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Yehya N, Booth TJ, Ardhanari GD, Thompson JM, Lam LKM, Till JE, Mai MV, Keim G, McKeone DJ, Halstead ES, Lahni P, Varisco BM, Zhou W, Carpenter EL, Christie JD, Mangalmurti NS. Inflammatory and tissue injury marker dynamics in pediatric acute respiratory distress syndrome. J Clin Invest 2024:e177896. [PMID: 38573766 DOI: 10.1172/jci177896] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND The molecular signature of pediatric acute respiratory distress syndrome (ARDS) is poorly described, and the degree to which hyperinflammation or specific tissue injury contributes to outcomes is unknown. Therefore, we profiled inflammation and tissue injury dynamics over the first 7 days of ARDS, and associated specific biomarkers with mortality, persistent ARDS, and persistent multiple organ dysfunction syndrome (MODS). METHODS In a single-center prospective cohort of intubated pediatric ARDS, we collected plasma on days 0, 3, and 7. Nineteen biomarkers reflecting inflammation, tissue injury, and damage associated molecular patterns were measured. We assessed the relationship between biomarkers and trajectories with mortality, persistent ARDS, or persistent MODS using multivariable mixed effect models. RESULTS In 279 subjects (64 [23%] non-survivors), hyperinflammatory cytokines, tissue injury markers, and DAMPs were higher in non-survivors. Survivors and non-survivors showed different biomarker trajectories. IL-1α, sTNFR1, ANG2, and SPD increased in non-survivors, while DAMPs remained persistently elevated. ANG2 and P3NP were associated with persistent ARDS, whereas multiple cytokines, tissue injury markers, and DAMPs were associated with persistent MODS. Corticosteroid use did not impact the association of biomarker levels or trajectory with mortality. CONCLUSIONS Pediatric ARDS survivors and non-survivors had distinct biomarker trajectories, with cytokines, endothelial and alveolar epithelial injury, and DAMPs elevated in non-survivors. Mortality markers overlapped with markers associated with persistent MODS, rather than persistent ARDS.
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Affiliation(s)
- Nadir Yehya
- Division of Pediatric Critical Care, Department of Anesthesiology and Criti, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, United States of America
| | - Thomas J Booth
- Division of Pediatric Critical Care, Department of Anesthesiology and Criti, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, United States of America
| | - Gnana D Ardhanari
- Division of Pediatric Cardiac Critical Care Medicine, Children's Heart Inst, Memorial Hermann Hospital, University of Texas Health McGovern Medical School, Houston, United States of America
| | - Jill M Thompson
- Division of Pediatric Critical Care, Department of Anesthesiology and Criti, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, United States of America
| | - L K Metthew Lam
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Jacob E Till
- Division of Hematology-Oncology, Department of Medicine, Abramson Cancer Ce, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Mark V Mai
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University, Atlanta, United States of America
| | - Garrett Keim
- Division of Pediatric Critical Care, Department of Anesthesiology and Criti, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, United States of America
| | - Daniel J McKeone
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, United States of America
| | - E Scott Halstead
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, United States of America
| | - Patrick Lahni
- Division of Critical Care Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Brian M Varisco
- Section of Critical Care, Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, United States of America
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, United States of America
| | - Erica L Carpenter
- Division of Hematology-Oncology, Department of Medicine, Abramson Cancer Ce, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Jason D Christie
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Nilam S Mangalmurti
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
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2
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van den Belt M, Gilchrist C, Booth TJ, Chooi YH, Medema MH, Alanjary M. CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters. BMC Bioinformatics 2023; 24:181. [PMID: 37131131 PMCID: PMC10155394 DOI: 10.1186/s12859-023-05311-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/27/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Co-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important examples include Biosynthetic Gene Clusters (BGCs) that produce specialized metabolites with medicinal, agricultural, and industrial value (e.g. antimicrobials). Comparative analysis of BGCs can aid in the discovery of novel metabolites by highlighting distribution and identifying variants in public genomes. Unfortunately, gene-cluster-level homology detection remains inaccessible, time-consuming and difficult to interpret. RESULTS The comparative gene cluster analysis toolbox (CAGECAT) is a rapid and user-friendly platform to mitigate difficulties in comparative analysis of whole gene clusters. The software provides homology searches and downstream analyses without the need for command-line or programming expertise. By leveraging remote BLAST databases, which always provide up-to-date results, CAGECAT can yield relevant matches that aid in the comparison, taxonomic distribution, or evolution of an unknown query. The service is extensible and interoperable and implements the cblaster and clinker pipelines to perform homology search, filtering, gene neighbourhood estimation, and dynamic visualisation of resulting variant BGCs. With the visualisation module, publication-quality figures can be customized directly from a web-browser, which greatly accelerates their interpretation via informative overlays to identify conserved genes in a BGC query. CONCLUSION Overall, CAGECAT is an extensible software that can be interfaced via a standard web-browser for whole region homology searches and comparison on continually updated genomes from NCBI. The public web server and installable docker image are open source and freely available without registration at: https://cagecat.bioinformatics.nl .
