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Yagound B, Sarma RR, Edwards RJ, Richardson MF, Rodriguez Lopez CM, Crossland MR, Brown GP, DeVore JL, Shine R, Rollins LA. Is developmental plasticity triggered by DNA methylation changes in the invasive cane toad ( Rhinella marina)? Ecol Evol 2024; 14:e11127. [PMID: 38450317 PMCID: PMC10917582 DOI: 10.1002/ece3.11127] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
Many organisms can adjust their development according to environmental conditions, including the presence of conspecifics. Although this developmental plasticity is common in amphibians, its underlying molecular mechanisms remain largely unknown. Exposure during development to either 'cannibal cues' from older conspecifics, or 'alarm cues' from injured conspecifics, causes reduced growth and survival in cane toad (Rhinella marina) tadpoles. Epigenetic modifications, such as changes in DNA methylation patterns, are a plausible mechanism underlying these developmental plastic responses. Here we tested this hypothesis, and asked whether cannibal cues and alarm cues trigger the same DNA methylation changes in developing cane toads. We found that exposure to both cannibal cues and alarm cues was associated with local changes in DNA methylation patterns. These DNA methylation changes affected genes putatively involved in developmental processes, but in different genomic regions for different conspecific-derived cues. Genetic background explains most of the epigenetic variation among individuals. Overall, the molecular mechanisms triggered by exposure to cannibal cues seem to differ from those triggered by alarm cues. Studies linking epigenetic modifications to transcriptional activity are needed to clarify the proximate mechanisms that regulate developmental plasticity in cane toads.
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Affiliation(s)
- Boris Yagound
- Evolution & Ecology Research Centre, Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Roshmi R. Sarma
- Evolution & Ecology Research Centre, Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Richard J. Edwards
- Evolution & Ecology Research Centre, School of Biotechnology and Biomedical SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Minderoo OceanOmics Centre at UWA, Oceans InstituteDeakin UniversityGeelongVictoriaAustralia
| | - Mark F. Richardson
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
- Minderoo OceanOmics Centre at UWA, Oceans InstituteDeakin UniversityGeelongVictoriaAustralia
- Deakin Genomics Research and Discovery FacilityDeakin University, Locked BagGeelongVICAustralia
| | - Carlos M. Rodriguez Lopez
- Deakin Genomics Research and Discovery FacilityDeakin University, Locked BagGeelongVICAustralia
- School of Agriculture, Food and Wine, Waite Research InstituteThe University of AdelaideGlen OsmondSouth AustraliaAustralia
- Environmental Epigenetics and Genetics Group, Department of HorticultureCollege of Agriculture, Food and Environment, University of KentuckyLexingtonKentuckyUSA
| | - Michael R. Crossland
- School of Agriculture, Food and Wine, Waite Research InstituteThe University of AdelaideGlen OsmondSouth AustraliaAustralia
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Gregory P. Brown
- School of Agriculture, Food and Wine, Waite Research InstituteThe University of AdelaideGlen OsmondSouth AustraliaAustralia
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Jayna L. DeVore
- School of Agriculture, Food and Wine, Waite Research InstituteThe University of AdelaideGlen OsmondSouth AustraliaAustralia
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
- UMR 241 EIOUniversity of French Polynesia, IFREMER, ILM, IRDFaa’aTahitiFrench Polynesia
| | - Richard Shine
- School of Agriculture, Food and Wine, Waite Research InstituteThe University of AdelaideGlen OsmondSouth AustraliaAustralia
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Lee A. Rollins
- Evolution & Ecology Research Centre, Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
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Cheung K, Amos TG, Shine R, DeVore JL, Ducatez S, Edwards RJ, Rollins LA. Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory. Ecol Evol 2024; 14:e11115. [PMID: 38435005 PMCID: PMC10909579 DOI: 10.1002/ece3.11115] [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: 10/16/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/05/2024] Open
Abstract
Invasive species offer insights into rapid adaptation to novel environments. The iconic cane toad (Rhinella marina) is an excellent model for studying rapid adaptation during invasion. Previous research using the mitochondrial NADH dehydrogenase 3 (ND3) gene in Hawai'ian and Australian invasive populations found a single haplotype, indicating an extreme genetic bottleneck following introduction. Nuclear genetic diversity also exhibited reductions across the genome in these two populations. Here, we investigated the mitochondrial genomics of cane toads across this invasion trajectory. We created the first reference mitochondrial genome for this species using long-read sequence data. We combined whole-genome resequencing data of 15 toads with published transcriptomic data of 125 individuals to construct nearly complete mitochondrial genomes from the native (French Guiana) and introduced (Hawai'i and Australia) ranges for population genomic analyses. In agreement with previous investigations of these populations, we identified genetic bottlenecks in both Hawai'ian and Australian introduced populations, alongside evidence of population expansion in the invasive ranges. Although mitochondrial genetic diversity in introduced populations was reduced, our results revealed that it had been underestimated: we identified 45 mitochondrial haplotypes in Hawai'ian and Australian samples, none of which were found in the native range. Additionally, we identified two distinct groups of haplotypes from the native range, separated by a minimum of 110 base pairs (0.6%). These findings enhance our understanding of how invasion has shaped the genetic landscape of this species.
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Affiliation(s)
- Kelton Cheung
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Timothy G. Amos
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Rick Shine
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Jayna L. DeVore
- Univ. Polynésie FrancaiseUMR 241 EIO (UPF, IRD, IFREMER, ILM) BP 6570 Faa'aTahitiFrench Polynesia
| | - Simon Ducatez
- Institut de Recherche pour le Développement (IRD)UMR 241 EIO (UPF, IRD, IFREMER, ILM) BP 6570 Faa'aTahitiFrench Polynesia
| | - Richard J. Edwards
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Minderoo OceanOmics Centre at UWA, Oceans InstituteThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Lee Ann Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
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de Jong E, Parata L, Bayer PE, Corrigan S, Edwards RJ. Toward genome assemblies for all marine vertebrates: current landscape and challenges. Gigascience 2024; 13:giad119. [PMID: 38280187 PMCID: PMC10821707 DOI: 10.1093/gigascience/giad119] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/29/2024] Open
Abstract
Marine vertebrate biodiversity is fundamental to ocean ecosystem health but is threatened by climate change, overharvesting, and habitat degradation. High-quality reference genomes are valuable foundational scientific resources that can inform conservation efforts. Consequently, global consortia are striving to produce reference genomes for representatives of all life. Here, we summarize the current landscape of available marine vertebrate reference genomes, including their phylogenetic diversity and geographic hotspots of production. We discuss key logistical and technical challenges that remain to be overcome if we are to realize the vision of a comprehensive reference genome library of all marine vertebrates.
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Affiliation(s)
- Emma de Jong
- Minderoo OceanOmics Centre at UWA, Oceans Institute, University of Western Australia, Perth, 6009, Australia
| | - Lara Parata
- Minderoo OceanOmics Centre at UWA, Oceans Institute, University of Western Australia, Perth, 6009, Australia
| | - Philipp E Bayer
- Minderoo OceanOmics Centre at UWA, Oceans Institute, University of Western Australia, Perth, 6009, Australia
- Minderoo Foundation, Perth, 6009, Australia
| | - Shannon Corrigan
- Minderoo OceanOmics Centre at UWA, Oceans Institute, University of Western Australia, Perth, 6009, Australia
- Minderoo Foundation, Perth, 6009, Australia
| | - Richard J Edwards
- Minderoo OceanOmics Centre at UWA, Oceans Institute, University of Western Australia, Perth, 6009, Australia
- Evolution and Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
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Loan JJM, Bacon A, van Beijnum J, Bhatt P, Bjornson A, Broomes N, Bullen A, Bulters D, Cahill J, Chavredakis E, Colombo F, Danciut M, Digpal R, Edwards RJ, Ferguson L, Forsyth L, Fouyas I, Ganesan V, Grover P, Gurusinghe N, Hall PS, Harkness K, Harris LS, Hayton T, Helmy A, Holsgrove D, Hutchinson PJ, Israni A, Kinsella E, Lewis S, Majeed S, Mallucci C, Mukerji N, Nair R, Neilson AR, Papadopoulos MC, Radatz M, Rossdeutsch A, Raza-Knight S, Stephen J, Stoddart A, Teo M, Turner C, Wade J, Walsh D, White D, White P, Wildman J, Wroe Wright O, Uff C, Ushewokunze S, Vindlacheruvu R, Kitchen N, Al-Shahi Salman R. Feasibility of comparing medical management and surgery (with neurosurgery or stereotactic radiosurgery) with medical management alone in people with symptomatic brain cavernoma - protocol for the Cavernomas: A Randomised Effectiveness (CARE) pilot trial. BMJ Open 2023; 13:e075187. [PMID: 37558454 PMCID: PMC10414059 DOI: 10.1136/bmjopen-2023-075187] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023] Open
Abstract
INTRODUCTION The top research priority for cavernoma, identified by a James Lind Alliance Priority setting partnership was 'Does treatment (with neurosurgery or stereotactic radiosurgery) or no treatment improve outcome for people diagnosed with a cavernoma?' This pilot randomised controlled trial (RCT) aims to determine the feasibility of answering this question in a main phase RCT. METHODS AND ANALYSIS We will perform a pilot phase, parallel group, pragmatic RCT involving approximately 60 children or adults with mental capacity, resident in the UK or Ireland, with an unresected symptomatic brain cavernoma. Participants will be randomised by web-based randomisation 1:1 to treatment with medical management and with surgery (neurosurgery or stereotactic radiosurgery) versus medical management alone, stratified by prerandomisation preference for type of surgery. In addition to 13 feasibility outcomes, the primary clinical outcome is symptomatic intracranial haemorrhage or new persistent/progressive focal neurological deficit measured at 6 monthly intervals. An integrated QuinteT Recruitment Intervention (QRI) evaluates screening logs, audio recordings of recruitment discussions, and interviews with recruiters and patients/parents/carers to identify and address barriers to participation. A Patient Advisory Group has codesigned the study and will oversee its progress. ETHICS AND DISSEMINATION This study was approved by the Yorkshire and The Humber-Leeds East Research Ethics Committee (21/YH/0046). We will submit manuscripts to peer-reviewed journals, describing the findings of the QRI and the Cavernomas: A Randomised Evaluation (CARE) pilot trial. We will present at national specialty meetings. We will disseminate a plain English summary of the findings of the CARE pilot trial to participants and public audiences with input from, and acknowledgement of, the Patient Advisory Group. TRIAL REGISTRATION NUMBER ISRCTN41647111.
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Affiliation(s)
- James J M Loan
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
- Department of Clinical Neurosciences, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | | | | | | | - Nicole Broomes
- University Hospital Southampton NHS Foundation Trust Wessex Neurological Centre, Southampton, UK
| | - Alistair Bullen
- Edinburgh Clinical Trials Unit, The University of Edinburgh Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Diederik Bulters
- University Hospital Southampton NHS Foundation Trust Wessex Neurological Centre, Southampton, UK
| | - Julian Cahill
- National Centre for Stereotactic Radiosurgery, Royal Hallamshire Hospital, Sheffield, UK
| | | | | | | | - Ronneil Digpal
- University Hospital Southampton NHS Foundation Trust Wessex Neurological Centre, Southampton, UK
| | | | | | - Laura Forsyth
- Edinburgh Clinical Trials Unit, The University of Edinburgh Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Ioannis Fouyas
- Department of Clinical Neurosciences, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Vijeya Ganesan
- Developmental Neurosciences Department, Great Ormond Street Hospital for Children, London, UK
| | - Patrick Grover
- The National Hospital for Neurology & Neurosurgery, London, UK
| | | | - Peter S Hall
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | | | - Tom Hayton
- Queen Elizabeth Hospital, Birmingham, UK
| | - Adel Helmy
- Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge, UK
| | - Daniel Holsgrove
- Centre for Clinical Neurosciences, Salford Royal Hospital Manchester, Salford, UK
| | - Peter J Hutchinson
- Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge, UK
| | - Anil Israni
- Alder Hey Children's Hospital, Liverpool, UK
| | - Elaine Kinsella
- Edinburgh Clinical Trials Unit, The University of Edinburgh Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Steff Lewis
- Edinburgh Clinical Trials Unit, The University of Edinburgh Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | | | | | | | | | - Aileen R Neilson
- Edinburgh Clinical Trials Unit, The University of Edinburgh Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | | | - Matthias Radatz
- National Centre for Stereotactic Radiosurgery, Royal Hallamshire Hospital, Sheffield, UK
| | | | | | - Jacqueline Stephen
- Edinburgh Clinical Trials Unit, The University of Edinburgh Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Andrew Stoddart
- Edinburgh Clinical Trials Unit, The University of Edinburgh Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Mario Teo
- Department of Neurosurgery, Southmead Hospital, Bristol, UK
| | - Carole Turner
- Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge, UK
| | - Julia Wade
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Daniel Walsh
- King's College Hospital, London, UK
- Institute of Psychiatry Psychology & Neuroscience, King's College London, London, UK
| | | | - Phil White
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Jack Wildman
- Department of Neurosurgery, Southmead Hospital, Bristol, UK
| | | | | | | | | | - Neil Kitchen
- The National Hospital for Neurology & Neurosurgery, London, UK
| | - Rustam Al-Shahi Salman
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
- Department of Clinical Neurosciences, Royal Infirmary of Edinburgh, Edinburgh, UK
- Edinburgh Clinical Trials Unit, The University of Edinburgh Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
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5
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Bennett AL, Edwards RJ, Kosheleva I, Saunders C, Bililign Y, Williams A, Manosouri K, Saunders KO, Haynes BF, Acharya P, Henderson R. Microsecond dynamics control the HIV-1 envelope conformation. bioRxiv 2023:2023.05.17.541130. [PMID: 37292605 PMCID: PMC10245784 DOI: 10.1101/2023.05.17.541130] [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] [Indexed: 06/10/2023]
Abstract
The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although significant progress has been made in understanding the structures of various Env conformations and transition intermediates that occur within the millisecond timescale, faster transitions in the microsecond timescale have not yet been observed. In this study, we employed time-resolved, temperature-jump small angle X-ray scattering to monitor structural rearrangements in an HIV-1 Env ectodomain construct with microsecond precision. We detected a transition correlated with Env opening that occurs in the hundreds of microseconds range and another more rapid transition that preceded this opening. Model fitting indicated that the early rapid transition involved an order-to-disorder transition in the trimer apex loop contacts, suggesting that conventional conformation-locking design strategies that target the allosteric machinery may be ineffective in preventing this movement. Utilizing this information, we engineered an envelope that locks the apex loop contacts to the adjacent protomer. This modification resulted in significant angle-of-approach shifts in the interaction of a neutralizing antibody. Our findings imply that blocking the intermediate state could be crucial for inducing antibodies with the appropriate bound state orientation through vaccination.
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Affiliation(s)
- Ashley L Bennett
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - R J Edwards
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Ave, Bld 434B, Lemont, IL 60439, USA
| | - Carrie Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Yishak Bililign
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Ashliegh Williams
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Katayoun Manosouri
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
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Ballard JWO, Field MA, Edwards RJ, Wilson LAB, Koungoulos LG, Rosen BD, Chernoff B, Dudchenko O, Omer A, Keilwagen J, Skvortsova K, Bogdanovic O, Chan E, Zammit R, Hayes V, Aiden EL. The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. Gigascience 2023; 12:7086663. [PMID: 36994871 DOI: 10.1093/gigascience/giad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/13/2023] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
Abstract
Background
One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed.
Findings
We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog.
Conclusions
These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
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Affiliation(s)
- J William O Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria 3052, Australia
- Department of Environment and Genetics, SABE, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, Queensland 4870, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Acton, ACT 2600, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Loukas G Koungoulos
- Department of Archaeology, School of Philosophical and Historical Inquiry, the University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705, USA
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth & Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Arina Omer
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg 06484, Germany
| | - Ksenia Skvortsova
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ozren Bogdanovic
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Eva Chan
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Statewide Genomics, New South Wales Health Pathology, Newcastle, NSW 2300, Australia
| | - Robert Zammit
- Vineyard Veterinary Hospital,Vineyard, NSW 2765, Australia
| | - Vanessa Hayes
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Charles Perkins Centre, Faculty of Medical Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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7
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Stuart KC, Edwards RJ, Sherwin WB, Rollins LA. Contrasting Patterns of Single Nucleotide Polymorphisms and Structural Variation Across Multiple Invasions. Mol Biol Evol 2023; 40:7052962. [PMID: 36814414 PMCID: PMC10037079 DOI: 10.1093/molbev/msad046] [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] [Received: 07/13/2022] [Revised: 12/20/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Genetic divergence is the fundamental process that drives evolution and ultimately speciation. Structural variants (SVs) are large-scale genomic differences within a species or population and can cause functionally important phenotypic differences. Characterizing SVs across invasive species will fill knowledge gaps regarding how patterns of genetic diversity and genetic architecture shape rapid adaptation under new selection regimes. Here, we seek to understand patterns in genetic diversity within the globally invasive European starling, Sturnus vulgaris. Using whole genome sequencing of eight native United Kingdom (UK), eight invasive North America (NA), and 33 invasive Australian (AU) starlings, we examine patterns in genome-wide SNPs and SVs between populations and within Australia. Our findings detail the landscape of standing genetic variation across recently diverged continental populations of this invasive avian. We demonstrate that patterns of genetic diversity estimated from SVs do not necessarily reflect relative patterns from SNP data, either when considering patterns of diversity along the length of the organism's chromosomes (owing to enrichment of SVs in subtelomeric repeat regions), or interpopulation diversity patterns (possibly a result of altered selection regimes or introduction history). Finally, we find that levels of balancing selection within the native range differ across SNP and SV of different classes and outlier classifications. Overall, our results demonstrate that the processes that shape allelic diversity within populations is complex and support the need for further investigation of SVs across a range of taxa to better understand correlations between often well-studied SNP diversity and that of SVs.
