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Madge Pimentel I, Baikova D, Buchner D, Burfeid Castellanos A, David GM, Deep A, Doliwa A, Hadžiomerović U, Mayombo NAS, Prati S, Spyra MA, Vermiert AM, Beisser D, Dunthorn M, Piggott JJ, Sures B, Tiegs SD, Leese F, Beermann AJ. Assessing the response of an urban stream ecosystem to salinization under different flow regimes. Sci Total Environ 2024; 926:171849. [PMID: 38537828 DOI: 10.1016/j.scitotenv.2024.171849] [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: 11/16/2023] [Revised: 02/08/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024]
Abstract
Urban streams are exposed to a variety of anthropogenic stressors. Freshwater salinization is a key stressor in these ecosystems that is predicted to be further exacerbated by climate change, which causes simultaneous changes in flow parameters, potentially resulting in non-additive effects on aquatic ecosystems. However, the effects of salinization and flow velocity on urban streams are still poorly understood as multiple-stressor experiments are often conducted at pristine rather than urban sites. Therefore, we conducted a mesocosm experiment at the Boye River, a recently restored stream located in a highly urbanized area in Western Germany, and applied recurrent pulses of salinity along a gradient (NaCl, 9 h daily of +0 to +2.5 mS/cm) in combination with normal and reduced current velocities (20 cm/s vs. 10 cm/s). Using a comprehensive assessment across multiple organism groups (macroinvertebrates, eukaryotic algae, fungi, parasites) and ecosystem functions (primary production, organic-matter decomposition), we show that flow velocity reduction has a pervasive impact, causing community shifts for almost all assessed organism groups (except fungi) and inhibiting organic-matter decomposition. Salinization affected only dynamic components of community assembly by enhancing invertebrate emigration via drift and reducing fungal reproduction. We caution that the comparatively small impact of salt in our study can be due to legacy effects from past salt pollution by coal mining activities >30 years ago. Nevertheless, our results suggest that urban stream management should prioritize the continuity of a minimum discharge to maintain ecosystem integrity. Our study exemplifies a holistic approach for the assessment of multiple-stressor impacts on streams, which is needed to inform the establishment of a salinity threshold above which mitigation actions must be taken.
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Affiliation(s)
- Iris Madge Pimentel
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
| | - Daria Baikova
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Dominik Buchner
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | | | - Gwendoline M David
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Department of Plankton and Microbial Ecology, Stechlin, Germany
| | - Aman Deep
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Annemie Doliwa
- Aquatic Ecology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Una Hadžiomerović
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | | | - Sebastian Prati
- Aquatic Ecology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | | | - Anna-Maria Vermiert
- Ruhr University Bochum, Department of Animal Ecology, Evolution and Biodiversity, Bochum, Germany
| | - Daniela Beisser
- Department of Engineering and Natural Sciences, Westphalian University of Applied Sciences, Recklinghausen, Germany
| | - Micah Dunthorn
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Jeremy J Piggott
- Zoology and Trinity Centre for the Environment, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Bernd Sures
- Aquatic Ecology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany; Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
| | - Scott D Tiegs
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
| | - Florian Leese
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Arne J Beermann
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
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2
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Hakimzadeh A, Asbun AA, Albanese D, Bernard M, Buchner D, Callahan B, Caporaso JG, Curd E, Djemiel C, Durling MB, Elbrecht V, Gold Z, Gweon HS, Hajibabaei M, Hildebrand F, Mikryukov V, Normandeau E, Özkurt E, Palmer JM, Pascal G, Porter TM, Straub D, Vasar M, Větrovský T, Zafeiropoulos H, Anslan S. A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Mol Ecol Resour 2023:10.1111/1755-0998.13847. [PMID: 37548515 PMCID: PMC10847385 DOI: 10.1111/1755-0998.13847] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/05/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023]
Abstract
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.
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Affiliation(s)
- Ali Hakimzadeh
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Italy
| | - Maria Bernard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- INRAE, SIGENAE, 78350, Jouy-en-Josas, France
| | - Dominik Buchner
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Benjamin Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - J. Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily Curd
- Vermont Biomedical Research Network, University of Vermont, Burlington, VT, USA
| | - Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Mikael B. Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden
| | - Vasco Elbrecht
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitaetsstrasse 5, 45141, Essen, Germany
| | - Zachary Gold
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hyun S. Gweon
- UK Centre for Ecology & Hydrology, Wallingford, Oxfordshire, OX10 8BB, UK
- School of Biological Sciences, University of Reading, Reading, RG6 6EX, UK
| | - Mehrdad Hajibabaei
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, Canada
| | - Falk Hildebrand
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | | | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Ezgi Özkurt
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Jonathan M. Palmer
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI USA (current address: Genencor Technology Center, IFF, Palo Alto, CA USA)
| | - Géraldine Pascal
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | - Teresita M. Porter
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, Canada
| | - Daniel Straub
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen D-72076, Germany
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Haris Zafeiropoulos
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
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Vos M, Hering D, Gessner MO, Leese F, Schäfer RB, Tollrian R, Boenigk J, Haase P, Meckenstock R, Baikova D, Bayat H, Beermann A, Beisser D, Beszteri B, Birk S, Boden L, Brauer V, Brauns M, Buchner D, Burfeid-Castellanos A, David G, Deep A, Doliwa A, Dunthorn M, Enß J, Escobar-Sierra C, Feld CK, Fohrer N, Grabner D, Hadziomerovic U, Jähnig SC, Jochmann M, Khaliq S, Kiesel J, Kuppels A, Lampert KP, Le TTY, Lorenz AW, Madariaga GM, Meyer B, Pantel JH, Pimentel IM, Mayombo NS, Nguyen HH, Peters K, Pfeifer SM, Prati S, Probst AJ, Reiner D, Rolauffs P, Schlenker A, Schmidt TC, Shah M, Sieber G, Stach TL, Tielke AK, Vermiert AM, Weiss M, Weitere M, Sures B. The Asymmetric Response Concept explains ecological consequences of multiple stressor exposure and release. Sci Total Environ 2023; 872:162196. [PMID: 36781140 DOI: 10.1016/j.scitotenv.2023.162196] [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: 12/14/2022] [Revised: 02/01/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Our capacity to predict trajectories of ecosystem degradation and recovery is limited, especially when impairments are caused by multiple stressors. Recovery may be fast or slow and either complete or partial, sometimes result in novel ecosystem states or even fail completely. Here, we introduce the Asymmetric Response Concept (ARC) that provides a basis for exploring and predicting the pace and magnitude of ecological responses to, and release from, multiple stressors. The ARC holds that three key mechanisms govern population, community and ecosystem trajectories. Stress tolerance is the main mechanism determining responses to increasing stressor intensity, whereas dispersal and biotic interactions predominantly govern responses to the release from stressors. The shifting importance of these mechanisms creates asymmetries between the ecological trajectories that follow increasing and decreasing stressor intensities. This recognition helps to understand multiple stressor impacts and to predict which measures will restore communities that are resistant to restoration.