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Affiliation(s)
- Matthias van den Belt
- Bioinformatics Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
| | - Cameron Gilchrist
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Thomas J Booth
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands.
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3
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Lacey HJ, Chen R, Vuong D, Lacey E, Rutledge PJ, Chooi YH, Piggott AM, Booth TJ. Resorculins: hybrid polyketide macrolides from Streptomyces sp. MST-91080. Org Biomol Chem 2023; 21:2531-2538. [PMID: 36876905 DOI: 10.1039/d2ob02332f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Fourteen-membered macrolides are a class of compounds with significant clinical value as antibacterial agents. As part of our ongoing investigation into the metabolites of Streptomyces sp. MST-91080, we report the discovery of resorculins A and B, unprecedented 3,5-dihydroxybenzoic acid (α-resorcylic acid)-containing 14-membered macrolides. We sequenced the genome of MST-91080 and identified the putative resorculin biosynthetic gene cluster (rsn BGC). The rsn BGC is hybrid of type I and type III polyketide synthases. Bioinformatic analysis revealed that the resorculins are relatives of known hybrid polyketides: kendomycin and venemycin. Resorculin A exhibited antibacterial activity against Bacillus subtilis (MIC 19.8 μg mL-1), while resorculin B showed cytotoxic activity against the NS-1 mouse myeloma cell line (IC50 3.6 μg mL-1).
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Affiliation(s)
- Heather J Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Rachel Chen
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
- School of Natural Sciences, Macquarie University, NSW 2109, Australia
| | - Peter J Rutledge
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, NSW 2109, Australia
| | - Thomas J Booth
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
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4
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Booth TJ, Bozhüyük KAJ, Liston JD, Batey SFD, Lacey E, Wilkinson B. Bifurcation drives the evolution of assembly-line biosynthesis. Nat Commun 2022; 13:3498. [PMID: 35715397 PMCID: PMC9205934 DOI: 10.1038/s41467-022-30950-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
Reprogramming biosynthetic assembly-lines is a topic of intense interest. This is unsurprising as the scaffolds of most antibiotics in current clinical use are produced by such pathways. The modular nature of assembly-lines provides a direct relationship between the sequence of enzymatic domains and the chemical structure of the product, but rational reprogramming efforts have been met with limited success. To gain greater insight into the design process, we wanted to examine how Nature creates assembly-lines and searched for biosynthetic pathways that might represent evolutionary transitions. By examining the biosynthesis of the anti-tubercular wollamides, we uncover how whole gene duplication and neofunctionalization can result in pathway bifurcation. We show that, in the case of the wollamide biosynthesis, neofunctionalization is initiated by intragenomic recombination. This pathway bifurcation leads to redundancy, providing the genetic robustness required to enable large structural changes during the evolution of antibiotic structures. Should the new product be non-functional, gene loss can restore the original genotype. However, if the new product confers an advantage, depreciation and eventual loss of the original gene creates a new linear pathway. This provides the blind watchmaker equivalent to the design, build, test cycle of synthetic biology.