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Affiliation(s)
- Katarina C Stuart
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Richard J Edwards
- Evolution & Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - William B Sherwin
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Lee A Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
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8
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Ballard JWO, Field MA, Edwards RJ, Wilson LA, Koungoulos LG, Rosen BD, Chernoff B, Dudchenko O, Omer A, Keilwagen J, Skvortsova K, Bogdanovic O, Chan E, Zammit R, Hayes V, Aiden EL. The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology. bioRxiv 2023:2023.01.26.525801. [PMID: 36747621 PMCID: PMC9900879 DOI: 10.1101/2023.01.26.525801] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Background One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. Findings We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on Chromosomes 11, 16, 25 and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and nine previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mtDNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified two differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphological data, comprising geometric morphometric assessment of cranial morphology place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue show she had a larger cranial capacity than a similar-sized domestic dog. Conclusions These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphological characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
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Affiliation(s)
- J. William O. Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria 3052, Australia,Department of Environment and Genetics, SABE, La Trobe University, Melbourne Victoria 3086, Australia
| | - Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, Queensland 4870, Australia,Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia
| | - Laura A.B. Wilson
- School of Archaeology and Anthropology, The Australian National University, Acton, ACT 2600, Australia,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Loukas G. Koungoulos
- Department of Archaeology, School of Philosophical and Historical Inquiry, the University of Sydney, Sydney, Australia 2006
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth & Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030 USA,Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Arina Omer
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27 06484 Quedlinburg, Germany
| | | | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Eva Chan
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia,Statewide Genomics, New South Wales Health Pathology, 45 Watt St, Newcastle NSW 2300, Australia
| | - Robert Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765, Australia
| | - Vanessa Hayes
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia,Charles Perkins Centre, Faculty of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030 USA,Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA,UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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9
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Stuart KC, Sherwin WB, Edwards RJ, Rollins LA. Evolutionary genomics: Insights from the invasive European starlings. Front Genet 2023; 13:1010456. [PMID: 36685843 PMCID: PMC9845568 DOI: 10.3389/fgene.2022.1010456] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/23/2022] [Indexed: 01/06/2023] Open
Abstract
Two fundamental questions for evolutionary studies are the speed at which evolution occurs, and the way that this evolution may present itself within an organism's genome. Evolutionary studies on invasive populations are poised to tackle some of these pressing questions, including understanding the mechanisms behind rapid adaptation, and how it facilitates population persistence within a novel environment. Investigation of these questions are assisted through recent developments in experimental, sequencing, and analytical protocols; in particular, the growing accessibility of next generation sequencing has enabled a broader range of taxa to be characterised. In this perspective, we discuss recent genetic findings within the invasive European starlings in Australia, and outline some critical next steps within this research system. Further, we use discoveries within this study system to guide discussion of pressing future research directions more generally within the fields of population and evolutionary genetics, including the use of historic specimens, phenotypic data, non-SNP genetic variants (e.g., structural variants), and pan-genomes. In particular, we emphasise the need for exploratory genomics studies across a range of invasive taxa so we can begin understanding broad mechanisms that underpin rapid adaptation in these systems. Understanding how genetic diversity arises and is maintained in a population, and how this contributes to adaptability, requires a deep understanding of how evolution functions at the molecular level, and is of fundamental importance for the future studies and preservation of biodiversity across the globe.
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Affiliation(s)
- Katarina C. Stuart
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia,*Correspondence: Katarina C. Stuart,
| | - William B. Sherwin
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Richard J. Edwards
- Evolution & Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Lee A Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
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10
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Chen SH, Martino AM, Luo Z, Schwessinger B, Jones A, Tolessa T, Bragg JG, Tobias PA, Edwards RJ. A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes. Gigascience 2022; 12:giad102. [PMID: 38096477 PMCID: PMC10720953 DOI: 10.1093/gigascience/giad102] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/11/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Melaleuca quinquenervia (broad-leaved paperbark) is a coastal wetland tree species that serves as a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. While extensively cultivated for its ornamental value, it has also become invasive in regions like Florida, USA. Long-lived trees face diverse pest and pathogen pressures, and plant stress responses rely on immune receptors encoded by the nucleotide-binding leucine-rich repeat (NLR) gene family. However, the comprehensive annotation of NLR encoding genes has been challenging due to their clustering arrangement on chromosomes and highly repetitive domain structure; expansion of the NLR gene family is driven largely by tandem duplication. Additionally, the allelic diversity of the NLR gene family remains largely unexplored in outcrossing tree species, as many genomes are presented in their haploid, collapsed state. RESULTS We assembled a chromosome-level pseudo-phased genome for M. quinquenervia and described the allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, distinct clustering patterns, and differences in the types and numbers of novel integrated domains. CONCLUSIONS The high-quality M. quinquenervia genome assembly establishes a new framework for functional and evolutionary studies of this significant tree species. Our findings suggest that maintaining allelic diversity within the NLR gene family is crucial for enabling responses to environmental stress, particularly in long-lived plants.
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Affiliation(s)
- Stephanie H Chen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington NSW 2052, Australia
- Research Centre for Ecosystem Resilience, Botanic Gardens of Sydney, Sydney NSW 2000, Australia
| | - Alyssa M Martino
- School of Life and Environmental Sciences, The University of Sydney, Camperdown NSW 2006, Australia
| | - Zhenyan Luo
- Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Benjamin Schwessinger
- Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Ashley Jones
- Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Tamene Tolessa
- Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
- School of Environment and Rural Science, University of New England, Armidale NSW 2351, Australia
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Botanic Gardens of Sydney, Sydney NSW 2000, Australia
- School of Biological, Earth and Environmental Sciences, UNSW Sydney, Kensington NSW 2052, Australia
| | - Peri A Tobias
- School of Life and Environmental Sciences, The University of Sydney, Camperdown NSW 2006, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington NSW 2052, Australia
- Minderoo OceanOmics Centre at UWA, UWA Oceans Institute, University of Western Australia, Crawley WA 6009, Australia
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11
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Holland SI, Vázquez-Campos X, Ertan H, Edwards RJ, Manefield MJ, Lee M. Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ' Candidatus Formimonas warabiya' strain DCMF. Front Microbiol 2022; 13:1035247. [PMID: 36569084 PMCID: PMC9768040 DOI: 10.3389/fmicb.2022.1035247] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood-Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, 'Candidatus Formimonas warabiya' strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.
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Affiliation(s)
- Sophie I. Holland
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Haluk Ertan
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia,Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael J. Manefield
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia,School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia,*Correspondence: Matthew Lee,
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12
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Stuart KC, Edwards RJ, Cheng Y, Warren WC, Burt DW, Sherwin WB, Hofmeister NR, Werner SJ, Ball GF, Bateson M, Brandley MC, Buchanan KL, Cassey P, Clayton DF, De Meyer T, Meddle SL, Rollins LA. Transcript- and annotation-guided genome assembly of the European starling. Mol Ecol Resour 2022; 22:3141-3160. [PMID: 35763352 PMCID: PMC9796300 DOI: 10.1111/1755-0998.13679] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/10/2022] [Indexed: 01/01/2023]
Abstract
The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short-read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Species-specific transcript mapping and gene annotation revealed good gene-level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.
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Affiliation(s)
- Katarina C. Stuart
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Richard J. Edwards
- Evolution & Ecology Research Centre, School of Biotechnology and Biomolecular SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Yuanyuan Cheng
- School of Life and Environmental SciencesThe University of Sydney, SydneyNew South WalesAustralia
| | - Wesley C. Warren
- Department of Animal Sciences, Institute for Data Science and InformaticsThe University of MissouriColumbiaMissouriUSA
| | - David W. Burt
- Office of the Deputy Vice‐Chancellor (Research and Innovation)The University of QueenslandBrisbaneAustralia
| | - William B. Sherwin
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Natalie R. Hofmeister
- Department of Ecology and Evolutionary BiologyCornell UniversityNew YorkUSA,Fuller Evolutionary Biology ProgramCornell Lab of OrnithologyNew YorkUSA
| | - Scott J. Werner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
| | | | - Melissa Bateson
- Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Matthew C. Brandley
- Section of Amphibians and ReptilesCarnegie Museum of Natural HistoryPittsburghPennsylvaniaUSA
| | - Katherine L. Buchanan
- School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Phillip Cassey
- Invasion Science & Wildlife Ecology LabUniversity of AdelaideAdelaideAustralia
| | - David F. Clayton
- Department of Genetics & BiochemistryClemson UniversitySouth CarolinaUSA
| | - Tim De Meyer
- Department of Data Analysis & Mathematical Modelling, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Simone L. Meddle
- The Roslin Institute, The Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Lee A. Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia,School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
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13
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Perera D, Clayton T, O'Kane PD, Greenwood JP, Weerackody R, Ryan M, Morgan HP, Dodd M, Evans R, Canter R, Arnold S, Dixon LJ, Edwards RJ, De Silva K, Spratt JC, Conway D, Cotton J, McEntegart M, Chiribiri A, Saramago P, Gershlick A, Shah AM, Clark AL, Petrie MC. Percutaneous Revascularization for Ischemic Left Ventricular Dysfunction. N Engl J Med 2022; 387:1351-1360. [PMID: 36027563 DOI: 10.1056/nejmoa2206606] [Citation(s) in RCA: 145] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND Whether revascularization by percutaneous coronary intervention (PCI) can improve event-free survival and left ventricular function in patients with severe ischemic left ventricular systolic dysfunction, as compared with optimal medical therapy (i.e., individually adjusted pharmacologic and device therapy for heart failure) alone, is unknown. METHODS We randomly assigned patients with a left ventricular ejection fraction of 35% or less, extensive coronary artery disease amenable to PCI, and demonstrable myocardial viability to a strategy of either PCI plus optimal medical therapy (PCI group) or optimal medical therapy alone (optimal-medical-therapy group). The primary composite outcome was death from any cause or hospitalization for heart failure. Major secondary outcomes were left ventricular ejection fraction at 6 and 12 months and quality-of-life scores. RESULTS A total of 700 patients underwent randomization - 347 were assigned to the PCI group and 353 to the optimal-medical-therapy group. Over a median of 41 months, a primary-outcome event occurred in 129 patients (37.2%) in the PCI group and in 134 patients (38.0%) in the optimal-medical-therapy group (hazard ratio, 0.99; 95% confidence interval [CI], 0.78 to 1.27; P = 0.96). The left ventricular ejection fraction was similar in the two groups at 6 months (mean difference, -1.6 percentage points; 95% CI, -3.7 to 0.5) and at 12 months (mean difference, 0.9 percentage points; 95% CI, -1.7 to 3.4). Quality-of-life scores at 6 and 12 months appeared to favor the PCI group, but the difference had diminished at 24 months. CONCLUSIONS Among patients with severe ischemic left ventricular systolic dysfunction who received optimal medical therapy, revascularization by PCI did not result in a lower incidence of death from any cause or hospitalization for heart failure. (Funded by the National Institute for Health and Care Research Health Technology Assessment Program; REVIVED-BCIS2 ClinicalTrials.gov number, NCT01920048.).
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Affiliation(s)
- Divaka Perera
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Tim Clayton
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Peter D O'Kane
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - John P Greenwood
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Roshan Weerackody
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Matthew Ryan
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Holly P Morgan
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Matthew Dodd
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Richard Evans
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Ruth Canter
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Sophie Arnold
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Lana J Dixon
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Richard J Edwards
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Kalpa De Silva
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - James C Spratt
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Dwayne Conway
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - James Cotton
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Margaret McEntegart
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Amedeo Chiribiri
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Pedro Saramago
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Anthony Gershlick
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Ajay M Shah
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Andrew L Clark
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
| | - Mark C Petrie
- From the National Institute for Health and Care Research Biomedical Research Centre and the British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine and Sciences, King's College London (D.P., M.R., H.P.M., A.C., A.M.S.), Guy's and St. Thomas' NHS Foundation Trust (D.P., S.A., K.D.S.), the London School of Hygiene and Tropical Medicine (T.C., M.D., R.E., R.C.), Barts Health NHS Trust (R.W.), St. George's University Hospitals NHS Foundation Trust (J.C.S.), and King's College Hospital NHS Foundation Trust (A.M.S.), London, University Hospitals Dorset NHS Foundation Trust, Bournemouth (P.D.O.), Leeds Teaching Hospitals NHS Trust, Leeds (J.P.G.), Belfast Health and Social Care NHS Trust, Belfast (L.J.D.), Newcastle Hospitals NHS Foundation Trust, Newcastle (R.J.E.), University Hospitals Bristol NHS Foundation Trust, Bristol (K.D.S.), Mid Yorkshire Hospitals NHS Trust, Wakefield (D.C.), Royal Wolverhampton NHS Trust, Wolverhampton (J.C.), the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow (M.M., M.C.P.), the University of York, York (P.S.), University Hospitals of Leicester NHS Trust, Leicester (A.G.), and Hull University Teaching Hospitals NHS Trust, Hull (A.L.C.) - all in the United Kingdom
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14
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Bell MJ, Rosario BL, Kochanek PM, Adelson PD, Morris KP, Au AK, Schober M, Butt W, Edwards RJ, Zimmerman J, Pineda J, Le TM, Dean N, Whalen MJ, Figaji A, Luther J, Beers SR, Gupta DK, Carpenter J, Buttram S, Wisniewski SR. Comparative Effectiveness of Diversion of Cerebrospinal Fluid for Children With Severe Traumatic Brain Injury. JAMA Netw Open 2022; 5:e2220969. [PMID: 35802371 PMCID: PMC9270700 DOI: 10.1001/jamanetworkopen.2022.20969] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
IMPORTANCE Diversion of cerebrospinal fluid (CSF) has been used for decades as a treatment for children with severe traumatic brain injury (TBI) and is recommended by evidenced-based guidelines. However, these recommendations are based on limited studies. OBJECTIVE To determine whether CSF diversion is associated with improved Glasgow Outcome Score-Extended for Pediatrics (GOS-EP) and decreased intracranial pressure (ICP) in children with severe TBI. DESIGN, SETTING, AND PARTICIPANTS This observational comparative effectiveness study was performed at 51 clinical centers that routinely care for children with severe TBI in 8 countries (US, United Kingdom, Spain, the Netherlands, Australia, New Zealand, South Africa, and India) from February 2014 to September 2017, with follow-up at 6 months after injury (final follow-up, October 22, 2021). Children with severe TBI were included if they had Glasgow Coma Scale (GCS) scores of 8 or lower, had intracranial pressure (ICP) monitor placed on-site, and were aged younger than 18 years. Children were excluded if they were pregnant or an ICP monitor was not placed at the study site. Consecutive children were screened and enrolled, data regarding treatments were collected, and at discharge, consent was obtained for outcomes testing. Propensity matching for pretreatment characteristics was performed to develop matched pairs for primary analysis. Data analyses were completed on April 18, 2022. EXPOSURES Clinical care followed local standards, including the use of CSF diversion (or not), with patients stratified at the time of ICP monitor placement (CSF group vs no CSF group). MAIN OUTCOMES AND MEASURES The primary outcome was GOS-EP at 6 months, while ICP was considered as a secondary outcome. CSF vs no CSF was treated as an intention-to-treat analysis, and a sensitivity analysis was performed for children who received delayed CSF diversion. RESULTS A total of 1000 children with TBI were enrolled, including 314 who received CSF diversion (mean [SD] age, 7.18 [5.45] years; 208 [66.2%] boys) and 686 who did not (mean [SD] age, 7.79 [5.33] years; 437 [63.7%] boys). The propensity-matched analysis included 98 pairs. In propensity score-matched analyses, there was no difference between groups in GOS-EP (median [IQR] difference, 0 [-3 to 1]; P = .08), but there was a decrease in overall ICP in the CSF group (mean [SD] difference, 3.97 [0.12] mm Hg; P < .001). CONCLUSIONS AND RELEVANCE In this comparative effectiveness study, CSF diversion was not associated with improved outcome at 6 months after TBI, but a decrease in ICP was observed. Given the higher quality of evidence generated by this study, current evidence-based guidelines related to CSF diversion should be reconsidered.