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Affiliation(s)
- Matthijs Vos
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Theoretical and Applied Biodiversity Research, Bochum, Germany
| | - Daniel Hering
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), Essen, Germany.
| | - Mark O Gessner
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany; Department of Ecology, Berlin Institute of Technology (TU Berlin), Berlin, Germany
| | - Florian Leese
- Centre for Water and Environmental Research (ZWU), Essen, Germany; Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Ralf B Schäfer
- Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany
| | - Ralph Tollrian
- Department of Animal Ecology, Ruhr University Bochum, Evolution and Biodiversity, Germany
| | - Jens Boenigk
- Centre for Water and Environmental Research (ZWU), Essen, Germany; Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Peter Haase
- Centre for Water and Environmental Research (ZWU), Essen, Germany; Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany; Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Rainer Meckenstock
- Centre for Water and Environmental Research (ZWU), Essen, Germany; Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Daria Baikova
- Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Helena Bayat
- Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany
| | - Arne Beermann
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Daniela Beisser
- Centre for Water and Environmental Research (ZWU), Essen, Germany; Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Bánk Beszteri
- Centre for Water and Environmental Research (ZWU), Essen, Germany; Phycology, University of Duisburg-Essen, Essen, Germany
| | - Sebastian Birk
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), Essen, Germany
| | - Lisa Boden
- Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Verena Brauer
- Centre for Water and Environmental Research (ZWU), Essen, Germany; Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Mario Brauns
- Helmholtz Centre for Environmental Research - UFZ, Department River Ecology, Magdeburg, Germany
| | - Dominik Buchner
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | | | - Gwendoline David
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
| | - Aman Deep
- Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Annemie Doliwa
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany
| | - Micah Dunthorn
- Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany; Natural History Museum, University of Oslo, Oslo, Norway
| | - Julian Enß
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany
| | | | - Christian K Feld
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), Essen, Germany
| | - Nicola Fohrer
- Department of Hydrology and Water Resources Management, Institute of Natural Resource Conservation, CAU Kiel, Germany
| | - Daniel Grabner
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), Essen, Germany
| | - Una Hadziomerovic
- Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Sonja C Jähnig
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Humboldt-Universität zu Berlin, Berlin, Germany
| | - Maik Jochmann
- Centre for Water and Environmental Research (ZWU), Essen, Germany; Instrumental Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Shaista Khaliq
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Jens Kiesel
- Department of Hydrology and Water Resources Management, Institute of Natural Resource Conservation, CAU Kiel, Germany
| | - Annabel Kuppels
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Theoretical and Applied Biodiversity Research, Bochum, Germany
| | | | - T T Yen Le
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany
| | - Armin W Lorenz
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany
| | - Graciela Medina Madariaga
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Humboldt-Universität zu Berlin, Berlin, Germany
| | - Benjamin Meyer
- Aquatic Microbial Ecology, University of Duisburg-, Essen, Germany
| | - Jelena H Pantel
- Ecological Modelling, University of Duisburg-Essen, Essen, Germany
| | | | | | - Hong Hanh Nguyen
- Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany; Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Kristin Peters
- Department of Hydrology and Water Resources Management, Institute of Natural Resource Conservation, CAU Kiel, Germany
| | | | - Sebastian Prati
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany
| | | | - Dominik Reiner
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany
| | - Peter Rolauffs
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany
| | - Alexandra Schlenker
- Helmholtz Centre for Environmental Research - UFZ, Department River Ecology, Magdeburg, Germany
| | - Torsten C Schmidt
- Centre for Water and Environmental Research (ZWU), Essen, Germany; Instrumental Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Manan Shah
- Biodiversity, University of Duisburg-Essen, Essen, Germany; Aquatic Microbial Ecology, University of Duisburg-, Essen, Germany
| | - Guido Sieber
- Biodiversity, University of Duisburg-Essen, Essen, Germany
| | | | - Ann-Kathrin Tielke
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Theoretical and Applied Biodiversity Research, Bochum, Germany
| | - Anna-Maria Vermiert
- Department of Animal Ecology, Ruhr University Bochum, Evolution and Biodiversity, Germany
| | - Martina Weiss
- Centre for Water and Environmental Research (ZWU), Essen, Germany; Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Markus Weitere
- Helmholtz Centre for Environmental Research - UFZ, Department River Ecology, Magdeburg, Germany
| | - Bernd Sures
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), Essen, Germany
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Thomas MN, Datta RR, Wahba R, Buchner D, Chiapponi C, Kurschat C, Grundmann F, Urbanski A, Tolksdorf S, Müller R, Henze J, Petrescu-Jipa VM, Meyer F, Bruns CJ, Stippel DL. Introduction of laparoscopic nephrectomy for autosomal dominant polycystic kidney disease as the standard procedure. Langenbecks Arch Surg 2023; 408:8. [PMID: 36602631 PMCID: PMC9816232 DOI: 10.1007/s00423-022-02737-9] [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: 06/20/2022] [Accepted: 10/18/2022] [Indexed: 01/06/2023]
Abstract