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Affiliation(s)
- Thomas J Booth
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.,School of Molecular Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Kenan A J Bozhüyük
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
| | - Jonathon D Liston
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Sibyl F D Batey
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
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5
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Gilchrist CLM, Booth TJ, van Wersch B, van Grieken L, Medema MH, Chooi YH. cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters. Bioinform Adv 2021; 1:vbab016. [PMID: 36700093 PMCID: PMC9710679 DOI: 10.1093/bioadv/vbab016] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 01/28/2023]
Abstract
Motivation Genes involved in coordinated biological pathways, including metabolism, drug resistance and virulence, are often collocalized as gene clusters. Identifying homologous gene clusters aids in the study of their function and evolution, however, existing tools are limited to searching local sequence databases. Tools for remotely searching public databases are necessary to keep pace with the rapid growth of online genomic data. Results Here, we present cblaster, a Python-based tool to rapidly detect collocated genes in local and remote databases. cblaster is easy to use, offering both a command line and a user-friendly graphical user interface. It generates outputs that enable intuitive visualizations of large datasets and can be readily incorporated into larger bioinformatic pipelines. cblaster is a significant update to the comparative genomics toolbox. Availability and implementation cblaster source code and documentation is freely available from GitHub under the MIT license (github.com/gamcil/cblaster). Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Cameron L M Gilchrist
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia,To whom correspondence should be addressed. or or
| | - Thomas J Booth
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Bram van Wersch
- Bioinformatics Group, Wageningen University, Wageningen 6708PB, The Netherlands
| | - Liana van Grieken
- Bioinformatics Group, Wageningen University, Wageningen 6708PB, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen 6708PB, The Netherlands,To whom correspondence should be addressed. or or
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia,To whom correspondence should be addressed. or or
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6
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Morshed MT, Lacey E, Vuong D, Lacey AE, Lean SS, Moggach SA, Karuso P, Chooi YH, Booth TJ, Piggott AM. Chlorinated metabolites from Streptomyces sp. highlight the role of biosynthetic mosaics and superclusters in the evolution of chemical diversity. Org Biomol Chem 2021; 19:6147-6159. [PMID: 34180937 DOI: 10.1039/d1ob00600b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
LCMS-guided screening of a library of biosynthetically talented bacteria and fungi identified Streptomyces sp. MST- as a prolific producer of chlorinated metabolites. We isolated and characterised six new and nine reported compounds from MST-, belonging to three discrete classes - the depsipeptide svetamycins, the indolocarbazole borregomycins and the aromatic polyketide anthrabenzoxocinones. Following genome sequencing of MST-, we describe, for the first time, the svetamycin biosynthetic gene cluster (sve), its mosaic structure and its relationship to several distantly related gene clusters. Our analysis of the sve cluster suggested that the reported stereostructures of the svetamycins may be incorrect. This was confirmed by single-crystal X-ray diffraction analysis, allowing us to formally revise the absolute configurations of svetamycins A-G. We also show that the borregomycins and anthrabenzoxocinones are encoded by a single supercluster (bab) implicating superclusters as potential nucleation points for the evolution of biosynthetic gene clusters. These clusters highlight how individual enzymes and functional subclusters can be co-opted during the formation of biosynthetic gene clusters, providing a rare insight into the poorly understood mechanisms underpinning the evolution of chemical diversity.
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Affiliation(s)
- Mahmud T Morshed
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
| | - Ernest Lacey
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia. and Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Alastair E Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Soo Sum Lean
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.
| | - Stephen A Moggach
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.
| | - Peter Karuso
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.
| | - Thomas J Booth
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia.