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Affiliation(s)
- Michael J. Bell
- Division of Critical Care Medicine, Department of Pediatrics, Children’s National Medical Center, Washington, District of Columbia
| | - Bedda L. Rosario
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Patrick M. Kochanek
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - P. David Adelson
- Barrow Neurological Institute at Phoenix Children’s Hospital, Phoenix, Arizona
| | - Kevin P. Morris
- Division of Pediatric Critical Care, Birmingham Children’s Hospital NHS Foundation, Birmingham, United Kingdom
| | - Alicia K. Au
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Michelle Schober
- Division of Pediatric Critical Care Medicine, University of Utah, Salt Lake City
| | - Warwick Butt
- Division of Pediatric Critical Care Medicine, The Royal Children’s Hospital, Melbourne, Australia
| | - Richard J. Edwards
- Division of Paediatric Neurosurgery, Bristol Royal Hospital for Children, Bristol, United Kingdom
| | - Jerry Zimmerman
- Division of Pediatric Critical Care Medicine, Harborview Medical Center, Seattle, Washington
| | - Jose Pineda
- Division of Pediatric Critical Care Medicine, St Louis Children’s Hospital, St Louis, Missouri
| | - Truc M. Le
- Division of Critical Care Medicine, Department of Pediatrics, Vanderbilt University, Nashville, Tennessee
| | - Nathan Dean
- Division of Critical Care Medicine, Department of Pediatrics, Children’s National Medical Center, Washington, District of Columbia
| | - Michael J. Whalen
- Division of Pediatric Critical Care Medicine, Massachusetts General Hospital, Boston
| | - Anthony Figaji
- Department of Neurosurgery, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - James Luther
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sue R. Beers
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Deepak K. Gupta
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | | | - Sandra Buttram
- Barrow Neurological Institute at Phoenix Children’s Hospital, Phoenix, Arizona
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15
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Toff WD, Hildick-Smith D, Kovac J, Mullen MJ, Wendler O, Mansouri A, Rombach I, Abrams KR, Conroy SP, Flather MD, Gray AM, MacCarthy P, Monaghan MJ, Prendergast B, Ray S, Young CP, Crossman DC, Cleland JGF, de Belder MA, Ludman PF, Jones S, Densem CG, Tsui S, Kuduvalli M, Mills JD, Banning AP, Sayeed R, Hasan R, Fraser DGW, Trivedi U, Davies SW, Duncan A, Curzen N, Ohri SK, Malkin CJ, Kaul P, Muir DF, Owens WA, Uren NG, Pessotto R, Kennon S, Awad WI, Khogali SS, Matuszewski M, Edwards RJ, Ramesh BC, Dalby M, Raja SG, Mariscalco G, Lloyd C, Cox ID, Redwood SR, Gunning MG, Ridley PD. Effect of Transcatheter Aortic Valve Implantation vs Surgical Aortic Valve Replacement on All-Cause Mortality in Patients With Aortic Stenosis: A Randomized Clinical Trial. JAMA 2022; 327:1875-1887. [PMID: 35579641 PMCID: PMC9115619 DOI: 10.1001/jama.2022.5776] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
IMPORTANCE Transcatheter aortic valve implantation (TAVI) is a less invasive alternative to surgical aortic valve replacement and is the treatment of choice for patients at high operative risk. The role of TAVI in patients at lower risk is unclear. OBJECTIVE To determine whether TAVI is noninferior to surgery in patients at moderately increased operative risk. DESIGN, SETTING, AND PARTICIPANTS In this randomized clinical trial conducted at 34 UK centers, 913 patients aged 70 years or older with severe, symptomatic aortic stenosis and moderately increased operative risk due to age or comorbidity were enrolled between April 2014 and April 2018 and followed up through April 2019. INTERVENTIONS TAVI using any valve with a CE mark (indicating conformity of the valve with all legal and safety requirements for sale throughout the European Economic Area) and any access route (n = 458) or surgical aortic valve replacement (surgery; n = 455). MAIN OUTCOMES AND MEASURES The primary outcome was all-cause mortality at 1 year. The primary hypothesis was that TAVI was noninferior to surgery, with a noninferiority margin of 5% for the upper limit of the 1-sided 97.5% CI for the absolute between-group difference in mortality. There were 36 secondary outcomes (30 reported herein), including duration of hospital stay, major bleeding events, vascular complications, conduction disturbance requiring pacemaker implantation, and aortic regurgitation. RESULTS Among 913 patients randomized (median age, 81 years [IQR, 78 to 84 years]; 424 [46%] were female; median Society of Thoracic Surgeons mortality risk score, 2.6% [IQR, 2.0% to 3.4%]), 912 (99.9%) completed follow-up and were included in the noninferiority analysis. At 1 year, there were 21 deaths (4.6%) in the TAVI group and 30 deaths (6.6%) in the surgery group, with an adjusted absolute risk difference of -2.0% (1-sided 97.5% CI, -∞ to 1.2%; P < .001 for noninferiority). Of 30 prespecified secondary outcomes reported herein, 24 showed no significant difference at 1 year. TAVI was associated with significantly shorter postprocedural hospitalization (median of 3 days [IQR, 2 to 5 days] vs 8 days [IQR, 6 to 13 days] in the surgery group). At 1 year, there were significantly fewer major bleeding events after TAVI compared with surgery (7.2% vs 20.2%, respectively; adjusted hazard ratio [HR], 0.33 [95% CI, 0.24 to 0.45]) but significantly more vascular complications (10.3% vs 2.4%; adjusted HR, 4.42 [95% CI, 2.54 to 7.71]), conduction disturbances requiring pacemaker implantation (14.2% vs 7.3%; adjusted HR, 2.05 [95% CI, 1.43 to 2.94]), and mild (38.3% vs 11.7%) or moderate (2.3% vs 0.6%) aortic regurgitation (adjusted odds ratio for mild, moderate, or severe [no instance of severe reported] aortic regurgitation combined vs none, 4.89 [95% CI, 3.08 to 7.75]). CONCLUSIONS AND RELEVANCE Among patients aged 70 years or older with severe, symptomatic aortic stenosis and moderately increased operative risk, TAVI was noninferior to surgery with respect to all-cause mortality at 1 year. TRIAL REGISTRATION isrctn.com Identifier: ISRCTN57819173.
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Affiliation(s)
| | - William D Toff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, England
- National Institute for Health Research Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, England
| | - David Hildick-Smith
- Sussex Cardiac Centre, Brighton and Sussex University Hospitals NHS Trust, Brighton, England
| | - Jan Kovac
- Department of Cardiovascular Sciences, University of Leicester, Leicester, England
- National Institute for Health Research Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, England
| | - Michael J Mullen
- Institute of Cardiovascular Science, University College London, London, England
| | - Olaf Wendler
- Department of Cardiothoracic Surgery, King's College Hospital NHS Foundation Trust, London, England
| | - Anita Mansouri
- Oxford Clinical Trials Research Unit, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, England
| | - Ines Rombach
- Oxford Clinical Trials Research Unit, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, England
| | - Keith R Abrams
- Centre for Health Economics, University of York, York, England
- Department of Statistics, University of Warwick, Coventry, England
- Department of Health Sciences, University of Leicester, Leicester, England
| | - Simon P Conroy
- Department of Health Sciences, University of Leicester, Leicester, England
| | - Marcus D Flather
- Norwich Medical School, University of East Anglia, Norwich, England
| | - Alastair M Gray
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, England
| | - Philip MacCarthy
- Department of Cardiology, King's College Hospital NHS Foundation Trust, London, England
| | - Mark J Monaghan
- Department of Cardiology, King's College Hospital NHS Foundation Trust, London, England
| | | | - Simon Ray
- Department of Cardiology, Manchester University NHS Foundation Trust, Manchester, England
| | | | | | - John G F Cleland
- Robertson Centre for Biostatistics and Glasgow Clinical Trials Unit, Institute of Health and Wellbeing, University of Glasgow, Glasgow, Scotland
| | - Mark A de Belder
- National Institute for Cardiovascular Outcomes Research, Barts Health NHS Trust, London, England
| | - Peter F Ludman
- Institute of Cardiovascular Sciences, Birmingham University, Birmingham, England
| | - Stephen Jones
- Surgical Intervention Trials Unit, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, England
| | - Cameron G Densem
- Department of Cardiology, Royal Papworth Hospital, Cambridge, England
| | - Steven Tsui
- Department of Cardiothoracic Surgery, Royal Papworth Hospital, Cambridge, England
| | - Manoj Kuduvalli
- Department of Cardiothoracic Surgery, Liverpool Heart and Chest Hospital NHS Foundation Trust, Liverpool, England
| | - Joseph D Mills
- Department of Cardiology, Liverpool Heart and Chest Hospital NHS Foundation Trust, Liverpool, England
| | - Adrian P Banning
- Department of Cardiology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Rana Sayeed
- Department of Cardiothoracic Surgery, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Ragheb Hasan
- Department of Cardiothoracic Surgery, Manchester University NHS Foundation Trust, Manchester, England
| | - Douglas G W Fraser
- Department of Cardiovascular Medicine, University of Manchester, Manchester, England
| | - Uday Trivedi
- Sussex Cardiac Centre, Brighton and Sussex University Hospitals NHS Trust, Brighton, England
| | - Simon W Davies
- Cardiac Department, Royal Brompton Hospital, Royal Brompton and Harefield NHS Foundation Trust, London, England
| | - Alison Duncan
- Cardiac Department, Royal Brompton Hospital, Royal Brompton and Harefield NHS Foundation Trust, London, England
| | - Nick Curzen
- Wessex Cardiothoracic Centre, University Hospital Southampton, Southampton, England
| | - Sunil K Ohri
- Wessex Cardiothoracic Centre, University Hospital Southampton, Southampton, England
| | | | - Pankaj Kaul
- Department of Cardiac Surgery, Leeds Teaching Hospitals NHS Trust, Leeds, England
| | - Douglas F Muir
- Department of Cardiology, James Cook University Hospital, South Tees Hospitals NHS Foundation Trust, Middlesbrough, England
| | - W Andrew Owens
- Department of Cardiothoracic Surgery, James Cook University Hospital, South Tees Hospitals NHS Foundation Trust, Middlesbrough, England
| | - Neal G Uren
- Edinburgh Heart Centre, Royal Infirmary of Edinburgh, Edinburgh, Scotland
| | - Renzo Pessotto
- Edinburgh Heart Centre, Royal Infirmary of Edinburgh, Edinburgh, Scotland
| | - Simon Kennon
- Barts Heart Centre, Barts Health NHS Trust, London, England
| | - Wael I Awad
- Barts Heart Centre, Barts Health NHS Trust, London, England
| | - Saib S Khogali
- Heart and Lung Centre, New Cross Hospital, Wolverhampton, England
| | | | - Richard J Edwards
- Cardiothoracic Department, Newcastle upon Tyne Hospitals, Newcastle upon Tyne, England
| | | | - Miles Dalby
- Department of Cardiology, Harefield Hospital, Royal Brompton and Harefield NHS Foundation Trust, London, England
| | - Shahzad G Raja
- Department of Cardiac Surgery, Harefield Hospital, Royal Brompton and Harefield NHS Foundation Trust, London, England
| | - Giovanni Mariscalco
- Department of Cardiovascular Sciences, University of Leicester, Leicester, England
- National Institute for Health Research Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, England
| | - Clinton Lloyd
- Department of Cardiothoracic Surgery, Derriford Hospital, Plymouth, England
| | - Ian D Cox
- Department of Cardiology, Derriford Hospital, Plymouth, England
| | - Simon R Redwood
- Cardiovascular Division, King's College London, British Heart Foundation Centre of Research Excellence, Rayne Institute, St Thomas' Hospital, London, England
| | - Mark G Gunning
- Cardiology Department, Royal Stoke University Hospital, Stoke-on-Trent, England
| | - Paul D Ridley
- Department of Cardiothoracic Surgery, Royal Stoke University Hospital, Stoke-on-Trent, England
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16
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Field MA, Yadav S, Dudchenko O, Esvaran M, Rosen BD, Skvortsova K, Edwards RJ, Keilwagen J, Cochran BJ, Manandhar B, Bustamante S, Rasmussen JA, Melvin RG, Chernoff B, Omer A, Colaric Z, Chan EKF, Minoche AE, Smith TPL, Gilbert MTP, Bogdanovic O, Zammit RA, Thomas T, Aiden EL, Ballard JWO. The Australian dingo is an early offshoot of modern breed dogs. Sci Adv 2022; 8:eabm5944. [PMID: 35452284 PMCID: PMC9032958 DOI: 10.1126/sciadv.abm5944] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/09/2022] [Indexed: 06/11/2023]
Abstract
Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.
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Affiliation(s)
- Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD 4878, Australia
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Sonu Yadav
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Meera Esvaran
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Blake J. Cochran
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bikash Manandhar
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacob Agerbo Rasmussen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- Center for Evolutionary Hologenomics, Faculty of Health and Medical Sciences, The GLOBE Institute University of Copenhagen, Copenhagen, Denmark
| | - Richard G. Melvin
- Department of Biomedical Sciences, University of Minnesota Medical School, 1035 University Drive, Duluth, MN 55812, USA
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth and Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Arina Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zane Colaric
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eva K. F. Chan
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Statewide Genomics, New South Wales Health Pathology, 45 Watt St, Newcastle, NSW 2300, Australia
| | - Andre E. Minoche
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Timothy P. L. Smith
- U.S. Meat Animal Research Center, Agricultural Research Service, USDA, Rd 313, Clay Center, NE 68933, USA
| | - M. Thomas P. Gilbert
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Robert A. Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765, Australia
| | - Torsten Thomas
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Erez L. Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Pudong 201210, China
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J. William O. Ballard
- Department of Environment and Genetics, SABE, La Trobe University, Melbourne, VIC 3086, Australia
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, VIC 3052, Australia
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17
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Williams MA, Nagel SJ, Golomb J, Jensen H, Dasher NA, Holubkov R, Edwards RJ, Luciano MG, Zwimpfer TJ, Katzen H, Moghekar A, Wisoff JH, McKhann GM, Hamilton MG. Safety and effectiveness of the assessment and treatment of idiopathic normal pressure hydrocephalus in the Adult Hydrocephalus Clinical Research Network. J Neurosurg 2022; 137:1-13. [PMID: 35276651 DOI: 10.3171/2022.1.jns212782] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/24/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE The aim of this study was to describe the processes and outcomes associated with patients at five sites in the Adult Hydrocephalus Clinical Research Network (AHCRN) who had undergone evaluation and treatment for suspected idiopathic normal pressure hydrocephalus (iNPH) and had 1-year postoperative follow-up. METHODS Subjects with possible iNPH who had been prospectively enrolled in the AHCRN registry between November 19, 2014, and December 31, 2018, were evaluated by CSF drainage via either lumbar puncture or external lumbar drainage, consistent with recommendations of the international iNPH guidelines. Standardized clinical evaluations of gait, cognition, urinary symptoms, depression, and functional outcomes were conducted at baseline, before and after CSF drainage, and at 4-month intervals after shunt surgery. Complications of CSF drainage and shunt surgery were recorded. RESULTS Seventy-four percent (424/570) of patients with possible iNPH had CSF drainage, and 46% of them (193/424) underwent shunt surgery. The mean change in gait velocity with CSF drainage was 0.18 m/sec in patients who underwent shunt surgery versus 0.08 m/sec in patients who did not. For shunt surgery patients, gait velocity increased by 54% from 0.67 m/sec before CSF drainage to 0.96 m/sec 8-12 months after surgery, and 80% of patients had an increase of at least 0.1 m/sec by the first postoperative visit. Evaluation of cognition, urinary symptoms, depression, and functional outcomes also revealed improvement after shunt surgery. Of 193 patients who had undergone shunt surgery, 176 (91%) had no complications and 17 (9%) had 28 complications. Eleven patients (6%) had 14 serious complications that resulted in the need for surgery or an extended hospital stay. The 30-day reoperation rate was 3%. CONCLUSIONS Using criteria recommended by the international iNPH guidelines, the authors found that evaluation and treatment of iNPH are safe and effective. Testing with CSF drainage and treatment with shunt surgery are associated with a high rate of sustained improvement and a low rate of complications for iNPH in the 1st year after shunt surgery. Patients who had undergone shunt surgery for iNPH experienced improvement in gait, cognitive function, bladder symptoms, depression, and functional outcome measures. Gait velocity, which is an easily measured, objective, continuous variable, should be used as a standard outcome measure to test a patient's response to CSF drainage and shunt surgery in iNPH.
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Affiliation(s)
- Michael A Williams
- 1Departments of Neurology and Neurological Surgery, University of Washington School of Medicine, Seattle, Washington
| | - Sean J Nagel
- 2Department of Neurosurgery, Center for Neurological Restoration, Cleveland Clinic, Cleveland, Ohio
| | - James Golomb
- 3Department of Neurology, New York University School of Medicine, New York, New York
| | - Hailey Jensen
- 4Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Nickolas A Dasher
- 5Department of Rehabilitation Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Richard Holubkov
- 4Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Richard J Edwards
- 6Department of Neurosurgery, Southmead Hospital, Bristol, United Kingdom
| | - Mark G Luciano
- 7Department of Neurosurgery, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Thomas J Zwimpfer
- 8Division of Neurosurgery, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Heather Katzen
- 9Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida
| | - Abhay Moghekar
- 10Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jeffrey H Wisoff
- 11Division of Pediatric Neurosurgery, Hassenfeld Children's Hospital at NYU Langone Health, New York, New York
| | - Guy M McKhann
- 12Department of Neurological Surgery, Columbia University School of Medicine, New York, New York; and
| | - Mark G Hamilton
- 13Department of Clinical Neurosciences, Division of Neurosurgery, University of Calgary School of Medicine, Calgary, Alberta, Canada
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18
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Galbraith JD, Ludington AJ, Sanders KL, Amos TG, Thomson VA, Enosi Tuipulotu D, Dunstan N, Edwards RJ, Suh A, Adelson DL. Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes. Genes (Basel) 2022; 13:genes13020217. [PMID: 35205262 PMCID: PMC8872380 DOI: 10.3390/genes13020217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/23/2022] [Accepted: 01/23/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~30 Mya and have since rapidly diversified into six amphibious, ~60 marine and ~100 terrestrial species that fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.
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Affiliation(s)
- James D. Galbraith
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Alastair J. Ludington
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Kate L. Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Timothy G. Amos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Vicki A. Thomson
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Division of Immunity, Inflammation and Infection, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | | | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology-Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
| | - David L. Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
- South Australian Museum, Adelaide, SA 5000, Australia
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
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19
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Chen SH, Rossetto M, van der Merwe M, Lu-Irving P, Yap JYS, Sauquet H, Bourke G, Amos TG, Bragg JG, Edwards RJ. Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C. Mol Ecol Resour 2022; 22:1836-1854. [PMID: 35016262 DOI: 10.1111/1755-0998.13574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/31/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022]
Abstract
Telopea speciosissima, the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8% of Embryophyta BUSCOs "Complete". We present a new method in Diploidocus (https://github.com/slimsuite/diploidocus) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome size estimation from the read depth of single-copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1% of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA (CYC) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 "Duplicated" BUSCO genes using a new tool, DepthKopy (https://github.com/slimsuite/depthkopy), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level T. speciosissima reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.
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Affiliation(s)
- Stephanie H Chen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales, Australia.,Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia
| | - Marlien van der Merwe
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Patricia Lu-Irving
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Jia-Yee S Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia.,School of Biological, Earth and Environmental Sciences, UNSW Sydney, New South Wales, Australia
| | - Greg Bourke
- Blue Mountains Botanic Garden, Mount Tomah, New South Wales, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales, Australia
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia.,School of Biological, Earth and Environmental Sciences, UNSW Sydney, New South Wales, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales, Australia
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20
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Ashida R, Walsh P, Brooks JCW, Cerminara NL, Apps R, Edwards RJ. Sensory and motor electrophysiological mapping of the cerebellum in humans. Sci Rep 2022; 12:177. [PMID: 34997137 PMCID: PMC8742093 DOI: 10.1038/s41598-021-04220-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Cerebellar damage during posterior fossa surgery in children can lead to ataxia and risk of cerebellar mutism syndrome. Compartmentalisation of sensorimotor and cognitive functions within the cerebellum have been demonstrated in animal electrophysiology and human imaging studies. Electrophysiological monitoring was carried out under general anaesthesia to assess the limb sensorimotor representation within the human cerebellum for assessment of neurophysiological integrity to reduce the incidence of surgical morbidities. Thirteen adult and paediatric patients undergoing posterior fossa surgery were recruited. Sensory evoked field potentials were recorded in response to mapping (n = 8) to electrical stimulation of limb nerves or muscles. For motor mapping (n = 5), electrical stimulation was applied to the surface of the cerebellum and evoked EMG responses were sought in facial and limb muscles. Sensory evoked potentials were found in two patients (25%). Responses were located on the surface of the right inferior posterior cerebellum to stimulation of the right leg in one patient, and on the left inferior posterior lobe in another patient to stimulation of left forearm. No evoked EMG responses were found for the motor mapping. The present study identifies challenges with using neurophysiological methods to map functional organization within the human cerebellum and considers ways to improve success.