PURPOSE Autosomal dominant polycystic kidney disease (ADPKD) is a common hereditary disorder and accounts for 5-10% of all cases of kidney failure. 50% of ADPKD patients reach kidney failure by the age of 58 years requiring dialysis or transplantation. Nephrectomy is performed in up to 20% of patients due to compressive symptoms, renal-related complications or in preparation for kidney transplantation. However, due to the large kidney size in ADPKD, nephrectomy can come with a considerable burden. Here we evaluate our institution's experience of laparoscopic nephrectomy (LN) as an alternative to open nephrectomy (ON) for ADPKD patients. MATERIALS AND METHODS We report the results of the first 12 consecutive LN for ADPKD from August 2020 to August 2021 in our institution. These results were compared with the 12 most recent performed ON for ADPKD at the same institution (09/2017 to 07/2020). Intra- and postoperative parameters were collected and analyzed. Health related quality of life (HRQoL) was assessed using the SF36 questionnaire. RESULTS Age, sex, and median preoperative kidney volumes were not significantly different between the two analyzed groups. Intraoperative estimated blood loss was significantly less in the laparoscopic group (33 ml (0-200 ml)) in comparison to the open group (186 ml (0-800 ml)) and postoperative need for blood transfusion was significantly reduced in the laparoscopic group (p = 0.0462). Operative time was significantly longer if LN was performed (158 min (85-227 min)) compared to the open procedure (107 min (56-174 min)) (p = 0.0079). In both groups one postoperative complication Clavien Dindo ≥ 3 occurred with the need of revision surgery. SF36 HRQol questionnaire revealed excellent postoperative quality of life after LN. CONCLUSION LN in ADPKD patients is a safe and effective operative procedure independent of kidney size with excellent postoperative outcomes and benefits of minimally invasive surgery. Compared with the open procedure patients profit from significantly less need for transfusion with comparable postoperative complication rates. However significant longer operation times need to be taken in account.
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Affiliation(s)
- M N Thomas
- Department of General-, Visceral-, Tumor- and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital of Cologne, University Hospital of Cologne, Cologne, Germany.
| | - R R Datta
- Department of General-, Visceral-, Tumor- and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital of Cologne, University Hospital of Cologne, Cologne, Germany
| | - R Wahba
- Department of General-, Visceral-, Tumor- and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital of Cologne, University Hospital of Cologne, Cologne, Germany
| | - D Buchner
- Department of General-, Visceral-, Tumor- and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital of Cologne, University Hospital of Cologne, Cologne, Germany
| | - C Chiapponi
- Department of General-, Visceral-, Tumor- and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital of Cologne, University Hospital of Cologne, Cologne, Germany
| | - C Kurschat
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
| | - F Grundmann
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
| | - A Urbanski
- Department of General-, Visceral-, Tumor- and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital of Cologne, University Hospital of Cologne, Cologne, Germany
| | - S Tolksdorf
- Department of General-, Visceral-, Tumor- and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital of Cologne, University Hospital of Cologne, Cologne, Germany
| | - R Müller
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
| | - J Henze
- Department of Radiology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, University Hospital of Cologne, Cologne, Germany
| | - V-M Petrescu-Jipa
- Department of Transfusionsmedizin, University of Cologne, Cologne, Germany
| | - F Meyer
- Department of Radiology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, University Hospital of Cologne, Cologne, Germany
| | - C J Bruns
- Department of General-, Visceral-, Tumor- and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital of Cologne, University Hospital of Cologne, Cologne, Germany
| | - D L Stippel
- Department of General-, Visceral-, Tumor- and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital of Cologne, University Hospital of Cologne, Cologne, Germany
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5
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Buchner D, Macher TH, Leese F. APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA Meta-barcoding data. Bioinformatics 2022; 38:4817-4819. [PMID: 36029248 PMCID: PMC9563694 DOI: 10.1093/bioinformatics/btac588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 08/19/2022] [Accepted: 08/26/2022] [Indexed: 11/28/2022] Open
Abstract
Summary DNA metabarcoding is an emerging approach to assess and monitor biodiversity worldwide and consequently the number and size of data sets increases exponentially. To date, no published DNA metabarcoding data processing pipeline exists that is (i) platform independent, (ii) easy to use [incl. graphical user interface (GUI)], (iii) fast (does scale well with dataset size) and (iv) complies with data protection regulations of e.g. environmental agencies. The presented pipeline APSCALE meets these requirements and handles the most common tasks of sequence data processing, such as paired-end merging, primer trimming, quality filtering, clustering and denoising of any popular metabarcoding marker, such as internal transcribed spacer, 16S or cytochrome c oxidase subunit I. APSCALE comes in a command line and a GUI version. The latter provides the user with additional summary statistics options and links to GUI-based downstream applications. Availability and implementation APSCALE is written in Python, a platform-independent language, and integrates functions of the open-source tools, VSEARCH (Rognes et al., 2016), cutadapt (Martin, 2011) and LULU (Frøslev et al., 2017). All modules support multithreading to allow fast processing of larger DNA metabarcoding datasets. Further information and troubleshooting are provided on the respective GitHub pages for the command-line version (https://github.com/DominikBuchner/apscale) and the GUI-based version (https://github.com/TillMacher/apscale_gui), including a detailed tutorial. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dominik Buchner
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstr. 5, Essen, 45141, Germany
| | - Till-Hendrik Macher
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstr. 5, Essen, 45141, Germany
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstr. 5, Essen, 45141, Germany.,Centre for Water and Environmental Research (ZWU), Universitaetsstr. 3, Essen, 45141, Germany
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6
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Buchner D, Macher TH, Beermann AJ, Werner MT, Leese F. Standardized high-throughput biomonitoring using DNA metabarcoding: Strategies for the adoption of automated liquid handlers. Environ Sci Ecotechnol 2021; 8:100122. [PMID: 36156998 PMCID: PMC9488008 DOI: 10.1016/j.ese.2021.100122] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 05/11/2023]
Abstract