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7
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Booth TJ, Kalaitzis JA, Vuong D, Crombie A, Lacey E, Piggott AM, Wilkinson B. Production of novel pladienolide analogues through native expression of a pathway-specific activator. Chem Sci 2020; 11:8249-8255. [PMID: 34094178 PMCID: PMC8163091 DOI: 10.1039/d0sc01928c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Aberrant splicing of pre-mRNA is implicated in many human genetic disorders. Small molecules that target the spliceosome are important leads as therapeutics and research tools, and one compound of significant interest is the polyketide natural product pladienolide B. Here, we describe the reactivation of quiescent pladienolide B production in the domesticated lab strain Streptomyces platensis AS6200 by overexpression of the pathway-specific activator PldR. The resulting dysregulation of the biosynthetic genes led to the accumulation and isolation of five additional intermediate or shunt metabolites of pladienolide B biosynthesis, including three previously unreported congeners. These compounds likely comprise the entire pladienolide biosynthetic pathway and demonstrate the link between polyketide tailoring reactions and bioactivity, particularly the importance of the 18,19-epoxide. Each congener demonstrated specific inhibitory activity against mammalian cell lines, with successive modifications leading to increased activity (IC50: 8 mM to 5 μM). Reactivation of quiescent polyketide production in a domesticated lab strain.![]()
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Affiliation(s)
- Thomas J Booth
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - John A Kalaitzis
- Department of Molecular Sciences, Macquarie University NSW 2109 Australia
| | - Daniel Vuong
- Microbial Screening Technologies Smithfield NSW 2164 Australia
| | - Andrew Crombie
- Microbial Screening Technologies Smithfield NSW 2164 Australia
| | - Ernest Lacey
- Microbial Screening Technologies Smithfield NSW 2164 Australia
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University NSW 2109 Australia
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
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8
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Lacey HJ, Booth TJ, Vuong D, Rutledge PJ, Lacey E, Chooi YH, Piggott AM. Conglobatins B-E: cytotoxic analogues of the C 2-symmetric macrodiolide conglobatin. J Antibiot (Tokyo) 2020; 73:756-765. [PMID: 32555501 DOI: 10.1038/s41429-020-0332-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/04/2020] [Accepted: 05/09/2020] [Indexed: 01/19/2023]
Abstract
Chemical investigation of a previously unreported indigenous Australian Streptomyces strain MST-91080 has identified six novel analogues related to the oxazole-pendanted macrodiolide, conglobatin. Phylogenetic analysis of the 16S rRNA gene sequence identified MST-91080 as a species of Streptomyces, distinct from reported conglobatin producer, Streptomyces conglobatus ATCC 31005. Conglobatins B-E diverge from conglobatin through differing patterns of methylation on the macrodiolide skeleton. The altered methyl positions suggest a deviation from the published biosynthetic pathway, which proposed three successive methylmalonyl-CoA extender unit additions to the conglobatin monomer. Conglobatins B1, C1 and C2 exhibited more potent cytotoxic activity selectively against the NS-1 myeloma cell line (IC50 0.084, 1.05 and 0.45 µg ml-1, respectively) compared with conglobatin (IC50 1.39 µg ml-1).
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Affiliation(s)
- Heather J Lacey
- Microbial Screening Technologies, Smithfield, Sydney, NSW, 2164, Australia. .,School of Chemistry, The University of Sydney, Camperdown, Sydney, NSW, 2006, Australia.
| | - Thomas J Booth
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, Sydney, NSW, 2164, Australia
| | - Peter J Rutledge
- School of Chemistry, The University of Sydney, Camperdown, Sydney, NSW, 2006, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, Sydney, NSW, 2164, Australia.,Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
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9
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Qin Z, Devine R, Booth TJ, Farrar EHE, Grayson MN, Hutchings MI, Wilkinson B. Formicamycin biosynthesis involves a unique reductive ring contraction. Chem Sci 2020; 11:8125-8131. [PMID: 33033611 PMCID: PMC7504897 DOI: 10.1039/d0sc01712d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/08/2020] [Indexed: 11/24/2022] Open
Abstract
Using a combination of biomimetic chemistry and molecular genetics we demonstrate that formicamycin biosynthesis proceeds via reductive Favorskii-like reaction.