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Affiliation(s)
- Reiko Ashida
- Neurosurgery Department, Southmead Hospital, North Bristol Trust, Bristol, UK.
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK.
| | - Peter Walsh
- Neurophysiology Department, Southmead Hospital, North Bristol Trust, Bristol, UK
| | | | - Nadia L Cerminara
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Richard Apps
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Richard J Edwards
- Neurosurgery Department, Southmead Hospital, North Bristol Trust, Bristol, UK
- Neurosurgery Department, Bristol Royal Hospital for Children, University of Bristol NHS Foundation Trust, Bristol, UK
- Bristol Medical School, University of Bristol, Bristol, UK
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21
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Potter S, Bragg JG, Turakulov R, Eldridge MDB, Deakin J, Kirkpatrick M, Edwards RJ, Moritz C. Limited introgression between rock-wallabies with extensive chromosomal rearrangements. Mol Biol Evol 2021; 39:6448774. [PMID: 34865126 PMCID: PMC8788226 DOI: 10.1093/molbev/msab333] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in speciation. Here, we pursue that goal using an extensive sampling of populations and genomes of Petrogale from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their divergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated divergence compared with autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in evaluating the role of Robertsonian fusions and structural variation in divergence, speciation, and patterns of molecular evolution.
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Affiliation(s)
- Sally Potter
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia.,Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Jason G Bragg
- National Herbarium of New South Wales, The Royal Botanical Gardens and Domain Trust, Sydney, NSW, Australia
| | - Rustamzhon Turakulov
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Janine Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX, United States of America
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
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22
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Zwimpfer TJ, Salterio N, Williams MA, Holubkov R, Katzen H, Luciano MG, Moghekar A, Nagel SJ, Wisoff JH, Golomb J, McKhann GM, Edwards RJ, Hamilton MG. Cognitive and gait outcomes after primary endoscopic third ventriculostomy in adults with chronic obstructive hydrocephalus. J Neurosurg 2021; 136:887-894. [PMID: 34534954 DOI: 10.3171/2021.3.jns203424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/10/2020] [Accepted: 03/10/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVE The object of this study was to determine the short- and long-term efficacy of primary endoscopic third ventriculostomy (ETV) on cognition and gait in adults with chronic obstructive hydrocephalus. METHODS Patients were prospectively accrued through the Adult Hydrocephalus Clinical Research Network patient registry. Patients with previously untreated congenital or acquired obstructive hydrocephalus were included in this study. Gait velocity was assessed using a 10-m walk test. Global cognition was assessed with the Montreal Cognitive Assessment (MoCA). Only patients with documented pre- and post-ETV gait analysis and/or pre- and post-ETV MoCA were included. RESULTS A total of 74 patients had undergone primary ETV, 42 of whom were analyzed. The remaining 32 patients were excluded, as they could not complete both pre- and post-ETV assessments. The mean age of the 42 patients, 19 (45.2%) of whom were female, was 51.9 ± 17.1 years (range 19-79 years). Most patients were White (37 [88.1%]), and the remainder were Asian. Surgical complications were minor. Congenital etiologies occurred in 31 patients (73.8%), with aqueductal stenosis in 23 of those patients (54.8%). The remaining 11 patients (26.2%) had acquired cases. The gait short-term follow-up cohort (mean 4.7 ± 4.1 months, 35 patients) had a baseline median gait velocity of 0.9 m/sec (IQR 0.7-1.3 m/sec) and a post-ETV median velocity of 1.3 m/sec (IQR 1.1-1.4 m/sec). Gait velocity significantly improved post-ETV with a median within-patient change of 0.3 m/sec (IQR 0.0-0.6 m/sec, p < 0.001). Gait velocity improvements were sustained in the long term (mean 14 ± 2.8 months, 12 patients) with a baseline median velocity of 0.7 m/sec (IQR 0.6-1.3 m/sec), post-ETV median of 1.3 m/sec (IQR 1.1-1.7 m/sec), and median within-patient change of 0.4 m/sec (IQR 0.2-0.6 m/sec, p < 0.001). The cognitive short-term follow-up cohort (mean 4.6 ± 4.0 months, 38 patients) had a baseline median MoCA total score (MoCA TS) of 24/30 (IQR 23-27) that improved to 26/30 (IQR 24-28) post-ETV. The median within-patient change was +1 point (IQR 0-2 points, p < 0.001). However, this change is not clinically significant. The cognitive long-term follow-up cohort (mean 14 ± 3.1 months, 15 patients) had a baseline median MoCA TS of 23/30 (IQR 22-27), which improved to 26/30 (IQR 25-28) post-ETV. The median within-patient change was +2 points (IQR 1-3 points, p = 0.007), which is both statistically and clinically significant. CONCLUSIONS Primary ETV can safely improve symptoms of gait and cognitive dysfunction in adults with chronic obstructive hydrocephalus. Gait velocity and global cognition were significantly improved, and the worsening of either was rare following ETV.
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Affiliation(s)
- Thomas J Zwimpfer
- 1Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas Salterio
- 1Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael A Williams
- 2Departments of Neurology and Neurological Surgery, University of Washington, Seattle, Washington
| | - Richard Holubkov
- 3Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Heather Katzen
- 4Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Abhay Moghekar
- 6Neurology, Johns Hopkins University, Baltimore, Maryland
| | - Sean J Nagel
- 7Department of Neurosurgery, Center for Neurological Restoration, Cleveland Clinic, Cleveland, Ohio
| | | | - James Golomb
- 9Neurology, New York University School of Medicine, New York, New York
| | - Guy M McKhann
- 10Department of Neurological Surgery, Columbia University Irving Medical Center, New York, New York
| | - Richard J Edwards
- 11Department of Neurosurgery, Southmead Hospital, Bristol, United Kingdom; and
| | - Mark G Hamilton
- 12Department of Clinical Neurosciences, Division of Neurosurgery, University of Calgary Cumming School of Medicine, Calgary, Alberta, Canada
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23
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Williams WB, Meyerhoff RR, Edwards RJ, Li H, Manne K, Nicely NI, Henderson R, Zhou Y, Janowska K, Mansouri K, Gobeil S, Evangelous T, Hora B, Berry M, Abuahmad AY, Sprenz J, Deyton M, Stalls V, Kopp M, Hsu AL, Borgnia MJ, Stewart-Jones GBE, Lee MS, Bronkema N, Moody MA, Wiehe K, Bradley T, Alam SM, Parks RJ, Foulger A, Oguin T, Sempowski GD, Bonsignori M, LaBranche CC, Montefiori DC, Seaman M, Santra S, Perfect J, Francica JR, Lynn GM, Aussedat B, Walkowicz WE, Laga R, Kelsoe G, Saunders KO, Fera D, Kwong PD, Seder RA, Bartesaghi A, Shaw GM, Acharya P, Haynes BF. Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell 2021; 184:2955-2972.e25. [PMID: 34019795 PMCID: PMC8135257 DOI: 10.1016/j.cell.2021.04.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/22/2021] [Accepted: 04/23/2021] [Indexed: 01/03/2023]
Abstract
Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (VH) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without VH-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM+IgD+CD27+, thus suggesting that they originated from a pool of antigen-experienced IgM+ or marginal zone B cells.
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Affiliation(s)
- Wilton B Williams
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA.
| | - R Ryan Meyerhoff
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - R J Edwards
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Rory Henderson
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | | | | | | | | | - Bhavna Hora
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | | | | | | | | | - Megan Kopp
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | | | - Matthew S Lee
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Naomi Bronkema
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | | | - Thomas Oguin
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Michael Seaman
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - John Perfect
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - Geoffrey M Lynn
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA; Avidea Technologies, Inc., Baltimore, MD, USA
| | | | | | - Richard Laga
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Peter D Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University, Durham, NC 27705, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA.
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24
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Sarma RR, Crossland MR, Eyck HJF, DeVore JL, Edwards RJ, Cocomazzo M, Zhou J, Brown GP, Shine R, Rollins LA. Intergenerational effects of manipulating DNA methylation in the early life of an iconic invader. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200125. [PMID: 33866803 DOI: 10.1098/rstb.2020.0125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In response to novel environments, invasive populations often evolve rapidly. Standing genetic variation is an important predictor of evolutionary response but epigenetic variation may also play a role. Here, we use an iconic invader, the cane toad (Rhinella marina), to investigate how manipulating epigenetic status affects phenotypic traits. We collected wild toads from across Australia, bred them, and experimentally manipulated DNA methylation of the subsequent two generations (G1, G2) through exposure to the DNA methylation inhibitor zebularine and/or conspecific tadpole alarm cues. Direct exposure to alarm cues (an indicator of predation risk) increased the potency of G2 tadpole chemical cues, but this was accompanied by reductions in survival. Exposure to alarm cues during G1 also increased the potency of G2 tadpole cues, indicating intergenerational plasticity in this inducible defence. In addition, the negative effects of alarm cues on tadpole viability (i.e. the costs of producing the inducible defence) were minimized in the second generation. Exposure to zebularine during G1 induced similar intergenerational effects, suggesting a role for alteration in DNA methylation. Accordingly, we identified intergenerational shifts in DNA methylation at some loci in response to alarm cue exposure. Substantial demethylation occurred within the sodium channel epithelial 1 subunit gamma gene (SCNN1G) in alarm cue exposed individuals and their offspring. This gene is a key to the regulation of sodium in epithelial cells and may help to maintain the protective epidermal barrier. These data suggest that early life experiences of tadpoles induce intergenerational effects through epigenetic mechanisms, which enhance larval fitness. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Roshmi R Sarma
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Michael R Crossland
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Harrison J F Eyck
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Jayna L DeVore
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
| | - Michael Cocomazzo
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong 3216, Australia
| | - Jia Zhou
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia.,School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB 1 Glen Osmond, 5064, Australia
| | - Gregory P Brown
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia
| | - Richard Shine
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia
| | - Lee A Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong 3216, Australia
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25
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Edwards RJ, Field MA, Ferguson JM, Dudchenko O, Keilwagen J, Rosen BD, Johnson GS, Rice ES, Hillier LD, Hammond JM, Towarnicki SG, Omer A, Khan R, Skvortsova K, Bogdanovic O, Zammit RA, Aiden EL, Warren WC, Ballard JWO. Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics 2021; 22:188. [PMID: 33726677 PMCID: PMC7962210 DOI: 10.1186/s12864-021-07493-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/28/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. RESULTS Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. CONCLUSIONS The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.
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Affiliation(s)
- Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878 Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - James M. Ferguson
- Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str, 27 06484 Quedlinburg, Germany
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705 USA
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211 USA
| | - Edward S. Rice
- Department of Surgery, University of Missouri, Columbia, MO 65211 USA
| | | | - Jillian M. Hammond
- Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Samuel G. Towarnicki
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Arina Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
| | - Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2010 Australia
| | - Ozren Bogdanovic
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Robert A. Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765 Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX USA
- Faculty of Science, UWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009 Australia
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Wesley C. Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO 65211 Australia
| | - J. William O. Ballard
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086 Australia
- School of Biosciences, University of Melbourne, Parkville, Victoria 3052 Australia
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26
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Benaud N, Edwards RJ, Amos TG, D'Agostino PM, Gutiérrez-Chávez C, Montgomery K, Nicetic I, Ferrari BC. Antarctic desert soil bacteria exhibit high novel natural product potential, evaluated through long-read genome sequencing and comparative genomics. Environ Microbiol 2020; 23:3646-3664. [PMID: 33140504 DOI: 10.1111/1462-2920.15300] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 11/30/2022]
Abstract
Actinobacteria and Proteobacteria are important producers of bioactive natural products (NP), and these phyla dominate in the arid soils of Antarctica, where metabolic adaptations influence survival under harsh conditions. Biosynthetic gene clusters (BGCs) which encode NPs, are typically long and repetitious high G + C regions difficult to sequence with short-read technologies. We sequenced 17 Antarctic soil bacteria from multi-genome libraries, employing the long-read PacBio platform, to optimize capture of BGCs and to facilitate a comprehensive analysis of their NP capacity. We report 13 complete bacterial genomes of high quality and contiguity, representing 10 different cold-adapted genera including novel species. Antarctic BGCs exhibited low similarity to known compound BGCs (av. 31%), with an abundance of terpene, non-ribosomal peptide and polyketide-encoding clusters. Comparative genome analysis was used to map BGC variation between closely related strains from geographically distant environments. Results showed the greatest biosynthetic differences to be in a psychrotolerant Streptomyces strain, as well as a rare Actinobacteria genus, Kribbella, while two other Streptomyces spp. were surprisingly similar to known genomes. Streptomyces and Kribbella BGCs were predicted to encode antitumour, antifungal, antibacterial and biosurfactant-like compounds, and the synthesis of NPs with antibacterial, antifungal and surfactant properties was confirmed through bioactivity assays.
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Affiliation(s)
- Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Paul M D'Agostino
- Technische Universität Dresden, Chair of Technical Biochemistry, Bergstraße 66, 01602 Dresden, Germany
| | | | - Kate Montgomery
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Iskra Nicetic
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
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Nunn AC, Jones HE, Morosanu CO, Singleton WGB, Williams MA, Nagel SJ, Luciano MG, Zwimpfer TJ, Holubkov R, Wisoff JH, McKhann GM, Hamilton MG, Edwards RJ. Extended lumbar drainage in idiopathic normal pressure hydrocephalus: a systematic review and meta-analysis of diagnostic test accuracy. Br J Neurosurg 2020; 35:285-291. [PMID: 32643967 DOI: 10.1080/02688697.2020.1787948] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND When appropriately selected, a high proportion of patients with suspected idiopathic normal pressure hydrocephalus (iNPH) will respond to cerebrospinal fluid diversion with a shunt. Extended lumbar drainage (ELD) is regarded as the most accurate test for this condition, however, varying estimates of its accuracy are found in the current literature. Here, we review the literature in order to provide summary estimates of sensitivity, specificity, positive- and negative predictive value for this test through meta-analysis of suitably rigorous studies. METHODS Studies involving a population of NPH patients with predominantly idiopathic aetiology (>80%) in which the intention of the study was to shunt patients regardless of the outcome of ELD were included in the review. Various literature databases were searched to identify diagnostic test accuracy studies addressing ELD in the diagnosis of iNPH. Those studies passing screening and eligibility were assessed using the QUADAS-2 tool and data extracted for bivariate random effects meta-analysis. RESULTS Four small studies were identified. They showed disparate results concerning diagnostic test accuracy. The summary estimates for sensitivity and specificity were 94% (CI 41-100%) and 85% (CI 33-100%), respectively. The summary estimates of positive and negative predictive value were both 90% (CIs 65-100% and 48-100%, respectively). CONCLUSION Large, rigorous studies addressing the diagnostic accuracy of ELD are lacking, and little robust evidence exists to support the use of ELD in diagnostic algorithms for iNPH. Therefore, a large cohort study, or ideally an RCT, is needed to determine best practice in selecting patients for shunt surgery.
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Affiliation(s)
- Adam C Nunn
- Department of Neurosurgery, Southmead Hospital, Bristol, UK
| | - Hayley E Jones
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | | | - Michael A Williams
- Departments of Neurology and Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA.,Adult Hydrocephalus Clinical Research Network, Hydrocephalus Association, Bethesda, MD, USA
| | - Sean J Nagel
- Adult Hydrocephalus Clinical Research Network, Hydrocephalus Association, Bethesda, MD, USA.,Department of Neurosurgery, Center for Neurological Restoration, Cleveland Clinic, Cleveland, OH, USA
| | - Mark G Luciano
- Adult Hydrocephalus Clinical Research Network, Hydrocephalus Association, Bethesda, MD, USA.,Department of Neurosurgery, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas J Zwimpfer
- Adult Hydrocephalus Clinical Research Network, Hydrocephalus Association, Bethesda, MD, USA.,Division of Neurosurgery, Department of Surgery, University of British Columbia, Vancouver, Canada
| | - Richard Holubkov
- Adult Hydrocephalus Clinical Research Network, Hydrocephalus Association, Bethesda, MD, USA.,Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Jeffrey H Wisoff
- Adult Hydrocephalus Clinical Research Network, Hydrocephalus Association, Bethesda, MD, USA.,Division of Pediatric Neurosurgery, Hassenfeld Children's Hospital at NYU Langone Health, New York, NY, USA
| | - Guy M McKhann
- Adult Hydrocephalus Clinical Research Network, Hydrocephalus Association, Bethesda, MD, USA.,Department of Neurological Surgery, Columbia University School of Medicine, New York, NY, USA
| | - Mark G Hamilton
- Adult Hydrocephalus Clinical Research Network, Hydrocephalus Association, Bethesda, MD, USA.,Department of Clinical Neurosciences, Division of Neurosurgery, University of Calgary School of Medicine, Calgary, Canada
| | - Richard J Edwards
- Department of Neurosurgery, Southmead Hospital, Bristol, UK.,Adult Hydrocephalus Clinical Research Network, Hydrocephalus Association, Bethesda, MD, USA
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Sarma RR, Edwards RJ, Crino OL, Eyck HJF, Waters PD, Crossland MR, Shine R, Rollins LA. Do Epigenetic Changes Drive Corticosterone Responses to Alarm Cues in Larvae of an Invasive Amphibian? Integr Comp Biol 2020; 60:1481-1494. [PMID: 32544233 DOI: 10.1093/icb/icaa082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The developmental environment can exert powerful effects on animal phenotype. Recently, epigenetic modifications have emerged as one mechanism that can modulate developmentally plastic responses to environmental variability. For example, the DNA methylation profile at promoters of hormone receptor genes can affect their expression and patterns of hormone release. Across taxonomic groups, epigenetic alterations have been linked to changes in glucocorticoid (GC) physiology. GCs are metabolic hormones that influence growth, development, transitions between life-history stages, and thus fitness. To date, relatively few studies have examined epigenetic effects on phenotypic traits in wild animals, especially in amphibians. Here, we examined the effects of exposure to predation threat (alarm cues) and experimentally manipulated DNA methylation on corticosterone (CORT) levels in tadpoles and metamorphs of the invasive cane toad (Rhinella marina). We included offspring of toads sampled from populations across the species' Australian range. In these animals, exposure to chemical cues from injured conspecifics induces shifts in developmental trajectories, putatively as an adaptive response that lessens vulnerability to predation. We exposed tadpoles to these alarm cues, and measured changes in DNA methylation and CORT levels, both of which are mechanisms that have been implicated in the control of phenotypically plastic responses in tadpoles. To test the idea that DNA methylation drives shifts in GC physiology, we also experimentally manipulated methylation levels with the drug zebularine. We found differentially methylated regions (DMRs) between control tadpoles and their full-siblings exposed to alarm cues, zebularine, or both treatments. However, the effects of these manipulations on methylation patterns were weaker than clutch (e.g., genetic, maternal, etc.) effects. CORT levels were higher in larval cane toads exposed to alarm cues and zebularine. We found little evidence of changes in DNA methylation across the GC receptor gene (NR3C1) promoter region in response to alarm cue or zebularine exposure. In both alarm cue and zebularine-exposed individuals, we found differentially methylated DNA in the suppressor of cytokine signaling 3 gene (SOCS3), which may be involved in predator avoidance behavior. In total, our data reveal that alarm cues have significant impacts on tadpole physiology, but show only weak links between DNA methylation and CORT levels. We also identify genes containing DMRs in tadpoles exposed to alarm cues and zebularine, particularly in range-edge populations, that warrant further investigation.