Reliable and comprehensive monitoring data are required to trace and counteract biodiversity loss. High-throughput metabarcoding using DNA extracted from community samples (bulk) or from water or sediment (environmental DNA) has revolutionized biomonitoring, given the capability to assess biodiversity across the tree of life rapidly with feasible effort and at a modest price. DNA metabarcoding can be upscaled to process hundreds of samples in parallel. However, while automated high-throughput analysis workflows are well-established in the medical sector, manual sample processing still predominates in biomonitoring laboratory workflows limiting the upscaling and standardization for routine monitoring applications. Here we present an automated, scalable, and reproducible metabarcoding workflow to extract DNA from bulk samples, perform PCR and library preparation on a liquid handler. Key features are the independent sample replication throughout the workflow and the use of many negative controls for quality assurance and quality control. We generated two datasets: i) a validation dataset consisting of 42 individual arthropod specimens of different species, and ii) a routine monitoring dataset consisting of 60 stream macroinvertebrate bulk samples. As a marker, we used the mitochondrial COI gene. Our results show that the developed single-deck workflow is free of laboratory-derived contamination and produces highly consistent results. Minor deviations between replicates are mostly due to stochastic differences for low abundant OTUs. Thus, we successfully demonstrated that robotic liquid handling can be used reliably from DNA extraction to final library preparation on a single deck, thereby substantially increasing throughput, reducing costs, and increasing data robustness for biodiversity assessments and monitoring.
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Affiliation(s)
- Dominik Buchner
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
| | - Till-Hendrik Macher
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
| | - Arne J. Beermann
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
- University of Duisburg-Essen, Centre for Water and Environmental Research (ZWU), Universitätsstr. 3, 45141, Essen, Germany
| | - Marie-Thérése Werner
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
- University of Duisburg-Essen, Centre for Water and Environmental Research (ZWU), Universitätsstr. 3, 45141, Essen, Germany
- Corresponding author. University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141 Essen, Germany.
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7
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Buchner D, Haase P, Leese F. Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics. MBMG 2021. [DOI: 10.3897/mbmg.5.67533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most metabarcoding protocols for invertebrate bulk samples start with sample homogenisation, followed by DNA extraction, amplification of a specific marker region, and sequencing. Many of the above-mentioned laboratory steps have been verified thoroughly and best practice strategies exist, yet, no clear recommendation for the basis of almost all metabarcoding studies exists: the homogenisation of samples itself. Two different categories of devices are typically used for homogenisation: bead mills or blenders. Both have upsides and downsides. Bead mills rely on single-use plastics and therefore produce a lot of waste and are expensive. In addition to that, processing times can go up to 30 minutes making them unsuitable for large-scale studies. Blenders can handle larger sample volumes in a shorter time, and be cleaned – yet suffer from an increased risk of cross-contamination. We aimed to develop a fast, robust, cheap, and reliable sample homogenisation protocol that overcomes limitations of both approaches, i.e. does not produce difficult to discard waste and avoid single-use plastics while reducing overall costs. We tested the performance of the new protocol using six size-sorted Malaise trap samples and six unsorted stream macroinvertebrate kick-net samples. We used 14 replicates per sample and included many negative controls at different steps of the protocol to quantify the impacts of i) insufficient homogenisation and ii) cross-contamination. Our results show that 3-min homogenisation is sufficient to recover about 80% of OTUs per sample in each replicate and that a non-hazardous DIY cleaning solution provides an effective and efficient way of cleaning. The improvements of the protocol in terms of speed, ease of handling, an overall reduction of costs as well as the documented reliability and robustness make it an important candidate for sample homogenisation after sampling in particular for large-scale and regulatory metabarcoding but also metagenomics biodiversity assessments and monitoring.
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8
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Buchner D, Beermann AJ, Leese F, Weiss M. Cooking small and large portions of “biodiversity‐soup”: Miniaturized DNA metabarcoding PCRs perform as good as large‐volume PCRs. Ecol Evol 2021. [DOI: 10.1002/ece3.7753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Dominik Buchner
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
| | - Arne J. Beermann
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
| | - Florian Leese
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
| | - Martina Weiss
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
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Abstract
DNA metabarcoding workflows produce hundreds to ten-thousands of Operational Taxonomic Units (OTUs) or Exact Sequence Variants (ESVs) per analysis. In most workflows, a taxonomic assignment to these generated sequences is needed. This is typically done using publicly available databases. Especially, yet not exclusively, for Eumetazoan metabarcoding, the Barcode of Life Data system (BOLD) is the most comprehensive and curated reference barcode database and, therefore, typically the first choice for taxonomic assignment. While an application programme interface (API) exists to query data in large batches, no information on the many and important unpublished data are obtained through the API. The alternative approach using the BOLD identification engine on the website provides full access, yet it is restricted to 100 sequences at once. We developed a small platform-independent and graphical user interface (GUI) software package, BOLDigger, which aims to solve this problem by automating the process of sending successive requests of up to 100 sequences without surpassing the capacities of BOLD. BOLDigger can be used to download the results of the identification engine, as well as metadata for the obtained hits. For the selection of the best fitting hit, three different methods are implemented. A new approach, combining a threshold-based approach with the metadata information, was implemented to make use of the metadata.
