilm community, and enables key syntrophic relationships, including anammox.
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Wong LL, Mugunthan S, Kundukad B, Ho JCS, Rice SA, Hinks J, Seviour T, Parikh AN, Kjelleberg S. Microbial biofilms are shaped by the constant dialogue between biological and physical forces in the extracellular matrix. Environ Microbiol 2023; 25:199-208. [PMID: 36502515 DOI: 10.1111/1462-2920.16306] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Affiliation(s)
- Lan Li Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sudarsan Mugunthan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Binu Kundukad
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - James Chin Shing Ho
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, Singapore
| | - Scott A Rice
- CSIRO, Agriculture and Food, Microbiomes for One Systems Health, Canberra, Australia
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,WATEC Aarhus University Centre for Water Technology, Aarhus, Denmark
| | - Atul N Parikh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, Singapore.,Department of Biomedical Engineering, University of California, Davis, California, USA
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Lu Y, Natarajan G, Nguyen TQN, Thi SS, Arumugam K, Seviour T, Williams RBH, Wuertz S, Law Y. Controlling anammox speciation and biofilm attachment strategy using N-biotransformation intermediates and organic carbon levels. Sci Rep 2022; 12:21720. [PMID: 36522527 PMCID: PMC9755228 DOI: 10.1038/s41598-022-26069-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Conventional nitrogen removal in wastewater treatment requires a high oxygen and energy input. Anaerobic ammonium oxidation (anammox), the single-step conversion of ammonium and nitrite to nitrogen gas, is a more energy and cost effective alternative applied extensively to sidestream wastewater treatment. It would also be a mainstream treatment option if species diversity and physiology were better understood. Anammox bacteria were enriched up to 80%, 90% and 50% relative abundance, from a single inoculum, under standard enrichment conditions with either stepwise-nitrite and ammonia concentration increases (R1), nitric oxide supplementation (R2), or complex organic carbon from mainstream wastewater (R3), respectively. Candidatus Brocadia caroliniensis predominated in all reactors, but a shift towards Ca. Brocadia sinica occurred at ammonium and nitrite concentrations > 270 mg NH4-N L-1 and 340 mg NO2-N L-1 respectively. With NO present, heterotrophic growth was inhibited, and Ca. Jettenia coexisted with Ca. B. caroliniensis before diminishing as nitrite increased to 160 mg NO2-N L-1. Organic carbon supplementation led to the emergence of heterotrophic communities that coevolved with Ca. B. caroliniensis. Ca. B. caroliniensis and Ca. Jettenia preferentially formed biofilms on surfaces, whereas Ca. Brocadia sinica formed granules in suspension. Our results indicate that multiple anammox bacteria species co-exist and occupy sub-niches in anammox reactors, and that the dominant population can be reversibly shifted by, for example, changing nitrogen load (i.e. high nitrite concentration favors Ca. Brocadia caroliniensis). Speciation has implications for wastewater process design, where the optimum cell immobilization strategy (i.e. carriers vs granules) depends on which species dominates.
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Affiliation(s)
- Yang Lu
- grid.484638.50000 0004 7703 9448Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551 Singapore ,grid.1003.20000 0000 9320 7537Present Address: The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072 Australia
| | - Gayathri Natarajan
- grid.484638.50000 0004 7703 9448Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551 Singapore
| | - Thi Quynh Ngoc Nguyen
- grid.484638.50000 0004 7703 9448Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551 Singapore ,grid.185448.40000 0004 0637 0221Present Address: Agency for Science, Technology and Research, Singapore, 138632 Singapore
| | - Sara Swa Thi
- grid.484638.50000 0004 7703 9448Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551 Singapore
| | - Krithika Arumugam
- grid.484638.50000 0004 7703 9448Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551 Singapore
| | - Thomas Seviour
- grid.484638.50000 0004 7703 9448Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551 Singapore ,grid.7048.b0000 0001 1956 2722Centre for Water Technology (WATEC) & Department of Biological and Chemical Engineering, Aarhus University, Universitetsbyen 36, 8000 Aarhus C, Denmark
| | - Rohan B. H. Williams
- grid.484638.50000 0004 7703 9448Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077 Singapore
| | - Stefan Wuertz
- grid.484638.50000 0004 7703 9448Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551 Singapore ,grid.59025.3b0000 0001 2224 0361School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798 Singapore
| | - Yingyu Law
- grid.484638.50000 0004 7703 9448Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551 Singapore
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6
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Vazquez DS, Toledo PL, Gianotti AR, Ermácora MR. Protein conformation and biomolecular condensates. Curr Res Struct Biol 2022; 4:285-307. [PMID: 36164646 PMCID: PMC9508354 DOI: 10.1016/j.crstbi.2022.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 10/27/2022] Open
Abstract
Protein conformation and cell compartmentalization are fundamental concepts and subjects of vast scientific endeavors. In the last two decades, we have witnessed exciting advances that unveiled the conjunction of these concepts. An avalanche of studies highlighted the central role of biomolecular condensates in membraneless subcellular compartmentalization that permits the spatiotemporal organization and regulation of myriads of simultaneous biochemical reactions and macromolecular interactions. These studies have also shown that biomolecular condensation, driven by multivalent intermolecular interactions, is mediated by order-disorder transitions of protein conformation and by protein domain architecture. Conceptually, protein condensation is a distinct level in protein conformational landscape in which collective folding of large collections of molecules takes place. Biomolecular condensates arise by the physical process of phase separation and comprise a variety of bodies ranging from membraneless organelles to liquid condensates to solid-like conglomerates, spanning lengths from mesoscopic clusters (nanometers) to micrometer-sized objects. In this review, we summarize and discuss recent work on the assembly, composition, conformation, material properties, thermodynamics, regulation, and functions of these bodies. We also review the conceptual framework for future studies on the conformational dynamics of condensed proteins in the regulation of cellular processes.