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Affiliation(s)
- Roshmi R Sarma
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ondi L Crino
- Centre for Integrative Ecology, School of Life and Environmental Sciences (LES), Deakin University, Geelong, Victoria, Australia.,Department of Biological Sciences, Macquarie University, NSW 2052, Australia
| | - Harrison J F Eyck
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael R Crossland
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Richard Shine
- Department of Biological Sciences, Macquarie University, NSW 2052, Australia
| | - Lee A Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Williams MA, Nagel SJ, Luciano MG, Relkin N, Zwimpfer TJ, Katzen H, Holubkov R, Moghekar A, Wisoff JH, McKhann GM, Golomb J, Edwards RJ, Hamilton MG. The clinical spectrum of hydrocephalus in adults: report of the first 517 patients of the Adult Hydrocephalus Clinical Research Network registry. J Neurosurg 2020; 132:1773-1784. [DOI: 10.3171/2019.2.jns183538] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 02/25/2019] [Indexed: 11/06/2022]
Abstract
OBJECTIVEThe authors describe the demographics and clinical characteristics of the first 517 patients enrolled in the Adult Hydrocephalus Clinical Research Network (AHCRN) during its first 2 years.METHODSAdults ≥ 18 years were nonconsecutively enrolled in a registry at 6 centers. Four categories of adult hydrocephalus were defined: transition (treated before age 18 years), unrecognized congenital (congenital pattern, not treated before age 18 years), acquired (secondary to known risk factors, treated or untreated), and suspected idiopathic normal pressure hydrocephalus (iNPH) (≥ age 65 years, not previously treated). Data include etiology, symptoms, examination findings, neuropsychology screening, comorbidities, treatment, complications, and outcomes. Standard evaluations were administered to all patients by trained examiners, including the Montreal Cognitive Assessment, the Symbol Digit Modalities Test, the Beck Depression Inventory–II, the Overactive Bladder Questionnaire Short Form symptom bother, the 10-Meter Walk Test, the Boon iNPH gait scale, the Lawton Activities of Daily Living/Instrumental Activities of Daily Living (ADL/IADL) questionnaire, the iNPH grading scale, and the modified Rankin Scale.RESULTSOverall, 517 individuals were enrolled. Age ranged from 18.1 to 90.7 years, with patients in the transition group (32.7 ± 10.0 years) being the youngest and those in the suspected iNPH group (76.5 ± 5.2 years) being the oldest. The proportion of patients in each group was as follows: 16.6% transition, 26.5% unrecognized congenital, 18.2% acquired, and 38.7% suspected iNPH. Excluding the 86 patients in the transition group, who all had received treatment, 79.4% of adults in the remaining 3 groups had not been treated at the time of enrollment. Patients in the suspected iNPH group had the poorest performance in cognitive evaluations, and those in the unrecognized congenital group had the best performance. The same pattern was seen in the Lawton ADL/IADL scores. Gait velocity was lowest in patients in the suspected iNPH group. Categories that had the most comorbidities (suspected iNPH) or etiologies of hydrocephalus that directly cause neurological injury (transition, acquired) had greater degrees of impairment compared to unrecognized congenital, which had the fewest comorbidities or etiologies associated with neurological injury.CONCLUSIONSThe clinical spectrum of hydrocephalus in adults comprises more than iNPH or acquired hydrocephalus. Only 39% of patients had suspected iNPH, whereas 43% had childhood onset (i.e., those in the transition and unrecognized congenital groups). The severity of symptoms and impairment was worsened when the etiology of the hydrocephalus or complications of treatment caused additional neurological injury or when multiple comorbidities were present. However, more than half of patients in the transition, unrecognized congenital, and acquired hydrocephalus groups had minimal or no impairment. Excluding the transition group, nearly 80% of patients in the AHCRN registry were untreated at the time of enrollment. A future goal for the AHCRN is to determine whether patients with unrecognized congenital and acquired hydrocephalus need treatment and which patients in the suspected iNPH cohort actually have possible hydrocephalus and should undergo further diagnostic testing. Future prospective research is needed in the diagnosis, treatment, outcomes, quality of life, and macroeconomics of all categories of adult hydrocephalus.
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Affiliation(s)
- Michael A. Williams
- 1Departments of Neurology and Neurological Surgery, University of Washington School of Medicine, Seattle, Washington
| | - Sean J. Nagel
- 2Department of Neurosurgery, Center for Neurological Restoration, Cleveland Clinic, Cleveland, Ohio
| | - Mark G. Luciano
- 3Department of Neurosurgery, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Norman Relkin
- 4Department of Neurology, Weill Cornell School of Medicine, New York, New York
| | - Thomas J. Zwimpfer
- 5Division of Neurosurgery, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Heather Katzen
- 6Department of Neurology, University of Miami Miller School of Medicine, Florida
| | - Richard Holubkov
- 7Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Abhay Moghekar
- 8Department of Neurology, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jeffrey H. Wisoff
- 9Division of Pediatric Neurosurgery, Hassenfeld Children’s Hospital at NYU Langone Health
| | - Guy M. McKhann
- 10Department of Neurological Surgery, Columbia University School of Medicine
| | - James Golomb
- 11Department of Neurology, New York University School of Medicine, New York, New York,
| | - Richard J. Edwards
- 12Department of Neurosurgery, Southmead Hospital, Bristol, United Kingdom; and
| | - Mark G. Hamilton
- 13Department of Clinical Neurosciences, Division of Neurosurgery, University of Calgary School of Medicine, Calgary, Alberta, Canada
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Field MA, Rosen BD, Dudchenko O, Chan EKF, Minoche AE, Edwards RJ, Barton K, Lyons RJ, Tuipulotu DE, Hayes VM, D. Omer A, Colaric Z, Keilwagen J, Skvortsova K, Bogdanovic O, Smith MA, Aiden EL, Smith TPL, Zammit RA, Ballard JWO. Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. Gigascience 2020; 9:giaa027. [PMID: 32236524 PMCID: PMC7111595 DOI: 10.1093/gigascience/giaa027] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/29/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance, and search-and-rescue. Yet, GSDs are well known to be susceptible to a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able to continue their duties. FINDINGS Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFam_GSD) utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly results show that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to ∼99%. Detailed examination of the evolutionarily important pancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestral copies and the disruption of 1 copy. CONCLUSIONS GSD genome assembly and annotation were produced with major improvement in completeness, continuity, and quality over the existing canid reference. This resource will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.
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Affiliation(s)
- Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield Road, Cairns, QLD 4878, Australia
- John Curtin School of Medical Research, Australian National University, Garran Rd, Canberra, ACT 2600, Australia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Baltimore Ave, Beltsville, MD 20705, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
- Center for Theoretical and Biological Physics, Rice University, Main St, Houston, TX 77005, USA
| | - Eva K F Chan
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Andre E Minoche
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of New South Wales Sydney, Victoria Street, Darlinghurst NSW 2010, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Kirston Barton
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Ruth J Lyons
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Vanessa M Hayes
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
- Central Clinical School, University of Sydney, Parramatta Road, Camperdown, NSW 2050, Australia
| | - Arina D. Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Martin A Smith
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
- Center for Theoretical and Biological Physics, Rice University, Main St, Houston, TX 77005, USA
- Broad Institute of MIT and Harvard, Main St, Cambridge, MA 02142, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, ShanghaiTech University, Huaxia Middle Rd, Pudong 201210, China
| | - Timothy P L Smith
- US Meat Animal Research Center, Agricultural Research Service USDA, Rd 313, Clay Center, NE 68933, USA
| | - Robert A Zammit
- Vineyard Veterinary Hospital, Windsor Rd, Vineyard, NSW 2765, Australia
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
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Lockey C, Edwards RJ, Roper DI, Dixon AM. The Extracellular Domain of Two-component System Sensor Kinase VanS from Streptomyces coelicolor Binds Vancomycin at a Newly Identified Binding Site. Sci Rep 2020; 10:5727. [PMID: 32235931 PMCID: PMC7109055 DOI: 10.1038/s41598-020-62557-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/11/2020] [Indexed: 11/24/2022] Open
Abstract
The glycopeptide antibiotic vancomycin has been widely used to treat infections of Gram-positive bacteria including Clostridium difficile and methicillin-resistant Staphylococcus aureus. However, since its introduction, high level vancomycin resistance has emerged. The genes responsible require the action of the two-component regulatory system VanSR to induce expression of resistance genes. The mechanism of detection of vancomycin by this two-component system has yet to be elucidated. Diverging evidence in the literature supports activation models in which the VanS protein binds either vancomycin, or Lipid II, to induce resistance. Here we investigated the interaction between vancomycin and VanS from Streptomyces coelicolor (VanSSC), a model Actinomycete. We demonstrate a direct interaction between vancomycin and purified VanSSC, and traced these interactions to the extracellular region of the protein, which we reveal adopts a predominantly α-helical conformation. The VanSSC-binding epitope within vancomycin was mapped to the N-terminus of the peptide chain, distinct from the binding site for Lipid II. In targeting a separate site on vancomycin, the effective VanS ligand concentration includes both free and lipid-bound molecules, facilitating VanS activation. This is the first molecular description of the VanS binding site within vancomycin, and could direct engineering of future therapeutics.
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Affiliation(s)
- Christine Lockey
- MOAC Doctoral Training Centre, University of Warwick, Coventry, CV4 7AL, UK
| | - Richard J Edwards
- Medical Research Council Doctoral Training Centre, University of Warwick, Coventry, CV4 7AL, UK
| | - David I Roper
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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Sivakumaran R, Mohamed AZ, Akhunbay-Fudge CY, Edwards RJ, Renowden SA, Nelson RJ. Internal Carotid Artery Test Balloon Occlusion Using Single Photon Emission Computed Tomography Scan in the Management of Complex Cerebral Aneurysms and Skull Base Tumors: A 20-Year Review. World Neurosurg 2020; 139:e32-e37. [PMID: 32169618 DOI: 10.1016/j.wneu.2020.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 01/11/2020] [Accepted: 03/02/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND Test balloon occlusion (TBO) is important in the management of complex cerebrovascular and skull base lesions when permanent occlusion (PO) of a parent artery may be indicated. Several adjuncts may be used to increase the sensitivity of TBO to predict whether PO will be tolerated. This is an observational study to evaluate the utility of internal carotid artery (ICA) TBO using single photon emission computed tomography (SPECT) scan in the management of complex vascular pathology and skull base tumors. METHODS All TBO procedures performed over a 20-year period were analyzed. Clinical assessment and angiographic collateral flow were combined with semi-quantitative cerebral blood flow analysis using 99mTc hexamethylpropylene-amine oxime SPECT scan during ICA TBO. Evaluation of collateral circulation after TBO, and the complications of TBO and the safety of PO after successful TBO were evaluated. RESULTS Eighty-three patients underwent TBO without complication. Of 45 patients with satisfactory TBO, 28 proceeded to PO. Three patients developed transient ischemic symptoms thought to be embolic in origin. Thirty-eight patients had unsatisfactory TBO, of whom 15 required PO accompanied by a bypass procedure. Forty patients in the series did not undergo permanent vessel occlusion. CONCLUSIONS SPECT scan-enhanced TBO is an important component of the management of complex vascular pathology and skull base tumors, permitting safe PO of the parent vessel and definitive treatment of the main pathology.
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Affiliation(s)
- Ram Sivakumaran
- Department of Neurosurgery, North Bristol Hospitals NHS Trust, Bristol, United Kingdom.
| | - Amr Z Mohamed
- Department of Neurosurgery, North Bristol Hospitals NHS Trust, Bristol, United Kingdom
| | | | - Richard J Edwards
- Department of Neurosurgery, North Bristol Hospitals NHS Trust, Bristol, United Kingdom
| | - Shelley A Renowden
- Department of Neuroradiology, North Bristol Hospitals NHS Trust, Bristol, United Kingdom
| | - Richard J Nelson
- Department of Neurosurgery, North Bristol Hospitals NHS Trust, Bristol, United Kingdom
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33
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Henderson R, Lu M, Zhou Y, Mu Z, Parks R, Han Q, Hsu AL, Carter E, Blanchard SC, Edwards RJ, Wiehe K, Saunders KO, Borgnia MJ, Bartesaghi A, Mothes W, Haynes BF, Acharya P, Munir Alam S. Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements. Nat Commun 2020; 11:520. [PMID: 31980614 PMCID: PMC6981184 DOI: 10.1038/s41467-019-14196-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/18/2019] [Indexed: 11/24/2022] Open
Abstract
The trimeric HIV-1 Envelope protein (Env) mediates viral-host cell fusion via a network of conformational transitions, with allosteric elements in each protomer orchestrating host receptor-induced exposure of the co-receptor binding site and fusion elements. To understand the molecular details of this allostery, here, we introduce Env mutations aimed to prevent CD4-induced rearrangements in the HIV-1 BG505 Env trimer. Binding analysis and single-molecule Förster Resonance Energy Transfer confirm that these mutations prevent CD4-induced transitions of the HIV-1 Env. Structural analysis by single-particle cryo-electron microscopy performed on the BG505 SOSIP mutant Env proteins shows rearrangements in the gp120 topological layer contacts with gp41. Displacement of a conserved tryptophan (W571) from its typical pocket in these Env mutants renders the Env insensitive to CD4 binding. These results reveal the critical function of W571 as a conformational switch in Env allostery and receptor-mediated viral entry and provide insights on Env conformation that are relevant for vaccine design.
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Affiliation(s)
- Rory Henderson
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC, 27708, USA
| | - Zekun Mu
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Qifeng Han
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Elizabeth Carter
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
- St. Jude Children's Research Hospital, Department of Structural Biology, 262 Danny Thomas Place, Memphis, TN, 38105-3678, USA
| | - R J Edwards
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin Wiehe
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, NC, 27708, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - Barton F Haynes
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - S Munir Alam
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
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Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE. An intrinsically disordered proteins community for ELIXIR. F1000Res 2019; 8. [PMID: 31824649 PMCID: PMC6880265 DOI: 10.12688/f1000research.20136.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2019] [Indexed: 01/20/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, Institute of Cancer Research, UK, London, SW3 6JB, UK
| | - M Madan Babu
- MRC Laboratory of Molecular Biology,, Cambridge, CB2 0QH, UK
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, 38000, France
| | - Alan Bridge
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Zsuzsanna Dosztanyi
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | | | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Isabella C Felli
- Department of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - John M Hancock
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Jen Harrow
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Desmond Higgins
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Philippe Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Balint Mészáros
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Marco Necci
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - Christos A Ouzounis
- BCPL-CPERI, Centre for Research & Technology Hellas (CERTH), Thessalonica, 57001, Greece
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Roberta Pierattelli
- Department of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Patrick Ruch
- HES-SO/HEG and SIB Text Mining, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Gabriella Rustici
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Pedro Romero
- University of Wisconsin-Madison, Madison, WI, 53706-1544, USA
| | | | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Malvika Sharan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Denis C Shields
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
| | - Joel L Sussman
- Department of Structural Biology and the Israel Structural Proteomics, Center (ISPC), Weizmann Institute of Science, Reḥovot, 7610001, Israel
| | | | - Peter Tompa
- VIB Center for Structural Biology (CSB), VIB Flemish Institute for Biotechnology, Brussels, 1050, Belgium
| | - Michael Turewicz
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, GesundheitsCampus 4, Bochum, 44801, Germany
| | - Jiri Vondrasek
- Institute of Organic Chemistry and Biochemistry, CAS, Prague, Czech Republic
| | - Wim F Vranken
- VUB/ULB Interuniversity Institute of Bioinformatics in Brussels and Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
| | - Bonnie Ann Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1H 0HA, UK
| | - Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
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Holland SI, Edwards RJ, Ertan H, Wong YK, Russell TL, Deshpande NP, Manefield MJ, Lee M. Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture. PeerJ 2019; 7:e7775. [PMID: 31592187 PMCID: PMC6778437 DOI: 10.7717/peerj.7775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/27/2019] [Indexed: 01/07/2023] Open
Abstract
Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CH2Cl2) are of great interest for potential bioremediation applications. A novel, strictly anaerobic, DCM-fermenting bacterium, "DCMF", was enriched from organochlorine-contaminated groundwater near Botany Bay, Australia. The enrichment culture was maintained in minimal, mineral salt medium amended with dichloromethane as the sole energy source. PacBio whole genome SMRTTM sequencing of DCMF allowed de novo, gap-free assembly despite the presence of cohabiting organisms in the culture. Illumina sequencing reads were utilised to correct minor indels. The single, circularised 6.44 Mb chromosome was annotated with the IMG pipeline and contains 5,773 predicted protein-coding genes. Based on 16S rRNA gene and predicted proteome phylogeny, the organism appears to be a novel member of the Peptococcaceae family. The DCMF genome is large in comparison to known DCM-fermenting bacteria. It includes an abundance of methyltransferases, which may provide clues to the basis of its DCM metabolism, as well as potential to metabolise additional methylated substrates such as quaternary amines. Full annotation has been provided in a custom genome browser and search tool, in addition to multiple sequence alignments and phylogenetic trees for every predicted protein, http://www.slimsuite.unsw.edu.au/research/dcmf/.