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10
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Buchner D, Beermann AJ, Laini A, Rolauffs P, Vitecek S, Hering D, Leese F. Analysis of 13,312 benthic invertebrate samples from German streams reveals minor deviations in ecological status class between abundance and presence/absence data. PLoS One 2019; 14:e0226547. [PMID: 31869356 PMCID: PMC6927632 DOI: 10.1371/journal.pone.0226547] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 06/06/2019] [Accepted: 11/28/2019] [Indexed: 11/18/2022] Open
Abstract
Benthic invertebrates are the most commonly used organisms used to assess ecological status as required by the EU Water Framework Directive (WFD). For WFD-compliant assessments, benthic invertebrate communities are sampled, identified and counted. Taxa × abundance matrices are used to calculate indices and the resulting scores are compared to reference values to determine the ecological status class. DNA-based tools, such as DNA metabarcoding, provide a new and precise method for species identification but cannot deliver robust abundance data. To evaluate the applicability of DNA-based tools to ecological status assessment, we evaluated whether the results derived from presence/absence data are comparable to those derived from abundance data. We analysed benthic invertebrate community data obtained from 13,312 WFD assessments of German streams. Broken down to 30 official stream types, we compared assessment results based on abundance and presence/absence data for the assessment modules “organic pollution” (i.e., the saprobic index) and “general degradation” (a multimetric index) as well as their underlying metrics. In 76.6% of cases, the ecological status class did not change after transforming abundance data to presence/absence data. In 12% of cases, the status class was reduced by one (e.g., from good to moderate), and in 11.2% of cases, the class increased by one. In only 0.2% of cases, the status shifted by two classes. Systematic stream type-specific deviations were found and differences between abundance and presence/absence data were most prominent for stream types where abundance information contributed directly to one or several metrics of the general degradation module. For a single stream type, these deviations led to a systematic shift in status from ‘good’ to ‘moderate’ (n = 201; with only n = 3 increasing). The systematic decrease in scores was observed, even when considering simulated confidence intervals for abundance data. Our analysis suggests that presence/absence data can yield similar assessment results to those for abundance-based data, despite type-specific deviations. For most metrics, it should be possible to intercalibrate the two data types without substantial efforts. Thus, benthic invertebrate taxon lists generated by standardised DNA-based methods should be further considered as a complementary approach.
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Affiliation(s)
- Dominik Buchner
- University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany
| | - Arne J. Beermann
- University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany
- Centre for Water and Environmental Research (ZWU), Essen, Germany
| | - Alex Laini
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parma, Italy
| | - Peter Rolauffs
- University of Duisburg-Essen, Aquatic Ecology, Essen, Germany
| | - Simon Vitecek
- WasserCluster Lunz, Lunz am See, Austria
- University of Natural Resources Vienna, Wien, Austria
| | - Daniel Hering
- Centre for Water and Environmental Research (ZWU), Essen, Germany
- University of Duisburg-Essen, Aquatic Ecology, Essen, Germany
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Essen, Germany
- Centre for Water and Environmental Research (ZWU), Essen, Germany
- * E-mail:
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Rosenberg DE, Di C, Rillamas-Sun E, Bellettiere J, LaMonte MJ, Buchner D, Zheng Y, LaCroix AZ. PATTERNS OF SEDENTARY TIME AND FALLS INCIDENCE IN OLDER WOMEN. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.3023] [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: 11/14/2022] Open
Affiliation(s)
- D E Rosenberg
- Kaiser Permanente Washington Health Research Institute (formerly the Group Health Research Institute), Seattle, Washington, United States
| | - C Di
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - E Rillamas-Sun
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - J Bellettiere
- University of California, San Diego, La Jolla, California, USA; Center for Behavioral Epidemiology and Community Health, San Diego, California, USA
| | - M J LaMonte
- University at Buffalo-SUNY, Buffalo, NY, USA
| | - D Buchner
- University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Y Zheng
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - A Z LaCroix
- University of California, San Diego, La Jolla, California, USA
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Dieplinger G, Mokhaberi N, Wahba R, Peltzer S, Buchner D, Schlösser H, Ditt V, von Borstel A, Bauerfeind U, Lange U, Arns W, Kurschat C, Stippel H, Vitinius F. Correlation Between the Transplant Evaluation Rating Scale (TERS) and Medical Outcomes in Living-Donor Kidney Transplant Recipients: A Retrospective Analysis. Transplant Proc 2018; 50:1276-1280. [DOI: 10.1016/j.transproceed.2018.02.082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 02/23/2018] [Indexed: 12/31/2022]
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13
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Lo JYL, Amour C, Buchner D, Cross D, Brenner JL, Matevelo D. MAPPING HEALTH FACILITY CHARACTERISTICS AND LOCATION IN RURAL TANZANIA. Paediatr Child Health 2017. [DOI: 10.1093/pch/pxx086.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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14
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Schlößer HA, Thelen M, Dieplinger G, von Bergwelt-Baildon A, Garcia-Marquez M, Reuter S, Shimabukuro-Vornhagen A, Wennhold K, Haustein N, Buchner D, Heiermann N, Kleinert R, Wahba R, Ditt V, Kurschat C, Cingöz T, Becker J, Stippel DL, von Bergwelt-Baildon M. Prospective Analyses of Circulating B Cell Subsets in ABO-Compatible and ABO-Incompatible Kidney Transplant Recipients. Am J Transplant 2017; 17:542-550. [PMID: 27529836 DOI: 10.1111/ajt.14013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 06/16/2016] [Revised: 07/24/2016] [Accepted: 08/09/2016] [Indexed: 01/25/2023]