Fasamycin natural products are biosynthetic precursors of the formicamycins. Both groups of compounds are polyketide natural products that exhibit potent antibacterial activity despite displaying different three-dimensional topologies. We show here that transformation of fasamycin into formicamycin metabolites requires two gene products and occurs via a novel two-step ring expansion-ring contraction pathway. Deletion of forX, encoding a flavin dependent monooxygenase, abolished formicamycin production and leads to accumulation of fasamycin E. Deletion of the adjacent gene forY, encoding a flavin dependent oxidoreductase, also abolished formicamycin biosynthesis and led to the accumulation of new lactone metabolites that represent Baeyer–Villiger oxidation products of the fasamycins. These results identify ForX as a Baeyer–Villiger monooxygenase capable of dearomatizing ring C of the fasamycins. Through in vivo cross feeding and biomimetic semi-synthesis experiments we showed that these lactone products represent biosynthetic intermediates that are reduced to formicamycins in a unique reductive ring contraction reaction catalyzed by ForY.
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Affiliation(s)
- Zhiwei Qin
- Department of Molecular Microbiology , John Innes Centre , Norwich Research Park , Norwich , NR4 7UH , UK .
| | - Rebecca Devine
- School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Thomas J Booth
- Department of Molecular Microbiology , John Innes Centre , Norwich Research Park , Norwich , NR4 7UH , UK .
| | - Elliot H E Farrar
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , UK
| | - Matthew N Grayson
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , UK
| | - Matthew I Hutchings
- Department of Molecular Microbiology , John Innes Centre , Norwich Research Park , Norwich , NR4 7UH , UK . .,School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Barrie Wilkinson
- Department of Molecular Microbiology , John Innes Centre , Norwich Research Park , Norwich , NR4 7UH , UK .
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10
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Brace S, Diekmann Y, Booth TJ, van Dorp L, Faltyskova Z, Rohland N, Mallick S, Olalde I, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Stewardson K, Martiniano R, Walsh S, Kayser M, Charlton S, Hellenthal G, Armit I, Schulting R, Craig OE, Sheridan A, Pearson MP, Stringer C, Reich D, Thomas MG, Barnes I. Author Correction: Ancient genomes indicate population replacement in Early Neolithic Britain. Nat Ecol Evol 2019; 3:986-987. [PMID: 31068681 DOI: 10.1038/s41559-019-0912-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this Article originally published, there were errors in the colour ordering of the legend in Fig. 5b, and in the positions of the target and surrogate populations in Fig. 5c. This has now been corrected. The conclusions of the study are in no way affected. The errors have been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Thomas J Booth
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Zuzana Faltyskova
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- UCL Genetics Institute, University College London, London, UK.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Sophy Charlton
- Department of Earth Sciences, Natural History Museum, London, UK.,Bioarch, University of York, York, UK
| | | | - Ian Armit
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, UK
| | - Rick Schulting
- Institute of Archaeology, University of Oxford, Oxford, UK
| | | | | | | | - Chris Stringer
- Department of Earth Sciences, Natural History Museum, London, UK
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, UK. .,UCL Genetics Institute, University College London, London, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK.
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11
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Brace S, Diekmann Y, Booth TJ, van Dorp L, Faltyskova Z, Rohland N, Mallick S, Olalde I, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Stewardson K, Martiniano R, Walsh S, Kayser M, Charlton S, Hellenthal G, Armit I, Schulting R, Craig OE, Sheridan A, Parker Pearson M, Stringer C, Reich D, Thomas MG, Barnes I. Ancient genomes indicate population replacement in Early Neolithic Britain. Nat Ecol Evol 2019; 3:765-771. [PMID: 30988490 DOI: 10.1038/s41559-019-0871-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/06/2019] [Indexed: 11/09/2022]
Abstract
The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Thomas J Booth
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Zuzana Faltyskova
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- UCL Genetics Institute, University College London, London, UK.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Sophy Charlton
- Department of Earth Sciences, Natural History Museum, London, UK.,Bioarch, University of York, York, UK
| | | | - Ian Armit
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, UK
| | - Rick Schulting
- Institute of Archaeology, University of Oxford, Oxford, UK
| | | | | | | | - Chris Stringer
- Department of Earth Sciences, Natural History Museum, London, UK
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, UK. .,UCL Genetics Institute, University College London, London, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK.