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Affiliation(s)
- Sophie I. Holland
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Haluk Ertan
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
- School of Chemical Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Yie Kuan Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Tonia L. Russell
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales, Australia
| | - Nandan P. Deshpande
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael J. Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, Australia
- School of Chemical Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, Australia
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Schneider MV, Griffin PC, Tyagi S, Flannery M, Dayalan S, Gladman S, Watson-Haigh N, Bayer PE, Charleston M, Cooke I, Cook R, Edwards RJ, Edwards D, Gorse D, McConville M, Powell D, Wilkins MR, Lonie A. Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Brief Bioinform 2019; 20:384-389. [PMID: 29106479 PMCID: PMC6433737 DOI: 10.1093/bib/bbx071] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
EMBL Australia Bioinformatics Resource (EMBL-ABR) is a developing national research infrastructure, providing bioinformatics resources and support to life science and biomedical researchers in Australia. EMBL-ABR comprises 10 geographically distributed national nodes with one coordinating hub, with current funding provided through Bioplatforms Australia and the University of Melbourne for its initial 2-year development phase. The EMBL-ABR mission is to: (1) increase Australia’s capacity in bioinformatics and data sciences; (2) contribute to the development of training in bioinformatics skills; (3) showcase Australian data sets at an international level and (4) enable engagement in international programs. The activities of EMBL-ABR are focussed in six key areas, aligning with comparable international initiatives such as ELIXIR, CyVerse and NIH Commons. These key areas—Tools, Data, Standards, Platforms, Compute and Training—are described in this article.
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Affiliation(s)
- Maria Victoria Schneider
- University of Melbourne Melbourne Institute, Carlton Victoria, Australia
- Corresponding author: Maria Victoria Schneider, University of Melbourne, Australia. Tel.:+61 3 8344 1395; E-mail: ; Andrew Lonie, University of Melbourne, Australia. Tel.: +61 3 8344 1395; E-mail:
| | - Philippa C Griffin
- EMBL Australia Bioinformatics Resource, EMBL-ABR Hub, Melbourne, Victoria, Australia
| | - Sonika Tyagi
- Australian Genome Research Facility, Bioinformatics, 1G royal Pde Parkville, Victoria, Australia
| | - Madison Flannery
- EMBL Australia Bioinformatics Resource, EMBL-ABR Hub, Melbourne, Victoria, Australia
| | - Saravanan Dayalan
- University of Melbourne Bio21 Molecular Science and Biotechnology Institute, Metabolomics Platform, Parkville Victoria, Australia
| | - Simon Gladman
- EMBL Australia Bioinformatics Resource, EMBL-ABR Hub, Melbourne, Victoria, Australia
| | | | - Philipp E Bayer
- University of Western Australia, School of Plant Biology, Crawley, Western Australia, Australia
| | - Michael Charleston
- University of Tasmania Menzies Institute for Medical Research, Hobart Tasmania, Australia
| | - Ira Cooke
- James Cook University, College of Public Health, Medical & Vet Sciences, Townsville, Queensland, Australia
| | - Rob Cook
- University of New South Wales, Sydney, Australia
| | | | - David Edwards
- University of Western Australia, School of Plant Biology, Crawley, Western Australia, Western Australia
| | - Dominique Gorse
- Queensland Facility for Advanced Bioinformatics, Brisbane, Queensland, Australia
| | - Malcolm McConville
- University of Melbourne Bio21 Molecular Science and Biotechnology Institute, Parkville Victoria, Australia
| | | | - Marc R Wilkins
- University of New South Wales, School of Biotechnology and Biomolecular Sciences, Sydney, Australia
| | - Andrew Lonie
- University of Melbourne Department of General Practice and Primary Health Care, Melbourne Bioinformatics, Carlton Victoria, Australia
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Ashida R, Cerminara NL, Edwards RJ, Apps R, Brooks JCW. Sensorimotor, language, and working memory representation within the human cerebellum. Hum Brain Mapp 2019; 40:4732-4747. [PMID: 31361075 PMCID: PMC6865458 DOI: 10.1002/hbm.24733] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 01/10/2023] Open
Abstract
The cerebellum is involved in a wide range of behaviours. A key organisational principle from animal studies is that somatotopically corresponding sensory input and motor output reside in the same cerebellar cortical areas. However, compelling evidence for a similar arrangement in humans and whether it extends to cognitive functions is lacking. To address this, we applied cerebellar optimised whole‐brain functional MRI in 20 healthy subjects. To assess spatial overlap within the sensorimotor and cognitive domains, we recorded activity to a sensory stimulus (vibrotactile) and a motor task; the Sternberg verbal working memory (VWM) task; and a verb generation paradigm. Consistent with animal data, sensory and motor activity overlapped with a somatotopic arrangement in ipsilateral areas of the anterior and posterior cerebellum. During the maintenance phase of the Sternberg task, a positive linear relationship between VWM load and activity was observed in right Lobule VI, extending into Crus I bilaterally. Articulatory movement gave rise to bilateral activity in medial Lobule VI. A conjunction of two independent language tasks localised activity during verb generation in right Lobule VI‐Crus I, which overlapped with activity during VWM. These results demonstrate spatial compartmentalisation of sensorimotor and cognitive function in the human cerebellum, with each area involved in more than one aspect of a given behaviour, consistent with an integrative function. Sensorimotor localisation was uniform across individuals, but the representation of cognitive tasks was more variable, highlighting the importance of individual scans for mapping higher order functions within the cerebellum.
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Affiliation(s)
- Reiko Ashida
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK.,Neurosurgery Department, Southmead Hospital, North Bristol Trust, Bristol, UK.,Neurosurgery Department, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Nadia L Cerminara
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Richard J Edwards
- Neurosurgery Department, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, UK.,Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard Apps
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
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38
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Song W, Thomas T, Edwards RJ. Complete genome sequences of pooled genomic DNA from 10 marine bacteria using PacBio long-read sequencing. Mar Genomics 2019; 48:100687. [PMID: 31129166 DOI: 10.1016/j.margen.2019.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 03/28/2019] [Revised: 05/15/2019] [Accepted: 05/15/2019] [Indexed: 11/27/2022]
Abstract
BACKGROUND High-quality, completed genomes are important to understand the functions of marine bacteria. PacBio sequencing technology provides a powerful way to obtain high-quality completed genomes. However individual library production is currently still costly, limiting the utility of the PacBio system for high-throughput genomics. Here we investigate how to generate high-quality genomes from pooled marine bacterial genomes. RESULTS Pooled genomic DNA from 10 marine bacteria were subjected to a single library production and sequenced with eight SMRT cells on the PacBio RS II sequencing platform. In total, 7.35 Gbp of long-read data was generated, which is equivalent to an approximate 168× average coverage for the input genomes. Genome assembly showed that eight genomes with average nucleotide identities (ANI) lower than 91.4% can be assembled with high-quality and completion using standard assembly algorithms (e.g. HGAP or Canu). A reference-based reads phasing step was developed and incorporated to assemble the complete genomes of the remaining two marine bacteria that had an ANI > 97% and whose initial assemblies were highly fragmented. CONCLUSIONS Ten complete high-quality genomes of marine bacteria were generated. The findings and developments made here, including the reference-based read phasing approach for the assembly of highly similar genomes, can be used in the future to design strategies to sequence pooled genomes using long-read sequencing.
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Affiliation(s)
- Weizhi Song
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia; Centre for Marine Bio-Innovation, University of New South Wales, Sydney, Australia.
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, Australia; School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia.
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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Jeffery SMT, Markia B, Pople IK, Aquilina K, Smith J, Mohamed AZ, Burchell A, Jenkins L, Walsh P, Clark N, Sacree J, Cramp M, Babiker MOE, Atherton WG, Clarke A, Edwards RJ. Surgical Outcomes of Single-Level Bilateral Selective Dorsal Rhizotomy for Spastic Diplegia in 150 Consecutive Patients. World Neurosurg 2019; 125:e60-e66. [PMID: 30659965 DOI: 10.1016/j.wneu.2018.12.187] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 05/28/2018] [Revised: 12/20/2018] [Accepted: 12/23/2018] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Selective dorsal rhizotomy (SDR) is used to improve spasticity, gait, and pain in children with spastic diplegia. There is growing evidence supporting its long-term benefits in terms of functional outcomes, independence, and quality of life. There is, however, little contemporary work describing the surgical morbidity of this irreversible procedure. The purpose of this study is to evaluate the surgical outcomes and complications of SDR at a single United Kingdom center. METHODS Demographics, surgical, postoperative, and follow-up data for all patients undergoing SDR between 2011 and 2016 were collected from medical records. RESULTS Preoperative Gross Motor Function Classification System levels in 150 consecutive patients were II (35%), III (65%), and IV (1%). Median age was 6 years and 58% were male patients. There were no deaths, cerebrospinal fluid leaks, returns to theater, or readmissions within 30 days. There were no new motor or sphincter deficits. Postoperative neuropathic pain was reported by 5.3% and sensory symptoms by 8.7%. Other complications included: postoperative nausea and vomiting (19.3%), superficial wound infection (3.3%), urinary retention (1.3%), headache (6.7%), and urine or chest infection (4.7%). Follow-up data were available for all patients (93% to 12 months, 72% to 24 months). Persistent neuropathic symptoms were reported in 6.5% at 24 months. CONCLUSIONS SDR using a single-level approach is a safe procedure with low surgical morbidity. This study complements the growing evidence base in support of SDR for spastic diplegia and should help inform decisions when considering treatment options.
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Affiliation(s)
- Samuel M T Jeffery
- Department of Neurosurgery, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom; Department of Neurosurgery, North Bristol NHS Trust, Bristol, United Kingdom; South West Neurosurgery Centre, Derriford Hospital, University Hospitals Plymouth NHS Trust, Plymouth, Devon, United Kingdom
| | - Balázs Markia
- Department of Neurosurgery, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom; National Institute for Clinical Neurosciences, Budapest, Hungary
| | - Ian K Pople
- Department of Neurosurgery, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom; Department of Neurosurgery, North Bristol NHS Trust, Bristol, United Kingdom
| | - Kristian Aquilina
- Department of Neurosurgery, North Bristol NHS Trust, Bristol, United Kingdom; Department of Neurosurgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Jenny Smith
- Department of Paediatric Physiotherapy, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Amr Z Mohamed
- Department of Neurosurgery, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom; Department of Neurosurgery, North Bristol NHS Trust, Bristol, United Kingdom
| | - Alison Burchell
- Department of Paediatric Physiotherapy, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Lyn Jenkins
- Department of Paediatric Physiotherapy, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Peter Walsh
- Department of Neurophysiology, North Bristol NHS Trust, Bristol, United Kingdom
| | - Natasha Clark
- Department of Paediatric Anaesthesia, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Jenny Sacree
- Department of Neurosurgery, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom; Department of Neurosurgery, North Bristol NHS Trust, Bristol, United Kingdom
| | - Mary Cramp
- Centre for Health and Clinical Research, University of the West of England, Bristol, United Kingdom
| | - Mohamed O E Babiker
- Department of Paediatric Neurology, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - William Guy Atherton
- Department of Orthopaedic Surgery, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Anna Clarke
- Department of Orthopaedic Surgery, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Richard J Edwards
- Department of Neurosurgery, Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom; Department of Neurosurgery, North Bristol NHS Trust, Bristol, United Kingdom; School of Clinical Sciences, University of Bristol, Bristol, United Kingdom.
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Idrees S, Pérez-Bercoff Å, Edwards RJ. Correction: SLiMEnrich: computational assessment of protein–protein interaction data as a source of domain-motif interactions. PeerJ 2018; 6:5858/correction-1. [PMID: 30488013 PMCID: PMC6248090 DOI: 10.7717/peerj.5858/correction-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Sobia Idrees
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Åsa Pérez-Bercoff
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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41
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Idrees S, Pérez-Bercoff Å, Edwards RJ. SLiM-Enrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions. PeerJ 2018; 6:e5858. [PMID: 30402352 PMCID: PMC6215436 DOI: 10.7717/peerj.5858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/02/2018] [Indexed: 01/21/2023] Open
Abstract
Many important cellular processes involve protein–protein interactions (PPIs) mediated by a Short Linear Motif (SLiM) in one protein interacting with a globular domain in another. Despite their significance, these domain-motif interactions (DMIs) are typically low affinity, which makes them challenging to identify by classical experimental approaches, such as affinity pulldown mass spectrometry (AP-MS) and yeast two-hybrid (Y2H). DMIs are generally underrepresented in PPI networks as a result. A number of computational methods now exist to predict SLiMs and/or DMIs from experimental interaction data but it is yet to be established how effective different PPI detection methods are for capturing these low affinity SLiM-mediated interactions. Here, we introduce a new computational pipeline (SLiM-Enrich) to assess how well a given source of PPI data captures DMIs and thus, by inference, how useful that data should be for SLiM discovery. SLiM-Enrich interrogates a PPI network for pairs of interacting proteins in which the first protein is known or predicted to interact with the second protein via a DMI. Permutation tests compare the number of known/predicted DMIs to the expected distribution if the two sets of proteins are randomly associated. This provides an estimate of DMI enrichment within the data and the false positive rate for individual DMIs. As a case study, we detect significant DMI enrichment in a high-throughput Y2H human PPI study. SLiM-Enrich analysis supports Y2H data as a source of DMIs and highlights the high false positive rates associated with naïve DMI prediction. SLiM-Enrich is available as an R Shiny app. The code is open source and available via a GNU GPL v3 license at: https://github.com/slimsuite/SLiMEnrich. A web server is available at: http://shiny.slimsuite.unsw.edu.au/SLiMEnrich/.
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Affiliation(s)
- Sobia Idrees
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Åsa Pérez-Bercoff
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Edwards RJ, Tuipulotu DE, Amos TG, O'Meally D, Richardson MF, Russell TL, Vallinoto M, Carneiro M, Ferrand N, Wilkins MR, Sequeira F, Rollins LA, Holmes EC, Shine R, White PA. Draft genome assembly of the invasive cane toad, Rhinella marina. Gigascience 2018; 7:5096832. [PMID: 30101298 PMCID: PMC6145236 DOI: 10.1093/gigascience/giy095] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 03/22/2018] [Accepted: 07/22/2018] [Indexed: 12/28/2022] Open
Abstract
Background The cane toad (Rhinella marina formerly Bufo marinus) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding of cane toad genetics. The availability of a genome would help to close these gaps and accelerate cane toad research. Findings We report a draft genome assembly for R. marina, the first of its kind for the Bufonidae family. We used a combination of long-read Pacific Biosciences RS II and short-read Illumina HiSeq X sequencing to generate 359.5 Gb of raw sequence data. The final hybrid assembly of 31,392 scaffolds was 2.55 Gb in length with a scaffold N50 of 168 kb. BUSCO analysis revealed that the assembly included full length or partial fragments of 90.6% of tetrapod universal single-copy orthologs (n = 3950), illustrating that the gene-containing regions have been well assembled. Annotation predicted 25,846 protein coding genes with similarity to known proteins in Swiss-Prot. Repeat sequences were estimated to account for 63.9% of the assembly. Conclusions The R. marina draft genome assembly will be an invaluable resource that can be used to further probe the biology of this invasive species. Future analysis of the genome will provide insights into cane toad evolution and enrich our understanding of their interplay with the ecosystem at large.