Abstract
Immunosuppressive strategies applied in renal transplantation traditionally focus on T cell inhibition. B cells were mainly examined in the context of antibody-mediated rejection, whereas the impact of antibody-independent B cell functions has only recently entered the field of transplantation. Similar to T cells, distinct B cell subsets can enhance or inhibit immune responses. In this study, we prospectively analyzed the evolution of B cell subsets in the peripheral blood of AB0-compatible (n = 27) and AB0-incompatible (n = 10) renal transplant recipients. Activated B cells were transiently decreased and plasmablasts were permanently decreased in patients without signs of rejection throughout the first year. In patients with histologically confirmed renal allograft rejection, activated B cells and plasmablasts were significantly elevated on day 365. Rituximab treatment in AB0-incompatible patients resulted in long-lasting B cell depletion and in a naïve phenotype of repopulating B cells 1 year following transplantation. Acute allograft rejection was correlated with an increase of activated B cells and plasmablasts and with a significant reduction of regulatory B cell subsets. Our study demonstrates the remarkable effects of standard immunosuppression on circulating B cell subsets. Furthermore, the B cell compartment was significantly altered in rejecting patients. A specific targeting of deleterious B cell subsets could be of clinical benefit in renal transplantation.
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Affiliation(s)
- H A Schlößer
- Department of General, Visceral and Cancer Surgery, University of Cologne, Köln, Germany.,Cologne Interventional Immunology, University of Cologne, Köln, Germany.,Cologne Transplant Center, University of Cologne, Köln, Germany
| | - M Thelen
- Cologne Interventional Immunology, University of Cologne, Köln, Germany
| | - G Dieplinger
- Department of General, Visceral and Cancer Surgery, University of Cologne, Köln, Germany.,Cologne Transplant Center, University of Cologne, Köln, Germany
| | - A von Bergwelt-Baildon
- Cologne Transplant Center, University of Cologne, Köln, Germany.,Department of Internal Medicine II, University of Cologne, Köln, Germany
| | - M Garcia-Marquez
- Cologne Interventional Immunology, University of Cologne, Köln, Germany
| | - S Reuter
- Cologne Interventional Immunology, University of Cologne, Köln, Germany
| | - A Shimabukuro-Vornhagen
- Cologne Interventional Immunology, University of Cologne, Köln, Germany.,Cologne Transplant Center, University of Cologne, Köln, Germany
| | - K Wennhold
- Cologne Interventional Immunology, University of Cologne, Köln, Germany
| | - N Haustein
- Cologne Interventional Immunology, University of Cologne, Köln, Germany
| | - D Buchner
- Department of General, Visceral and Cancer Surgery, University of Cologne, Köln, Germany.,Cologne Transplant Center, University of Cologne, Köln, Germany
| | - N Heiermann
- Department of General, Visceral and Cancer Surgery, University of Cologne, Köln, Germany.,Cologne Transplant Center, University of Cologne, Köln, Germany
| | - R Kleinert
- Department of General, Visceral and Cancer Surgery, University of Cologne, Köln, Germany.,Cologne Transplant Center, University of Cologne, Köln, Germany
| | - R Wahba
- Department of General, Visceral and Cancer Surgery, University of Cologne, Köln, Germany.,Cologne Transplant Center, University of Cologne, Köln, Germany
| | - V Ditt
- Institute for Clinical Transfusion Medicine, Merheim Medical Center Cologne, Köln, Germany
| | - C Kurschat
- Cologne Transplant Center, University of Cologne, Köln, Germany.,Department of Internal Medicine II, University of Cologne, Köln, Germany
| | - T Cingöz
- Cologne Transplant Center, University of Cologne, Köln, Germany.,Department of Internal Medicine II, University of Cologne, Köln, Germany
| | - J Becker
- Cologne Transplant Center, University of Cologne, Köln, Germany.,Institute of Pathology, University of Cologne, Köln, Germany
| | - D L Stippel
- Department of General, Visceral and Cancer Surgery, University of Cologne, Köln, Germany.,Cologne Transplant Center, University of Cologne, Köln, Germany
| | - M von Bergwelt-Baildon
- Cologne Interventional Immunology, University of Cologne, Köln, Germany.,Department of Internal Medicine I, University of Cologne, Köln, Germany
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15
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Buchner D, Drebber U, Chang DH, Stippel DL. Bile duct carcinoma recurrence in the papillary region in a long-term survivor of hilar cholangiocarcinoma: a case report. J Med Case Rep 2016; 10:299. [PMID: 27784337 PMCID: PMC5080686 DOI: 10.1186/s13256-016-1073-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 03/19/2016] [Accepted: 09/21/2016] [Indexed: 01/03/2023] Open
Abstract
Background Because of its high rate of early recurrence and its poor prognosis, long-term survival after cholangiocarcinoma is rare; therefore, only limited information on patients surviving more than 5 years after surgical therapy is available. Case presentation We report the case of a 57-year-old white man who developed a distal bile duct carcinoma 9 years after curative surgical therapy of intrahepatic cholangiocarcinoma. He had undergone a right lobe hemihepatectomy 11 years ago. Nine years later, he was diagnosed with a distal bile duct carcinoma and a duodenopancreatectomy was performed. On histologic examination both carcinomas revealed a tubular and papillary growth pattern with cancer-free resection margins and for both carcinomas there were no signs of lymphatic infiltration or metastatic spreading. Targeted next-generation sequencing showed an identical activating mutation pattern in both carcinomas. Conclusions Late recurrence of cholangiocarcinoma, even anatomically distant to the primary, in long-time survivors is possible and could be caused by a distinct tumor biology. A better understanding of the individual tumor biology could help hepatologists as well as hepatobiliary and pancreatic surgeons in their daily treatment of these patients.
