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Holman LE, Parker-Nance S, de Bruyn M, Creer S, Carvalho G, Rius M. Correction to: 'Managing human-mediatedrange shifts: understanding spatial,temporal and genetic variation in marinenon-native species' (2022) by Holman et al. Philos Trans R Soc Lond B Biol Sci 2022; 377:20220284. [PMID: 36126676 PMCID: PMC9489301 DOI: 10.1098/rstb.2022.0284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Wang Y, Korneliussen TS, Holman LE, Manica A, Pedersen MW.
ngs
LCA
—A toolkit for fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yucheng Wang
- Department of Zoology University of Cambridge Cambridge UK
- Lundbeck Foundation GeoGenetics Centre, Globe Institute University of Copenhagen Copenhagen K Denmark
- ALPHA, State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER) Institute of Tibetan Plateau Research (ITPCAS), Chinese Academy of Sciences (CAS) Beijing China
- BGI BGI‐Shenzhen Shanghai China
| | | | - Luke E. Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton University of Southampton Southampton UK
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Andrea Manica
- Department of Zoology University of Cambridge Cambridge UK
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute University of Copenhagen Copenhagen K Denmark
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Good E, Holman LE, Pusceddu A, Russo T, Rius M, Iacono CL. Detection of community-wide impacts of bottom trawl fishing on deep-sea assemblages using environmental DNA metabarcoding. Mar Pollut Bull 2022; 183:114062. [PMID: 36075115 DOI: 10.1016/j.marpolbul.2022.114062] [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] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Although considerable research progress on the effects of anthropogenic disturbance in the deep sea has been made in recent years, our understanding of these impacts at community level remains limited. Here, we studied deep-sea assemblages of Sicily (Mediterranean Sea) subject to different intensities of benthic trawling using environmental DNA (eDNA) metabarcoding and taxonomic identification of meiofauna communities. Firstly, eDNA metabarcoding data did not detect trawling impacts using alpha diversity whereas meiofauna data detected a significant effect of trawling. Secondly, both eDNA and meiofauna data detected significantly different communities across distinct levels of trawling intensity when we examined beta diversity. Taxonomic assignment of the eDNA data revealed that Bryozoa was present only at untrawled sites, highlighting their vulnerability to trawling. Our results provide evidence for community-wide impacts of trawling, with different trawling intensities leading to distinct deep-sea communities. Finally, we highlight the need for further studies to unravel understudied deep-sea biodiversity.
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Affiliation(s)
- Edward Good
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom.
| | - Luke E Holman
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom; Section for Molecular Ecology and Evolution, Faculty of Health and Medical Sciences, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antonio Pusceddu
- Department of Life and Environmental Sciences, University of Cagliari, Via T. Fiorelli, 1, 09126 Cagliari, Italy
| | - Tommaso Russo
- Laboratory of Experimental Ecology and Aquaculture, Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Marc Rius
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, United Kingdom; Centre for Advanced Studies of Blanes - Spanish National Research Council (CEAB-CSIC), Accés a la Cala Sant Francesc 14, 17300 Blanes (Girona), Spain; Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, South Africa
| | - Claudio Lo Iacono
- Marine Sciences Institute - Spanish National Research Council (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
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Holman LE, Parker-Nance S, de Bruyn M, Creer S, Carvalho G, Rius M. Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210025. [PMID: 35067092 PMCID: PMC8784926 DOI: 10.1098/rstb.2021.0025] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The use of molecular tools to manage natural resources is increasingly common. However, DNA-based methods are seldom used to understand the spatial and temporal dynamics of species' range shifts. This is important when managing range shifting species such as non-native species (NNS), which can have negative impacts on biotic communities. Here, we investigated the ascidian NNS Ciona robusta, Clavelina lepadiformis, Microcosmus squamiger and Styela plicata using a combined methodological approach. We first conducted non-molecular biodiversity surveys for these NNS along the South African coastline, and compared the results with historical surveys. We detected no consistent change in range size across species, with some displaying range stability and others showing range shifts. We then sequenced a section of cytochrome c oxidase subunit I (COI) from tissue samples and found genetic differences along the coastline but no change over recent times. Finally, we found that environmental DNA metabarcoding data showed broad congruence with both the biodiversity survey and the COI datasets, but failed to capture the complete incidence of all NNS. Overall, we demonstrated how a combined methodological approach can effectively detect spatial and temporal variation in genetic composition and range size, which is key for managing both thriving NNS and threatened species. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.