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Affiliation(s)
- Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Denis O'Meally
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camperdown, NSW, 2052, Australia
| | - Mark F Richardson
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3216, Australia.,Bioinformatics Core Research Group, Deakin University, Geelong, VIC, 3216, Australia
| | - Tonia L Russell
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Marcelo Vallinoto
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Laboratório de Evolução, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, South Africa
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,Ramaciotti Centre for Genomics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Fernando Sequeira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Lee A Rollins
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3216, Australia.,Evolution and Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Richard Shine
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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Affiliation(s)
- Richard J Edwards
- Department of Neurosurgery, Atkinson Morley's Hospital, Copse Hill, Wimbledon, London SW20 0NE
| | - Gavin W Britz
- Department of Neurological Surgery, University of Washington School of Medicine, and Harborview Medical Center, Seattle, Washington, USA
| | - Henry Marsh
- Department of Neurosurgery, Atkinson Morley's Hospital, Copse Hill, Wimbledon, London SW20 0NE
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44
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Glenn WK, Ngan CC, Amos TG, Edwards RJ, Swift J, Lutze-Mann L, Shang F, Whitaker NJ, Lawson JS. High risk human papilloma viruses (HPVs) are present in benign prostate tissues before development of HPV associated prostate cancer. Infect Agent Cancer 2017; 12:46. [PMID: 28811834 PMCID: PMC5553674 DOI: 10.1186/s13027-017-0157-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/05/2017] [Indexed: 12/31/2022] Open
Abstract
Background Although high risk HPVs are associated with an increased risk of prostate cancer it is not known if they have a causal role. The purpose of this study is to investigate the potential role of human papilloma viruses (HPVs) in prostate cancer. The aims are (i) to investigate the presence and confirm the identity of high risk HPVs in benign prostate tissues prior to the development of HPV positive prostate cancer in the same patients, and (ii) to determine if HPVs are biologically active. Methods We used polymerase chain reaction (PCR) to identify HPVs in specimens from 52 Australian men with benign prostate biopsies who 1 to 10 years later developed prostate cancer. Immunohistochemistry (IHC) was used to assess the expression of HPV E7 oncoproteins, cytokeratin and prostate specific antigen (PSA). We used RNASeq data from The Cancer Genome Atlas (TCGA) to identify possible HPV RNA sequences in prostate cancer. Results HPV screening using standard PCR was conducted on 28 of the 52 sets of benign and later prostate cancers. HPV L1 genes were identified in 13 (46%) benign and 8 (29%) of 28 later prostate cancers in the same patients. HPV E7 genes were identified in 23 (82%) benign and 19 (68%) of 28 subsequent prostate cancers in the same patients. The same HPV types were present in both the benign and subsequent prostate cancers in 9 sets of specimens. HPV type 16 was identified in 15% of benign and 3% of prostate cancers. HPV type 18 was identified in 26% of benign and 16% of prostate cancers. Small numbers of HPV types 45, 47, 76 and 115 were also identified. High confidence RNA-Seq evidence for high risk HPV types 16 and 18 was identified in 12 (2%) of the 502 TCGA prostate cancer transcriptomes. High risk HPV E7 oncoprotein was positively expressed in 23 (82%) of 28 benign prostate specimens but only in 8 (29%) of 28 of the later prostate cancer specimens. This difference is statistically significant (p = 0.001). Prostate specific antigen (PSA) was more highly expressed in 26 (50%) of 52 prostate cancer specimens as compared to prior benign prostate specimens in the same patients. Conclusions High risk HPVs are present in benign prostate tissues prior to the development of HPV positive prostate cancer. There is a significantly higher expression of HPV E7 oncoproteins in benign prostate tissues as compared to late prostate cancer that subsequently developed in the same patients. This observation suggests that HPV oncogenic activity is an early phenomenon in a majority of prostate oncogenesis. TCGA RNA-Seq data suggests that HPV is biologically active in some prostate tumour samples. Electronic supplementary material The online version of this article (doi:10.1186/s13027-017-0157-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wendy K Glenn
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Christopher C Ngan
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Joshua Swift
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Louise Lutze-Mann
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Fei Shang
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Noel J Whitaker
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - James S Lawson
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
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45
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Adam A, Robison J, Lu J, Jose R, Badran N, Vivas-Buitrago T, Rigamonti D, Sattar A, Omoush O, Hammad M, Dawood M, Maghaslah M, Belcher T, Carson K, Hoffberger J, Jusué Torres I, Foley S, Yasar S, Thai QA, Wemmer J, Klinge P, Al-Mutawa L, Al-Ghamdi H, Carson KA, Asgari M, de Zélicourt D, Kurtcuoglu V, Garnotel S, Salmon S, Balédent O, Lokossou A, Page G, Balardy L, Czosnyka Z, Payoux P, Schmidt EA, Zitoun M, Sevestre MA, Alperin N, Baudracco I, Craven C, Matloob S, Thompson S, Haylock Vize P, Thorne L, Watkins LD, Toma AK, Bechter K, Pong AC, Jugé L, Bilston LE, Cheng S, Bradley W, Hakim F, Ramón JF, Cárdenas MF, Davidson JS, García C, González D, Bermúdez S, Useche N, Mejía JA, Mayorga P, Cruz F, Martinez C, Matiz MC, Vallejo M, Ghotme K, Soto HA, Riveros D, Buitrago A, Mora M, Murcia L, Bermudez S, Cohen D, Dasgupta D, Curtis C, Domínguez L, Remolina AJ, Grijalba MA, Whitehouse KJ, Edwards RJ, Eleftheriou A, Lundin F, Fountas KN, Kapsalaki EZ, Smisson HF, Robinson JS, Fritsch MJ, Arouk W, Garzon M, Kang M, Sandhu K, Baghawatti D, Aquilina K, James G, Thompson D, Gehlen M, Schmid Daners M, Eklund A, Malm J, Gomez D, Guerra M, Jara M, Flores M, Vío K, Moreno I, Rodríguez S, Ortega E, Rodríguez EM, McAllister JP, Guerra MM, Morales DM, Sival D, Jimenez A, Limbrick DD, Ishikawa M, Yamada S, Yamamoto K, Junkkari A, Häyrinen A, Rauramaa T, Sintonen H, Nerg O, Koivisto AM, Roine RP, Viinamäki H, Soininen H, Luikku A, Jääskeläinen JE, Leinonen V, Kehler U, Lilja-Lund O, Kockum K, Larsson EM, Riklund K, Söderström L, Hellström P, Laurell K, Kojoukhova M, Sutela A, Vanninen R, Vanha KI, Timonen M, Rummukainen J, Korhonen V, Helisalmi S, Solje E, Remes AM, Huovinen J, Paananen J, Hiltunen M, Kurki M, Martin B, Loth F, Luciano M, Luikku AJ, Hall A, Herukka SK, Mattila J, Lötjönen J, Alafuzoff I, Jurjević I, Miyajima M, Nakajima M, Murai H, Shin T, Kawaguchi D, Akiba C, Ogino I, Karagiozov K, Arai H, Reis RC, Teixeira MJ, Valêncio CG, da Vigua D, Almeida-Lopes L, Mancini MW, Pinto FCG, Maykot RH, Calia G, Tornai J, Silvestre SSS, Mendes G, Sousa V, Bezerra B, Dutra P, Modesto P, Oliveira MF, Petitto CE, Pulhorn H, Chandran A, McMahon C, Rao AS, Jumaly M, Solomon D, Moghekar A, Relkin N, Hamilton M, Katzen H, Williams M, Bach T, Zuspan S, Holubkov R, Rigamonti A, Clemens G, Sharkey P, Sanyal A, Sankey E, Rigamonti K, Naqvi S, Hung A, Schmidt E, Ory-Magne F, Gantet P, Guenego A, Januel AC, Tall P, Fabre N, Mahieu L, Cognard C, Gray L, Buttner-Ennever JA, Takagi K, Onouchi K, Thompson SD, Thorne LD, Tully HM, Wenger TL, Kukull WA, Doherty D, Dobyns WB, Moran D, Vakili S, Patel MA, Elder B, Goodwin CR, Crawford JA, Pletnikov MV, Xu J, Blitz A, Herzka DA, Guerrero-Cazares H, Quiñones-Hinojosa A, Mori S, Saavedra P, Treviño H, Maitani K, Ziai WC, Eslami V, Nekoovaght-Tak S, Dlugash R, Yenokyan G, McBee N, Hanley DF. Abstracts from Hydrocephalus 2016. Fluids Barriers CNS 2017; 14:15. [PMID: 28929972 PMCID: PMC5471936 DOI: 10.1186/s12987-017-0054-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- A Adam
- Johns Hopkins University, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA.,Johns Hopkins Biostatistics Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - J Robison
- Johns Hopkins University, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - J Lu
- Johns Hopkins University, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - R Jose
- Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - N Badran
- Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - T Vivas-Buitrago
- Johns Hopkins University, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - D Rigamonti
- Johns Hopkins University, Baltimore, MD, USA.,Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.,Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.,Johns Hopkins Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - A Sattar
- Johns Hopkins Aramco Healthcare, Ras Tanura, Saudi Arabia.,Primary Care, Johns Hopkins Aramco Healthcare, Ras Tanura, Saudi Arabia
| | - O Omoush
- Johns Hopkins Aramco Healthcare, Ras Tanura, Saudi Arabia.,Primary Care, Johns Hopkins Aramco Healthcare, Ras Tanura, Saudi Arabia
| | - M Hammad
- Johns Hopkins Aramco Healthcare, Ras Tanura, Saudi Arabia
| | - M Dawood
- Johns Hopkins Aramco Healthcare, Ras Tanura, Saudi Arabia
| | - M Maghaslah
- Johns Hopkins Aramco Healthcare, Ras Tanura, Saudi Arabia
| | - T Belcher
- Johns Hopkins Aramco Healthcare, Ras Tanura, Saudi Arabia
| | - K Carson
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA.,Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - J Hoffberger
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
| | - I Jusué Torres
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - S Foley
- Department of Neurosurgery, Rhode Island Hospital, Providence, RI, USA
| | - S Yasar
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
| | - Q A Thai
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
| | - J Wemmer
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
| | - P Klinge
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
| | - L Al-Mutawa
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
| | - H Al-Ghamdi
- Department of Neurosurgery, Rhode Island Hospital, Providence, RI, USA
| | - K A Carson
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - M Asgari
- The Interface Group, Institute of PhysiologyUniversity of Zurich, Zurich, Switzerland
| | - D de Zélicourt
- The Interface Group, Institute of PhysiologyUniversity of Zurich, Zurich, Switzerland
| | - V Kurtcuoglu
- The Interface Group, Institute of PhysiologyUniversity of Zurich, Zurich, Switzerland.,Institute of Physiology, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich and the Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - S Garnotel
- BioFlowImage Laboratory, University of Picardie Jules Verne, Amiens, France.,Reims Mathematics Laboratory, University of Reims Champagne-Ardenne, Reims, France.,Image Processing Laboratory, University Hospital of Amiens-Picardie, Amiens, France.,BioFlowImage Laboratory, Department of Medical Image Processing, University Hospital of Picardie Jules Verne, Amiens, France
| | - S Salmon
- Reims Mathematics Laboratory, University of Reims Champagne-Ardenne, Reims, France
| | - O Balédent
- BioFlowImage Laboratory, University of Picardie Jules Verne, Amiens, France.,Image Processing Laboratory, University Hospital of Amiens-Picardie, Amiens, France.,BioFlowImage Laboratory, Department of Medical Image Processing, University Hospital of Picardie Jules Verne, Amiens, France
| | - A Lokossou
- BioFlowImage Laboratory, Department of Medical Image Processing, University Hospital of Picardie Jules Verne, Amiens, France
| | - G Page
- BioFlowImage Laboratory, Department of Medical Image Processing, University Hospital of Picardie Jules Verne, Amiens, France
| | - L Balardy
- Department of Geriatric, University Hospital of Toulouse, Toulouse, France.,Departments of Geriatric, University Hospital of Toulouse, Toulouse, France.,Department of Geriatry, University Hospital Toulouse, Toulouse, France
| | - Z Czosnyka
- Neurosciences department, University of Cambridge, Cambridge, UK.,Brain Physics Lab, Academic Neurosurgery, University of Cambridge, Cambridge, UK
| | - P Payoux
- Department of Nuclear Medicine, University Hospital of Toulouse, Toulouse, France.,Department of Nuclear Medicine, University Hospital Toulouse, Toulouse, France.,INSER TONIC 1014, Toulouse Neuroimaging Center, Toulouse, France
| | - E A Schmidt
- UMR 1214-INSERM/UPS-TONIC Toulouse Neuro-Imaging Center, Toulouse, France.,Department of Neurosurgery, University Hospital of Toulouse, Toulouse, France.,Department of Neurosurgery, University Hospital Toulouse, Toulouse, France
| | - M Zitoun
- BioFlowImage, University Hospital of Picardie Jules Verne, Amiens, France
| | - M A Sevestre
- BioFlowImage, University Hospital of Picardie Jules Verne, Amiens, France
| | - N Alperin
- University of Miami Health System, Miami, FL, USA
| | - I Baudracco
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UK
| | - C Craven
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UK
| | - S Matloob
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UK
| | - S Thompson
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UK
| | - P Haylock Vize
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UK
| | - L Thorne
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UK
| | - L D Watkins
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UK.,The National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - A K Toma
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UK.,The National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - Karl Bechter
- Department Psychiatry II/Bezirkskliniken, Ulm University, Günzburg, Germany
| | - A C Pong
- Neuroscience Research Australia, Randwick, Australia.,School of Medical Sciences, University of New South Wales, Kensington, Australia
| | - L Jugé
- Neuroscience Research Australia, Randwick, Australia.,School of Medical Sciences, University of New South Wales, Kensington, Australia
| | - L E Bilston
- Neuroscience Research Australia, Randwick, Australia.,Prince of Wales Clinical School, University of New South Wales, Kensington, Australia
| | - S Cheng
- Neuroscience Research Australia, Randwick, Australia.,Department of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - W Bradley
- Department of Radiology, University of California San Diego Health System, San Diego, CA, USA
| | - F Hakim
- Department of Surgery, Section of Neurosurgery, Fundación Santa Fe de Bogotá, Bogotá, Colombia.,Neurosurgery Department, Hospital Universitario, Fundación Santafe de Bogota, Bogota, Colombia
| | - J F Ramón
- Department of Surgery, Section of Neurosurgery, Fundación Santa Fe de Bogotá, Bogotá, Colombia.,Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia.,Neurosurgery Department, Hospital Universitario, Fundación Santafe de Bogota, Bogota, Colombia
| | - M F Cárdenas
- Department of Surgery, Section of Neurosurgery, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - J S Davidson
- Department of Surgery, Section of Neurosurgery, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - C García
- Department of Surgery, Section of Neurosurgery, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - D González
- Department of Surgery, Section of Neurosurgery, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - S Bermúdez
- Department of Diagnostic Imaging, Section of Neuroradiology, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - N Useche
- Department of Diagnostic Imaging, Section of Neuroradiology, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - J A Mejía
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - P Mayorga
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - F Cruz
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - C Martinez
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - M C Matiz
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - M Vallejo
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - K Ghotme
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - H A Soto
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - D Riveros
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - A Buitrago
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - M Mora
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - L Murcia
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - S Bermudez
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - D Cohen
- Grupo de Hidrocefalia con Presión Normal, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - D Dasgupta
- Victor Horsley Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, London, UK
| | - C Curtis
- Department of Microbiology, University College London Hospital NHS Foundation Trust, London, UK
| | - L Domínguez
- Neurosurgery Department, Cartagena University, Cartagena de Indias, Colombia
| | - A J Remolina
- Neurosurgery Department, Cartagena University, Cartagena de Indias, Colombia
| | - M A Grijalba
- Neurosurgery Department, Cartagena University, Cartagena de Indias, Colombia
| | - K J Whitehouse
- Department of Paediatric Neurosurgery, Bristol Royal Hospital for Children, Bristol, UK
| | - R J Edwards
- Department of Paediatric Neurosurgery, Bristol Royal Hospital for Children, Bristol, UK
| | - A Eleftheriou
- Department of Neurology, University Hospital, Linköping, Sweden
| | - F Lundin
- Division of Neuroscience, Department of Clinical and Experimental Medicine (IKE), Linköping University, Linköping, Sweden
| | - K N Fountas
- Department of Neurosurgery, School of Medicine, University of Thessaly, Larisa, Greece
| | - E Z Kapsalaki
- Department of Diagnostic Radiology, School of Medicine, University of Thessaly, Larisa, Greece
| | - H F Smisson
- Department of Neurosurgery, Georgia Neurosurgical Institute, Macon, GA, USA
| | - J S Robinson
- Department of Neurosurgery, Georgia Neurosurgical Institute, Macon, GA, USA
| | - M J Fritsch
- Klinik für Neurochirurgie, Dietrich-Bonhoeffer-Klinikum, Neubrandenburg, Germany
| | - W Arouk
- Klinik für Neurochirurgie, Dietrich-Bonhoeffer-Klinikum, Neubrandenburg, Germany
| | - M Garzon
- Great Ormond Street Hospital, London, UK
| | - M Kang
- Great Ormond Street Hospital, London, UK
| | - K Sandhu
- Great Ormond Street Hospital, London, UK
| | | | - K Aquilina
- Great Ormond Street Hospital, London, UK
| | - G James
- Great Ormond Street Hospital, London, UK
| | - D Thompson
- Great Ormond Street Hospital, London, UK
| | - M Gehlen
- Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland.,Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - M Schmid Daners
- Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland
| | - A Eklund
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - J Malm
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
| | - D Gomez
- Neurosurgery Department, Hospital Universitario, Fundación Santafe de Bogota, Bogota, Colombia
| | - M Guerra
- Instituto de Anatomía, Histología y Patología, Facultad de Medicina, UACh, Valdivia, Chile
| | - M Jara
- Instituto de Anatomía, Histología y Patología, Facultad de Medicina, UACh, Valdivia, Chile
| | - M Flores
- Laboratorio de Polímeros, Facultad de Ciencias, UACh, Valdivia, Chile
| | - K Vío
- Instituto de Anatomía, Histología y Patología, Facultad de Medicina, UACh, Valdivia, Chile
| | - I Moreno
- Laboratorio de Polímeros, Facultad de Ciencias, UACh, Valdivia, Chile
| | - S Rodríguez
- Instituto de Anatomía, Histología y Patología, Facultad de Medicina, UACh, Valdivia, Chile
| | - E Ortega
- Instituto de Neurociencias Clínicas, Facultad de Medicina, UACh, Valdivia, Chile
| | - E M Rodríguez
- Instituto de Anatomía, Histología y Patología, Facultad de Medicina, UACh, Valdivia, Chile.,Instituto de Histologia y Patologia, Facultad de Medicina, Universidad Austral de Chile, Valdivia, Chile
| | - J P McAllister
- Department of Neurosurgery, St. Louis Children's Hospital, St. Louis, MO, USA
| | - M M Guerra
- Instituto de Histologia y Patologia, Facultad de Medicina, Universidad Austral de Chile, Valdivia, Chile
| | - D M Morales
- Department of Neurosurgery, St. Louis Children's Hospital, St. Louis, MO, USA
| | - D Sival
- Department of Pediatrics Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - A Jimenez
- Departamento de Biología Celular, Genética y Fisiología Facultad de Ciencias, Universidad de Malaga, Malaga, Spain
| | - D D Limbrick
- Department of Neurosurgery, St. Louis Children's Hospital, St. Louis, MO, USA.,Department of Pediatrics, St. Louis Children's Hospital, St. Louis, MO, USA
| | - M Ishikawa
- Rakuwa Villa Ilios, Kyoto, Japan.,Normal Pressure Hydrocephalus Center, Otowa Hospital, Kyoto, Japan
| | - S Yamada
- Normal Pressure Hydrocephalus Center, Otowa Hospital, Kyoto, Japan.,Department of Neurosurgery, Otowa Hospital, Kyoto, Japan
| | - K Yamamoto
- Department of Neurosurgery, Otowa Hospital, Kyoto, Japan
| | - A Junkkari
- Neurosurgery of NeuroCenter, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland.,Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland
| | - A Häyrinen
- Neurosurgery of NeuroCenter, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - T Rauramaa
- Department of Pathology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland.,Department of Pathology, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine-Pathology, University of Eastern Finland, Kuopio, Finland
| | - H Sintonen
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - O Nerg
- Neurology of NeuroCenter, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland.,Neurology of NeuroCenter, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - A M Koivisto
- Neurology of NeuroCenter, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland.,Unit of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,Neurology of NeuroCenter, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland.,Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - R P Roine
- University of Eastern Finland, Kuopio Finland and Helsinki and Uusimaa Hospital DistrictGroup Administration, Helsinki, Finland
| | - H Viinamäki
- Department of Psychiatry, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - H Soininen
- Department of Neurology, University of Eastern Finland, Kuopio, Finland.,Unit of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,Neurology of NeuroCenter, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland.,Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - A Luikku
- Neurology of NeuroCenter, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - J E Jääskeläinen
- Neurosurgery of NeuroCenter, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland.,Department of Neurosurgery, Kuopio University Hospital, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland
| | - V Leinonen
- Neurosurgery of NeuroCenter, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland.,Department of Neurosurgery, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland.,Department of Neurosurgery, Kuopio University Hospital, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland