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Affiliation(s)
- D Buchner
- Department of General, Visceral and Cancer Surgery, University of Cologne, Kerpenerstr. 62, 50637, Cologne, Germany.
| | - U Drebber
- Department of General Pathology and Pathological Anatomy, University of Cologne, Cologne, Germany
| | - D H Chang
- Department of Diagnostic and Interventional Radiology, University of Cologne, Cologne, Germany
| | - D L Stippel
- Department of General, Visceral and Cancer Surgery, University of Cologne, Kerpenerstr. 62, 50637, Cologne, Germany
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16
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Brenner JL, Barigye C, Maling S, Kabakyenga J, Nettel-Aguirre A, Buchner D, Yomuhangi TK, Wotton K, Amon N, Singhal N. 208: Can Volunteer Community Health Workers in Rural Uganda Provide Integrated Community Case Management? Paediatr Child Health 2014. [DOI: 10.1093/pch/19.6.e35-203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Jackson J, Jain G, Balu S, Buchner D, Schwartzberg LS. Impact of 5-HT 3 receptor antagonist (5HT3-RA) selection within triple antiemetic regimens on the risk of uncontrolled chemotherapy-induced nausea and vomiting with highly emetogenic chemotherapy (HEC) in breast cancer patients. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.e16519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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18
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Miller P, Balu S, Buchner D, Walker M, Stepanski EJ, Schwartzberg LS. Willingness to pay to prevent chemotherapy-induced nausea and vomiting. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.6068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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19
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Balu S, Craver C, Gayle J, Buchner D. Palonosetron versus other 5-HT 3–receptor antagonists for chemotherapy-induced nausea and vomiting prevention in patients with noncolon gastrointestinal cancers. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.4_suppl.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
129 Background: This study analyzed the risk of chemotherapy induced nausea and vomiting (N&V) [CINV] associated with palonosetron versus other 5-HT3 receptor antagonists (5-HT3-RAs) initiation among patients with non-colon gastrointestinal cancers receiving chemotherapy (CT) in a hospital outpatient setting. Methods: Patients diagnosed with any non-colon gastrointestinal cancer initiating any CT and antiemetic prophylaxis with palonosetron (Group 1) or other 5-HT3-RAs (Group 2) for the first time (index date) between 4/1/2007-3/31/2009 were identified from the Premier Perspective database. Patients included were aged ≥ 18 years, with no evidence of N&V, CT, and antiemetic medication in the 6 month pre-index date period, and with at least 36 consecutive months of data. A negative binomial GLM regression analysis was done estimating the number of CINV events (identified through either ICD-9-CM codes for N&V and/or volume depletion or CINV-related rescue medications 1 day after CT administration) in the follow-up period (first of 8 CT cycles or 6 months post index date) between the 2 groups (after matching on CT and specific CT cycle). Results: Of 658 identified patients, 215 initiated on palonosetron (Group 1; 32.7%). Group 1 patients were significantly younger [61.7 (SD: 11.3) vs. 62.2 (12.1) years; p = 0.0073], a higher percent received highly emetogenic chemotherapy (27.4% vs. 19.4%; p < 0.0001), and comprised of less African Americans (7.0% vs. 13.3%). In the follow-up period, the unadjusted number of CINV events per patient per CT cycle for Group 1 patients was lower versus Group 2 patients, though statistically non-significant (4.7 vs. 5.2; p = 0.1714). However, after controlling for differences in demographic and clinical variables, the regression model predicted a statistically significant reduction (30.9%) in the total CINV events per patient per CT cycle in favor of Group 1 patients; p = 0.0086. Conclusions: In this analysis, patients with non-colon gastrointestinal cancers initiated on palonosetron were more likely to experience a significantly lower rate of CINV events per patient per CT cycle versus those initiated on other 5-HT3-RAs. [Table: see text]
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Affiliation(s)
- S. Balu
- Eisai, Inc., Woodcliff Lake, NJ; Premier, Inc., Charlotte, NC
| | - C. Craver
- Eisai, Inc., Woodcliff Lake, NJ; Premier, Inc., Charlotte, NC
| | - J. Gayle
- Eisai, Inc., Woodcliff Lake, NJ; Premier, Inc., Charlotte, NC
| | - D. Buchner
- Eisai, Inc., Woodcliff Lake, NJ; Premier, Inc., Charlotte, NC
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Gallmeier E, Bader D, Seeliger H, Assmann G, Buchner D, de Toni E, Kirchner T, Bruns CJ, Goke B, Schäfer C. Tissue microarray analysis to evaluate the role of heat shock protein 27 as a potential biomarker in pancreatic cancer. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.e21053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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21
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Hatoum HT, Lin S, Buchner D, Cox D. Chemotherapy-induced nausea and vomiting-associated hospital and ER visits in real-world practice: Palonosetron versus other 5-HT 3-RA anti-emetic regimens. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.9127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Bordoni R, Feinberg BA, Gilmore JW, Haislip S, Kim E, Jackson J, Farrelly E, Buchner D. Hematologic outcomes of MDS treatment with hypomethylating agents in community practice. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.6601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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23
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Brown DR, Pate RR, Pratt M, Wheeler F, Buchner D, Ainsworth B, Macera C. Physical activity and public health: training courses for researchers and practitioners. Public Health Rep 2002. [PMID: 12034908 DOI: 10.1016/s0033-3549(04)50034-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The authors explore development of courses in continuing education intended to provide additional research and practice capacity for addressing the growing burden of chronic disease and disability from physical inactivity. Two annual training courses on physical activity and public health are described. The courses are developed with funding from the Centers for Disease Control and Prevention, National Center for Chronic Disease Prevention and Health Promotion, Division of Nutrition and Physical Activity. The University of South Carolina, School of Public Health, Prevention Research Center has been an active collaborator and was responsible for developing and implementing the courses. An eight-day "Course on Research Directions and Strategies," is offered to postdoctoral researchers, and practitioners may take a six-day "Practitioners' Course on Community Interventions." Both courses are designed to increase the number of professionals qualified to implement physical activity community interventions and conduct physical activity and public health research.