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12
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Booth TJ, Alt S, Capon RJ, Wilkinson B. Synchronous intramolecular cycloadditions of the polyene macrolactam polyketide heronamide C. Chem Commun (Camb) 2016; 52:6383-6. [DOI: 10.1039/c6cc01930g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two spontaneous intramolecular cycloadditions lead to the biosynthetic congeners heronamide A and B.
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Affiliation(s)
- Thomas J. Booth
- Department of Molecular Microbiology
- John Innes Centre
- Norwich Research Park
- Norwich NR4 7UH
- UK
| | - Silke Alt
- Department of Molecular Microbiology
- John Innes Centre
- Norwich Research Park
- Norwich NR4 7UH
- UK
| | - Robert J. Capon
- Institute for Molecular Bioscience
- The University of Queensland
- Australia 4072
| | - Barrie Wilkinson
- Department of Molecular Microbiology
- John Innes Centre
- Norwich Research Park
- Norwich NR4 7UH
- UK
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13
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White L, Booth TJ. The origin of bacteria responsible for bioerosion to the internal bone microstructure: Results from experimentally-deposited pig carcasses. Forensic Sci Int 2014; 239:92-102. [PMID: 24763128 DOI: 10.1016/j.forsciint.2014.03.024] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 02/03/2014] [Accepted: 03/24/2014] [Indexed: 11/30/2022]
Abstract
It is unclear whether the principal forms of bioerosion that are often found within the internal microstructure of human bone are produced by intrinsic gut microbiota or exogenous bacteria from the soil. The aim of this study was to attempt to resolve this issue through the histological analysis of bone sampled from experimentally-deposited domestic pig (Sus scrofa) carcasses. Confirmation of either scenario will dictate how patterns of bone bioerosion can be used in reconstructions of taphonomic events. The results should also reveal the post mortem processes that promote the survival of bone biomolecules as well as the histomorphological structures that can be used in forensic identifications of human remains. Twelve pig carcasses were differentially buried and sub-aerially exposed for one year at Riseholme, Lincolnshire, U.K. Their femora were examined after one year using thin section light microscopy to investigate the patterns of microscopic bioerosion. The distribution and extent of degradation observed within the microstructures of the pig femora were consistent with bacterial bioerosion. The early occurrence of bioerosion within the Riseholme samples suggested that enteric putrefactive bacteria are primarily responsible for characteristic internal bone bioerosion. The distribution of bioerosion amongst the buried/unburied and stillborn/juvenile pig remains also supported an endogenous model. Bone from stillborn neonatal carcasses always demonstrated immaculate histological preservation due to the intrinsic sterility of newborn infant intestinal tracts. Bioerosion within the internal microstructure of mature bone will reflect the extent to which the skeletal element was exposed to putrefaction. Bone histology should be useful in reconstructing early taphonomic events. There is likely to be a relationship between post mortem processes that deny enteric gut bacteria access to internal bone microstructures and the survival of biomolecules.
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Affiliation(s)
- Lorraine White
- Department of Archaeology, Northgate House, West Street, Sheffield S1 4ET, S. Yorkshire, United Kingdom.
| | - Thomas J Booth
- Department of Archaeology, Northgate House, West Street, Sheffield S1 4ET, S. Yorkshire, United Kingdom.
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14
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Klarskov MB, Dam HF, Petersen DH, Hansen TM, Löwenborg A, Booth TJ, Schmidt MS, Lin R, Nielsen PF, Bøggild P. Fast and direct measurements of the electrical properties of graphene using micro four-point probes. Nanotechnology 2011; 22:445702. [PMID: 21975563 DOI: 10.1088/0957-4484/22/44/445702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present measurements of the electronic properties of graphene using a repositionable micro four-point probe system, which we show here to have unique advantages over measurements made on lithographically defined devices; namely speed, simplicity and lack of a need to pattern graphene. Measurements are performed in ambient, vacuum and controlled environmental conditions using an environmental scanning electron microscope (SEM). The results are comparable to previous results for microcleaved graphene on silicon dioxide (SiO(2)). We observe a pronounced hysteresis of the charge neutrality point, dependent on the sweep rate of the gate voltage; and environmental measurements provide insight into the sensor application prospects of graphene. The method offers a fast, local and non-destructive technique for electronic measurements on graphene, which can be positioned freely on a graphene flake.