| | - U Kehler
- Neurosurgical Department, Asklepios Klinik Hamburg Altona, Hamburg, Germany
| | - O Lilja-Lund
- Department of Pharmacology and Clinical Neuroscience, Unit of Neurology, Östersund, Umeå University, Umeå, Sweden
| | - K Kockum
- Department of Pharmacology and Clinical Neuroscience, Unit of Neurology, Östersund, Umeå University, Umeå, Sweden
| | - E M Larsson
- Department of Radiology, Uppsala University, Uppsala, Sweden
| | - K Riklund
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - L Söderström
- Department of Pharmacology and Clinical Neuroscience, Unit of Neurology, Östersund, Umeå University, Umeå, Sweden
| | - P Hellström
- Hydrocephalus Research Unit, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - K Laurell
- Department of Pharmacology and Clinical Neuroscience, Unit of Neurology, Östersund, Umeå University, Umeå, Sweden
| | - M Kojoukhova
- Neurosurgery of NeuroCenter, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland.,Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland.,Department of Radiology, Kuopio University Hospital, Kuopio, Finland
| | - A Sutela
- Department of Radiology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland.,Department of Radiology, Kuopio University Hospital, Kuopio, Finland
| | - R Vanninen
- Department of Radiology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - K I Vanha
- Neurosurgery of NeuroCenter, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - M Timonen
- Neurosurgery of NeuroCenter, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - J Rummukainen
- Department of Pathology, Kuopio University Hospital, Kuopio, Finland
| | - V Korhonen
- Department of Neurosurgery, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - S Helisalmi
- Unit of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland.,Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - E Solje
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland.,Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - A M Remes
- Unit of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,Neurology of NeuroCenter, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland.,Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - J Huovinen
- Department of Neurosurgery, Kuopio University Hospital, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - J Paananen
- Unit of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,Department of Neurology, Kuopio University Hospital, Kuopio, Finland.,Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - M Hiltunen
- Unit of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,Neurology of NeuroCenter, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland.,Department of Neurology, Kuopio University Hospital, Kuopio, Finland.,Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - M Kurki
- Department of Neurosurgery, Kuopio University Hospital, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute for Harvard and MIT, Cambridge, MA, USA
| | - B Martin
- Biological Engineering, University of Idaho, Moscow, ID, USA
| | - F Loth
- Mechanical Engineering, University of Akron, Akron, Ohio, USA
| | - M Luciano
- Neurosurgery, Johns Hopkins University, Baltimore, MA, USA.,Department of Neurosurgery, Johns Hopkins Hospital, Baltimore, MD, USA
| | - A J Luikku
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland.,Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland
| | - A Hall
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - S K Herukka
- Neurology of NeuroCenter, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - J Mattila
- VTT Technical Research Centre of Finland, Tampere, Finland.,Combinostics Ltd, Tampere, Finland
| | - J Lötjönen
- VTT Technical Research Centre of Finland, Tampere, Finland.,Combinostics Ltd, Tampere, Finland
| | - I Alafuzoff
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland.,Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.,Department of Pathology and Cytology, Uppsala University Hospital, Uppsala, Sweden
| | - I Jurjević
- Department of Neurosurgery, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Department of Pharmacology and Department of Neurology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - M Miyajima
- Department of Neurosurgery, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Department of Neurosurgery, Juntendo University School of Medicine, Tokyo, Japan
| | - M Nakajima
- Department of Neurosurgery, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Department of Neurosurgery, Juntendo University School of Medicine, Tokyo, Japan
| | - H Murai
- Department of Neurosurgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - T Shin
- Department of Neurosurgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - D Kawaguchi
- Department of Neurosurgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - C Akiba
- Department of Neurosurgery, Juntendo University School of Medicine, Tokyo, Japan
| | - I Ogino
- Department of Neurosurgery, Juntendo University School of Medicine, Tokyo, Japan
| | - K Karagiozov
- Department of Neurosurgery, Juntendo University School of Medicine, Tokyo, Japan
| | - H Arai
- Department of Neurosurgery, Juntendo University School of Medicine, Tokyo, Japan
| | - R C Reis
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - M J Teixeira
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - C G Valêncio
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - D da Vigua
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - L Almeida-Lopes
- Núcleo de Pesquisa e Ensino de Fototerapia nas Ciências da Saúde (NUPEN), São Carlos, Brazil
| | - M W Mancini
- Núcleo de Pesquisa e Ensino de Fototerapia nas Ciências da Saúde (NUPEN), São Carlos, Brazil
| | - F C G Pinto
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - R H Maykot
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - G Calia
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - J Tornai
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - S S S Silvestre
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - G Mendes
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - V Sousa
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - B Bezerra
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - P Dutra
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - P Modesto
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - M F Oliveira
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - C E Petitto
- Group of Cerebral Hydrodynamics, Division of Functional Neurosurgery, Institute of Psychiatry, Hospital das Clínicas, University of São Paulo, São Paulo, Brazil
| | - H Pulhorn
- Department of Neurosurgery, The Walton Centre, Liverpool, UK
| | - A Chandran
- Department of Neuroradiology, The Walton Centre, Liverpool, UK
| | - C McMahon
- Department of Neurosurgery, The Walton Centre, Liverpool, UK
| | - A S Rao
- The Johns Hopkins Hospital, Baltimore, MD, USA
| | - M Jumaly
- The Johns Hopkins Hospital, Baltimore, MD, USA
| | - D Solomon
- The Johns Hopkins Hospital, Baltimore, MD, USA.,Neurology, Johns Hopkins Hospital, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins Bayview Medical Center, Baltimore, MD, USA
| | - A Moghekar
- The Johns Hopkins Hospital, Baltimore, MD, USA
| | - N Relkin
- Department of Neurology, Weill Cornell Medical College, New York, NY, USA
| | - M Hamilton
- Department of Neurosurgery, University of Calgary, Alberta, Canada
| | - H Katzen
- Department of Neurology, University of Miami, Miami, FL, USA
| | - M Williams
- Department of Neurosurgery, Washington University, Seattle, WA, USA
| | - T Bach
- Utah Data Collection Center (DCC), University of Utah, Salt Lake City, UT, USA
| | - S Zuspan
- Utah Data Collection Center (DCC), University of Utah, Salt Lake City, UT, USA
| | - R Holubkov
- Utah Data Collection Center (DCC), University of Utah, Salt Lake City, UT, USA
| | | | - G Clemens
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - P Sharkey
- School of Business, Loyola University Maryland, Baltimore, MD, USA
| | - A Sanyal
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - E Sankey
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - K Rigamonti
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
| | - S Naqvi
- Primary Care, Johns Hopkins Aramco Healthcare, Abqaiq, Saudi Arabia
| | - A Hung
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - E Schmidt
- Department of Neurosurgery, University Hospital Toulouse, Toulouse, France
| | - F Ory-Magne
- Department of Neurology, University Hospital Toulouse, Toulouse, France.,INSER TONIC 1014, Toulouse Neuroimaging Center, Toulouse, France
| | - P Gantet
- Department of Nuclear Medicine, University Hospital Toulouse, Toulouse, France
| | - A Guenego
- Department of Neurosurgery, University Hospital Toulouse, Toulouse, France.,Department of Neuroradiology, University Hospital Toulouse, Toulouse, France
| | - A C Januel
- Department of Neuroradiology, University Hospital Toulouse, Toulouse, France
| | - P Tall
- Department of Neuroradiology, University Hospital Toulouse, Toulouse, France
| | - N Fabre
- Department of Neurology, University Hospital Toulouse, Toulouse, France
| | - L Mahieu
- Department of Ophtalmology, University Hospital Toulouse, Toulouse, France
| | - C Cognard
- Department of Neuroradiology, University Hospital Toulouse, Toulouse, France
| | - L Gray
- Department of Physiology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | | | - K Takagi
- Normal Pressure Hydrocephalus Center, Kashiwa-Tanaka Hospital, Kashiwa, Japan
| | - K Onouchi
- Department of Neurology, Kashiwa-Tanaka Hospital, Kashiwa, Japan
| | - S D Thompson
- The National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - L D Thorne
- The National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - H M Tully
- Department of Neurology, University of Washington, Seattle, WA, USA
| | - T L Wenger
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - W A Kukull
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - D Doherty
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - W B Dobyns
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - D Moran
- Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - S Vakili
- Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - M A Patel
- Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - B Elder
- Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - C R Goodwin
- Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - J A Crawford
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - M V Pletnikov
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - J Xu
- F. M. Kirby Research Center for Functional Brain Imaging at the Kennedy Krieger Institute, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - A Blitz
- Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - D A Herzka
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - H Guerrero-Cazares
- Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - A Quiñones-Hinojosa
- Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - S Mori
- Department of Radiology-Magnetic Resonance Research, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - P Saavedra
- Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - H Treviño
- Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - K Maitani
- Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.,Tohoku University School of Medicine, Sendai, Japan
| | - W C Ziai
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - V Eslami
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Nekoovaght-Tak
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - R Dlugash
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - G Yenokyan
- Department of Biostatistics, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - N McBee
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - D F Hanley
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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46
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Porretta E, Jeffery SM, Jordan SL, Male J, Edwards RJ, Love S, Scolding NJ, Rice CM. SAFETY AND UTILITY OF BRAINSTEM BIOPSY AND RESECTION. J Neurol Neurosurg Psychiatry 2016. [DOI: 10.1136/jnnp-2016-315106.196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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47
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Watson-Lazowski A, Lin Y, Miglietta F, Edwards RJ, Chapman MA, Taylor G. Plant adaptation or acclimation to rising CO 2 ? Insight from first multigenerational RNA-Seq transcriptome. Glob Chang Biol 2016; 22:3760-3773. [PMID: 27539677 DOI: 10.1111/gcb.13322] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 06/06/2023]
Abstract
Atmospheric carbon dioxide (CO2 ) directly determines the rate of plant photosynthesis and indirectly effects plant productivity and fitness and may therefore act as a selective pressure driving evolution, but evidence to support this contention is sparse. Using Plantago lanceolata L. seed collected from a naturally high CO2 spring and adjacent ambient CO2 control site, we investigated multigenerational response to future, elevated atmospheric CO2 . Plants were grown in either ambient or elevated CO2 (700 μmol mol-1 ), enabling for the first time, characterization of the functional and population genomics of plant acclimation and adaptation to elevated CO2 . This revealed that spring and control plants differed significantly in phenotypic plasticity for traits underpinning fitness including above-ground biomass, leaf size, epidermal cell size and number and stomatal density and index. Gene expression responses to elevated CO2 (acclimation) were modest [33-131 genes differentially expressed (DE)], whilst those between control and spring plants (adaptation) were considerably larger (689-853 DE genes). In contrast, population genomic analysis showed that genetic differentiation between spring and control plants was close to zero, with no fixed differences, suggesting that plants are adapted to their native CO2 environment at the level of gene expression. An unusual phenotype of increased stomatal index in spring but not control plants in elevated CO2 correlated with altered expression of stomatal patterning genes between spring and control plants for three loci (YODA, CDKB1;1 and SCRM2) and between ambient and elevated CO2 for four loci (ER, YODA, MYB88 and BCA1). We propose that the two positive regulators of stomatal number (SCRM2) and CDKB1;1 when upregulated act as key controllers of stomatal adaptation to elevated CO2 . Combined with significant transcriptome reprogramming of photosynthetic and dark respiration and enhanced growth in spring plants, we have identified the potential basis of plant adaptation to high CO2 likely to occur over coming decades.
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Affiliation(s)
| | - Yunan Lin
- Centre for Biological Sciences, University of Southampton, Life Sciences, Southampton, SO17 1BJ, UK
| | - Franco Miglietta
- Institute of Biometeorology (IBIMET), National Research Council (CNR), Via Caproni 8, Firenze, 50145, Italy
| | - Richard J Edwards
- Centre for Biological Sciences, University of Southampton, Life Sciences, Southampton, SO17 1BJ, UK
| | - Mark A Chapman
- Centre for Biological Sciences, University of Southampton, Life Sciences, Southampton, SO17 1BJ, UK
| | - Gail Taylor
- Centre for Biological Sciences, University of Southampton, Life Sciences, Southampton, SO17 1BJ, UK.
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48
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Mangion K, Carrick D, Hennigan BW, Payne AR, McClure J, Mason M, Das R, Wilson R, Edwards RJ, Petrie MC, McEntegart M, Eteiba H, Oldroyd KG, Berry C. Infarct size and left ventricular remodelling after preventive percutaneous coronary intervention. Heart 2016; 102:1980-1987. [PMID: 27504003 PMCID: PMC5256395 DOI: 10.1136/heartjnl-2015-308660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 06/17/2016] [Accepted: 06/22/2016] [Indexed: 11/05/2022] Open
Abstract
Objective We hypothesised that, compared with culprit-only primary percutaneous coronary intervention (PCI), additional preventive PCI in selected patients with ST-elevation myocardial infarction with multivessel disease would not be associated with iatrogenic myocardial infarction, and would be associated with reductions in left ventricular (LV) volumes in the longer term. Methods In the preventive angioplasty in myocardial infarction trial (PRAMI; ISRCTN73028481), cardiac magnetic resonance (CMR) was prespecified in two centres and performed (median, IQR) 3 (1, 5) and 209 (189, 957) days after primary PCI. Results From 219 enrolled patients in two sites, 84% underwent CMR. 42 (50%) were randomised to culprit-artery-only PCI and 42 (50%) were randomised to preventive PCI. Follow-up CMR scans were available in 72 (86%) patients. There were two (4.8%) cases of procedure-related myocardial infarction in the preventive PCI group. The culprit-artery-only group had a higher proportion of anterior myocardial infarctions (MIs) (55% vs 24%). Infarct sizes (% LV mass) at baseline and follow-up were similar. At follow-up, there was no difference in LV ejection fraction (%, median (IQR), (culprit-artery-only PCI vs preventive PCI) 51.7 (42.9, 60.2) vs 54.4 (49.3, 62.8), p=0.23), LV end-diastolic volume (mL/m2, 69.3 (59.4, 79.9) vs 66.1 (54.7, 73.7), p=0.48) and LV end-systolic volume (mL/m2, 31.8 (24.4, 43.0) vs 30.7 (23.0, 36.3), p=0.20). Non-culprit angiographic lesions had low-risk Syntax scores and 47% had non-complex characteristics. Conclusions Compared with culprit-only PCI, non-infarct-artery MI in the preventive PCI strategy was uncommon and LV volumes and ejection fraction were similar.
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Affiliation(s)
- Kenneth Mangion
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK.,West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital, Dunbartonshire, UK
| | - David Carrick
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK.,West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital, Dunbartonshire, UK
| | - Barry W Hennigan
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK.,West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital, Dunbartonshire, UK
| | - Alexander R Payne
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK.,West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital, Dunbartonshire, UK
| | - John McClure
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - Maureen Mason
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital, Dunbartonshire, UK
| | - Rajiv Das
- Therapeutics and Cardiac Research Team, Freeman Hospital, Newcastle upon Tyne, UK
| | - Rebecca Wilson
- Therapeutics and Cardiac Research Team, Freeman Hospital, Newcastle upon Tyne, UK
| | - Richard J Edwards
- Therapeutics and Cardiac Research Team, Freeman Hospital, Newcastle upon Tyne, UK
| | - Mark C Petrie
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK.,West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital, Dunbartonshire, UK
| | - Margaret McEntegart
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital, Dunbartonshire, UK
| | - Hany Eteiba
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital, Dunbartonshire, UK
| | - Keith G Oldroyd
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK.,West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital, Dunbartonshire, UK
| | - Colin Berry
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK.,West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital, Dunbartonshire, UK
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49
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Singleton WG, Barua NU, Morgan J, Bienemann AS, Killick-Cole CL, Asby DJ, Edwards RJ, Lowis SP, Gill SS. NS-21MULTI-CATHETER INTERMITTENT CONVECTION-ENHANCED DELIVERY OF CARBOPLATIN AS A TREATMENT FOR DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG): PRE-CLINICAL RATIONALE AND EARLY CLINICAL EXPERIENCE. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now078.21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Churton NWV, Misra RV, Howlin RP, Allan RN, Jefferies J, Faust SN, Gharbia SE, Edwards RJ, Clarke SC, Webb JS. Parallel Evolution in Streptococcus pneumoniae Biofilms. Genome Biol Evol 2016; 8:1316-26. [PMID: 27190203 PMCID: PMC4898793 DOI: 10.1093/gbe/evw072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Streptococcus pneumoniae is a commensal human pathogen and the causative agent of various invasive and noninvasive diseases. Carriage of the pneumococcus in the nasopharynx is thought to be mediated by biofilm formation, an environment where isogenic populations frequently give rise to morphological colony variants, including small colony variant (SCV) phenotypes. We employed metabolic characterization and whole-genome sequencing of biofilm-derived S. pneumoniae serotype 22F pneumococcal SCVs to investigate diversification during biofilm formation. Phenotypic profiling revealed that SCVs exhibit reduced growth rates, reduced capsule expression, altered metabolic profiles, and increased biofilm formation compared to the ancestral strain. Whole-genome sequencing of 12 SCVs from independent biofilm experiments revealed that all SCVs studied had mutations within the DNA-directed RNA polymerase delta subunit (RpoE). Mutations included four large-scale deletions ranging from 51 to 264 bp, one insertion resulting in a coding frameshift, and seven nonsense single-nucleotide substitutions that result in a truncated gene product. This work links mutations in the rpoE gene to SCV formation and enhanced biofilm development in S. pneumoniae and therefore may have important implications for colonization, carriage, and persistence of the organism. Furthermore, recurrent mutation of the pneumococcal rpoE gene presents an unprecedented level of parallel evolution in pneumococcal biofilm development.
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Affiliation(s)
- Nicholas W V Churton
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom
| | - Raju V Misra
- Genomics Research Unit, Microbiology Services, Public Health England, Colindale, United Kingdom
| | - Robert P Howlin
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
| | - Raymond N Allan
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom Southampton NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, United Kingdom
| | - Johanna Jefferies
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
| | - Saul N Faust
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom Southampton NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, United Kingdom
| | - Saheer E Gharbia
- Genomics Research Unit, Microbiology Services, Public Health England, Colindale, United Kingdom
| | - Richard J Edwards
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Stuart C Clarke
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom Public Health England, Southampton, United Kingdom
| | - Jeremy S Webb
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom Institute for Life Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, United Kingdom NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
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