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Affiliation(s)
- Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
| | - Shirley Parker-Nance
- Zoology Department, Institute for Coastal and Marine Research Nelson Mandela University Ocean Sciences Campus, Gqeberha (Port Elizabeth), South Africa.,South African Environmental Observation Network (SAEON) Elwandle Coastal Node, Nelson Mandela University Ocean Sciences Campus, Gqeberha (Port Elizabeth), South Africa
| | - Mark de Bruyn
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia.,Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Simon Creer
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Gary Carvalho
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, Bangor, UK
| | - Marc Rius
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK.,Centre for Advanced Studies of Blanes (CEAB, CSIC), Accés a la Cala Sant Francesc 14, 17300 Blanes, Spain.,Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, South Africa
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Fernandez S, Miller DL, Holman LE, Gittenberger A, Ardura A, Rius M, Mirimin L. Environmental DNA sampling protocols for the surveillance of marine non-indigenous species in Irish coastal waters. Mar Pollut Bull 2021; 172:112893. [PMID: 34464822 DOI: 10.1016/j.marpolbul.2021.112893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/02/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Understanding the spread and distribution of Non-Indigenous Species (NIS) is key when implementing legislation to maintain good ecosystem health. Environmental DNA (eDNA) has shown great potential to detect aquatic organisms in a rapid and cost-effective way, however their applicability to new environments must be validated prior to their implementation. Here, we tested different field sampling methods in combination with eDNA metabarcoding to develop a tool to detect NIS. Large and small volumes of seawater were filtered, in addition to the collection of sediment and horizontal tow net samples at 12 locations across four distinct geographic areas in Ireland. The biggest dissimilarity in the species recovered was found between sediment and town net samples. Tow nets showed to be the most efficient. A total of 357 taxa were identified, including 16 NIS. Fine mesh tow nets were identified as the most cost-efficient for large-scale monitoring and surveillance of NIS.
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Affiliation(s)
- Sara Fernandez
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland.
| | - Dulaney L Miller
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland
| | - Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre, European Way, Southampton SO14 3ZH, University of Southampton, United Kingdom
| | - Arjan Gittenberger
- GiMaRIS, Rijksstraatweg 75, 2171 AK Sassenheim, the Netherlands; Department of Marine Zoology, Naturalis Biodiversity Center, Pesthuislaan 7, 2333 BA Leiden, the Netherlands
| | - Alba Ardura
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Asturias, Spain
| | - Marc Rius
- School of Ocean and Earth Science, National Oceanography Centre, European Way, Southampton SO14 3ZH, University of Southampton, United Kingdom; Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland
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Rodriguez-Ezpeleta N, Morissette O, Bean CW, Manu S, Banerjee P, Lacoursière-Roussel A, Beng KC, Alter SE, Roger F, Holman LE, Stewart KA, Monaghan MT, Mauvisseau Q, Mirimin L, Wangensteen OS, Antognazza CM, Helyar SJ, de Boer H, Monchamp ME, Nijland R, Abbott CL, Doi H, Barnes MA, Leray M, Hablützel PI, Deiner K. Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on "Environmental DNA: What's behind the term?" by Pawlowski et al., (2020). Mol Ecol 2021; 30:4601-4605. [PMID: 34036646 PMCID: PMC8698002 DOI: 10.1111/mec.15942] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 12/08/2020] [Revised: 03/31/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring,” Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra‐organismal DNA from macro‐organisms. We agree with this view. However, we are concerned that their proposed two‐level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra‐organismal) from which ecological interpretations are derived.
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Affiliation(s)
| | - Olivier Morissette
- Direction de l'expertise sur la Faune Aquatique, Ministère des Forêt de la Faune et des Parcs, Québec, QC, Canada
| | - Colin W Bean
- Scottish Centre for Ecology and the Natural Environment, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Shivakumara Manu
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Pritam Banerjee
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan.,Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Anaïs Lacoursière-Roussel
- Government of Canada, Department of Fisheries and Oceans, St. Andrews Biological Station, St. Andrews, NB, Canada
| | - Kingsly C Beng
- Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - S Elizabeth Alter
- Department of Biology and Chemistry, California State University Monterey Bay, Seaside, CA, USA
| | - Fabian Roger
- Centre for Environmental and Climate Research (CEC), Lund University, Lund, Sweden
| | - Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
| | - Kathryn A Stewart
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, the Netherlands
| | - Michael T Monaghan
- Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | | | - Luca Mirimin
- Department of Natural Sciences, School of Science and Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Caterina M Antognazza
- Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Sarah J Helyar
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Hugo de Boer
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Reindert Nijland
- Marine Animal Ecology Group, Wageningen University, Wageningen, The Netherlands
| | - Cathryn L Abbott
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Matthew A Barnes
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX, USA
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Smithsonian Institution, Panama City, Panama
| | | | - Kristy Deiner
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
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Holman LE, de Bruyn M, Creer S, Carvalho G, Robidart J, Rius M. Animals, protists and bacteria share marine biogeographic patterns. Nat Ecol Evol 2021; 5:738-746. [PMID: 33859375 DOI: 10.1038/s41559-021-01439-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/08/2021] [Indexed: 01/22/2023]
Abstract
Over millennia, ecological and evolutionary mechanisms have shaped macroecological patterns across the tree of life. Research describing these patterns at both regional and global scales has traditionally focused on the study of metazoan species. Consequently, there is a limited understanding of cross-phylum biogeographic structuring and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, protists and bacteria along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life despite billions of years of evolution. Analyses investigating the drivers of these patterns for each taxonomic kingdom found that environmental conditions (such as temperature) and, to a lesser extent, anthropogenic stressors (such as fishing pressure and pollution) explained some of the observed variation. Additionally, metazoans displayed biogeographic patterns that suggested regional biotic homogenization. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of biodiversity patterns across broad taxonomic, ecological and geographical scales.