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Affiliation(s)
- Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
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7
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Xiao R, Zhu W, Zheng Y, Xu S, Lu H. Active assimilators of soluble microbial products produced by wastewater anammox bacteria and their roles revealed by DNA-SIP coupled to metagenomics. ENVIRONMENT INTERNATIONAL 2022; 164:107265. [PMID: 35526296 DOI: 10.1016/j.envint.2022.107265] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/11/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Heterotrophic bacteria grow on influent organics or soluble microbial products (SMP) in wastewater anammox processes, playing key roles in facilitating microbial aggregation and reducing excess nitrate. The overgrowth of heterotrophs represents one of the major causes of anammox process failure, while the metabolic functions of coexisting heterotrophs and their roles in anammox process remain vague. This study aimed at revealing metabolic interactions between AnAOB and active SMP assimilators by integrating 13C DNA-stable isotope probing, metabolomic and metagenomic approaches. Glycine, aspartate, and glutamate with low biosynthetic energy cost were the major SMP components produced by AnAOB (net yield: 44.8, 10.4, 8.1 mg·g NH4+-N-1). Glycine was likely synthesized by AnAOB via the reductive glycine pathway which is oxygen-tolerant, supporting heterotrophic growth. Fermentative Chloroflexi bacterium OLB13, denitrifying Gemmatimonadaceae and Burkholderiaceae bacterium JOSHI-001 were active SMP assimilators, which were prevalent in globally distributed wastewater anammox reactors as core taxa. They likely formed a mutualistic relationship with auxotrophic Ca. Kuenenia by providing necessities such as methionine, folate, 4'-phosphopantetheine, and molybdopterin cofactor, and receiving vitamin B12 for methionine synthesis. For the first time, the identify and metabolic features of SMP assimilators in wastewater anammox communities were revealed. Supplying necessities secreted by heterotrophs could be helpful to the endeavor of AnAOB enrichment. Practically, maintaining active but not overgrown SMP assimilators is critical to efficient and stable operation of wastewater anammox processes.
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Affiliation(s)
- Rui Xiao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Wanlu Zhu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yuanzhu Zheng
- Wenzhou Institute of Eco-environmental Sciences, Wenzhou, China
| | - Shaoyi Xu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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8
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Forman-Kay JD, Ditlev JA, Nosella ML, Lee HO. What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates? RNA (NEW YORK, N.Y.) 2022; 28:36-47. [PMID: 34772786 PMCID: PMC8675286 DOI: 10.1261/rna.079026.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Exciting recent work has highlighted that numerous cellular compartments lack encapsulating lipid bilayers (often called "membraneless organelles"), and that their structure and function are central to the regulation of key biological processes, including transcription, RNA splicing, translation, and more. These structures have been described as "biomolecular condensates" to underscore that biomolecules can be significantly concentrated in them. Many condensates, including RNA granules and processing bodies, are enriched in proteins and nucleic acids. Biomolecular condensates exhibit a range of material states from liquid- to gel-like, with the physical process of liquid-liquid phase separation implicated in driving or contributing to their formation. To date, in vitro studies of phase separation have provided mechanistic insights into the formation and function of condensates. However, the link between the often micron-sized in vitro condensates with nanometer-sized cellular correlates has not been well established. Consequently, questions have arisen as to whether cellular structures below the optical resolution limit can be considered biomolecular condensates. Similarly, the distinction between condensates and discrete dynamic hub complexes is debated. Here we discuss the key features that define biomolecular condensates to help understand behaviors of structures containing and generating RNA.
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Affiliation(s)
- Julie D Forman-Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jonathon A Ditlev
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Michael L Nosella
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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