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Affiliation(s)
- M B Klarskov
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Kongens Lyngby, Denmark
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15
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Nair RR, Blake P, Grigorenko AN, Novoselov KS, Booth TJ, Stauber T, Peres NMR, Geim AK. Fine Structure Constant Defines Visual Transparency of Graphene. Science 2008; 320:1308. [PMID: 18388259 DOI: 10.1126/science.1156965] [Citation(s) in RCA: 2675] [Impact Index Per Article: 167.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- R R Nair
- Manchester Centre for Mesoscience and Nanotechnology, University of Manchester, M13 9PL Manchester, UK
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16
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Meyer JC, Geim AK, Katsnelson MI, Novoselov KS, Booth TJ, Roth S. The structure of suspended graphene sheets. Nature 2007; 446:60-3. [PMID: 17330039 DOI: 10.1038/nature05545] [Citation(s) in RCA: 1840] [Impact Index Per Article: 108.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 12/21/2006] [Indexed: 11/09/2022]
Abstract
The recent discovery of graphene has sparked much interest, thus far focused on the peculiar electronic structure of this material, in which charge carriers mimic massless relativistic particles. However, the physical structure of graphene--a single layer of carbon atoms densely packed in a honeycomb crystal lattice--is also puzzling. On the one hand, graphene appears to be a strictly two-dimensional material, exhibiting such a high crystal quality that electrons can travel submicrometre distances without scattering. On the other hand, perfect two-dimensional crystals cannot exist in the free state, according to both theory and experiment. This incompatibility can be avoided by arguing that all the graphene structures studied so far were an integral part of larger three-dimensional structures, either supported by a bulk substrate or embedded in a three-dimensional matrix. Here we report on individual graphene sheets freely suspended on a microfabricated scaffold in vacuum or air. These membranes are only one atom thick, yet they still display long-range crystalline order. However, our studies by transmission electron microscopy also reveal that these suspended graphene sheets are not perfectly flat: they exhibit intrinsic microscopic roughening such that the surface normal varies by several degrees and out-of-plane deformations reach 1 nm. The atomically thin single-crystal membranes offer ample scope for fundamental research and new technologies, whereas the observed corrugations in the third dimension may provide subtle reasons for the stability of two-dimensional crystals.
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Affiliation(s)
- Jannik C Meyer
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany.
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Abstract
We report free-standing atomic crystals that are strictly 2D and can be viewed as individual atomic planes pulled out of bulk crystals or as unrolled single-wall nanotubes. By using micromechanical cleavage, we have prepared and studied a variety of 2D crystals including single layers of boron nitride, graphite, several dichalcogenides, and complex oxides. These atomically thin sheets (essentially gigantic 2D molecules unprotected from the immediate environment) are stable under ambient conditions, exhibit high crystal quality, and are continuous on a macroscopic scale.
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Affiliation(s)
- K S Novoselov
- Centre for Mesoscience and Nanotechnology and School of Physics and Astronomy, University of Manchester, Manchester M13 9PL, United Kingdom
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Abstract
This is a paper concerning the transport needs of people with disabilities. Whilst tracing to date the development of Dial-a-Ride, the door-to-door transport service for the disabled, it also examines the future of Dial-a-Ride and explores what progress is still to be achieved in the field of transport. The paper draws upon recent research undertaken by the London Dial-a-Ride Users' Association, the representative body of London Dial-a-Ride users.
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Affiliation(s)
- T J Booth
- London Dial-a-Ride Users' Association, Great Britain
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