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Affiliation(s)
- Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK.
| | - Mark de Bruyn
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.,Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, UK
| | - Julie Robidart
- Ocean Technology and Engineering Group, National Oceanography Centre Southampton, Southampton, UK
| | - Marc Rius
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK.,Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
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Holman LE, Hollenbeck CM, Ashton TJ, Johnston IA. Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster ( Ostrea edulis). Front Genet 2019; 10:1159. [PMID: 31803238 PMCID: PMC6877716 DOI: 10.3389/fgene.2019.01159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 07/04/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
Accurate SNP (single nucleotide polymorphism) genotype information is critical for a wide range of selective breeding applications in aquaculture, including parentage assignment, marker-assisted, and genomic selection. However, the sampling of tissue for genetic analysis can be invasive for juvenile animals or taxa where sampling tissue is difficult or may cause mortality (e.g. bivalve mollusks). Here, we demonstrate a novel, non-invasive technique for sampling DNA based on the collection of environmental DNA using European Flat Oysters (Ostrea edulis) as an example. The live animals are placed in individual containers until sufficient genetic material is released into the seawater which is then recovered by filtration. We compared the results of tissue and eDNA derived SNP genotype calls using a PCR based genotyping platform. We found that 100% accurate genotype calls from eDNA are possible, but depend on appropriate filtration and the dilution of the sample throughout the workflow. We also developed an additional low-cost DNA extraction technique which provided >99% correct SNP genotype calls in comparison to tissue. It was concluded that eDNA sampling can be used in hatchery and selective breeding programs applicable to any aquatic organism for which direct tissue sampling may result in animal welfare concerns or mortality.
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Affiliation(s)
- Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, United Kingdom
| | | | | | - Ian A Johnston
- Xelect Ltd, Horizon House, Scotland, United Kingdom.,Scottish Oceans Institute, School of Biology, University of St Andrews, Scotland, United Kingdom
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Holman LE, Rius M, Blackburn TM. Observations of a novel predatory gull behavior on an invasive ascidian: A new consequence of coastal urban sprawl? Ecosphere 2019; 10:e02636. [PMID: 35860719 PMCID: PMC9285467 DOI: 10.1002/ecs2.2636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 01/31/2019] [Accepted: 02/04/2019] [Indexed: 11/18/2022] Open
Abstract
Coastal urbanization has a dramatic effect on both terrestrial and marine ecosystems, altering resources such as food or space. Many species have shifted their ranges in response to anthropogenic pressures, resulting in novel species interactions. Here, we report an observation of a novel foraging behavior of the European Herring Gull (Larus argentatus): the capture and consumption of the widespread sea squirt Ciona intestinalis from under floating pontoons in a recreational marina in Ireland. Multiple gulls were observed performing a complex, multi‐step manipulation of several C. intestinalis individuals to remove their cellulose‐based tunic, which remained unconsumed. Further avenues of investigation are discussed, and hypotheses concerning possible ecosystem effects of novel ecological interactions occurring in proliferating artificial environments are presented.
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Affiliation(s)
- Luke E. Holman
- School of Ocean and Earth Science National Oceanography Centre Southampton University of Southampton Southampton UK
| | - Marc Rius
- School of Ocean and Earth Science National Oceanography Centre Southampton University of Southampton Southampton UK
- Centre for Ecological Genomics and Wildlife Conservation University of Johannesburg Johannesburg South Africa
| | - Tim M. Blackburn
- Centre for Biodiversity and Environment Research Department of Genetics, Evolution and Environment University College London London UK
- Institute of Zoology Zoological Society of London London UK
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Abstract
For the calibration of a compaction simulator for punch displacement measurements, the displacement of the punch must be related to the voltage output of a linear variable displacement transducer (LVDT) which is attached to the punch via its movable core, with correction for any deformation of the machine parts which are inherently incorporated in the LVDT readings. Contrary to common assumptions the relationship between the displacement of the movable core and the voltage output of the LVDTs used is not linear. Similarly, the deformation of the machine parts did not follow Hooke's law of linear elasticity but exhibited characteristics of nonlinear elasticity. The data demonstrate the need for careful validation of the calibration of a compaction simulator when accurate punch displacements are required.
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Affiliation(s)
- L E Holman
- SmithKline Beecham Pharmaceuticals, Pharmaceutical Sciences Department, King of Prussia, Pennsylvania 19406
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