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Affiliation(s)
- D R Brown
- Physical Activity and Health Branch, Division of Nutrition and Physical Activity, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30341-3724, USA.
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Abstract
BACKGROUND Asthma treatment has broadened from managing clinical markers to incorporate factors that are most meaningful to patients, collectively called health-related quality of life (HQL). OBJECTIVE To develop an asthma-specific HQL tool, meeting demands for brevity, usefulness and measurement precision. METHODS The 20-item Sydney Asthma Quality of Life Questionnaire (AQLQ) and six additional items were studied using factor analysis, reliability and validity tests among asthma patients 14 and older. RESULTS The 15-item Integrated Therapeutics Group Asthma Short Form (ITG-ASF) retains the validity of the AQLQ with improved scaling properties and interpretability. The ITG-ASF yields 6 scores: Symptom-Free Index, Functioning with Asthma, Psychosocial Impact of Asthma, Asthma Energy and Asthma-Confidence in Health and a Total. All items correlated 0.40 or higher with their hypothesized scales and passed discriminant validity tests, with scaling success rates from 75 to 100%. Reliability exceeded the minimum of 0.70 for group comparisons. Ceiling and floor effects were acceptable. Scales were valid in relation to changes in asthma severity and lung function. The best predictor of asthma severity (National Asthma Education and Prevention Program (NAEPP) staging) was the Symptom-Free Index. A Spanish translation is available, Chinese-American is forthcoming. The reading grade level is 4.8. CONCLUSIONS Development of the ITG-ASF was a data-driven process maximizing measurement precision and breadth while minimizing burden. The ITG-ASF is a brief, comprehensive and empirically valid tool that complements traditional markers of the outcomes of asthma care.
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Brown DR, Pate RR, Pratt M, Wheeler F, Buchner D, Ainsworth B, Macera C. Physical activity and public health: training courses for researchers and practitioners. Public Health Rep 2001; 116:197-202. [PMID: 12034908 PMCID: PMC1497315 DOI: 10.1093/phr/116.3.197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The authors explore development of courses in continuing education intended to provide additional research and practice capacity for addressing the growing burden of chronic disease and disability from physical inactivity. Two annual training courses on physical activity and public health are described. The courses are developed with funding from the Centers for Disease Control and Prevention, National Center for Chronic Disease Prevention and Health Promotion, Division of Nutrition and Physical Activity. The University of South Carolina, School of Public Health, Prevention Research Center has been an active collaborator and was responsible for developing and implementing the courses. An eight-day "Course on Research Directions and Strategies," is offered to postdoctoral researchers, and practitioners may take a six-day "Practitioners' Course on Community Interventions." Both courses are designed to increase the number of professionals qualified to implement physical activity community interventions and conduct physical activity and public health research.
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Affiliation(s)
- D R Brown
- Physical Activity and Health Branch, Division of Nutrition and Physical Activity, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30341-3724, USA.
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26
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Ferrucci L, Guralnik JM, Buchner D, Kasper J, Lamb SE, Simonsick EM, Corti MC, Bandeen-Roche K, Fried LP. Departures from linearity in the relationship between measures of muscular strength and physical performance of the lower extremities: the Women's Health and Aging Study. J Gerontol A Biol Sci Med Sci 1997; 52:M275-85. [PMID: 9310081 DOI: 10.1093/gerona/52a.5.m275] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Sarcopenia, an age-related reduction in muscular mass and strength, may cause a decline in physical functioning and subsequent loss of autonomy. It has been suggested that strength is associated with lower extremity function mainly in the lower portion of the range of strength. Identifying the threshold under which strength is most critical to function may help in targeting groups who may benefit most from exercise interventions. METHODS The study uses data from the Women's Health and Aging Study. The study population, recruited by screening a population-based sample aged 65 years and older, comprised 1,002 women who represent the one-third most disabled women without severe cognitive impairment living in the community. Knee extensor and hip flexor strength were assessed using a hand-held dynamometer. Lower extremity performance was evaluated using tests of walking, standing balance, and rising from a chair. RESULTS Among women tested for strength (n = 892), those who could walk (97%), do the side-by-side stand (87%), or complete 5 chair stands (74%) had significantly greater strength. Walking speed was linearly associated with knee extensor strength over the entire range of strength, but its association with hip strength was limited to values below 15 kg. Time for five chair stands was associated with knee extensor and hip flexor strength below 10 and 15 kg, respectively, and no significant association was detected above these values. Stronger women were more likely to hold balance for 10 sec in the side-by-side, semi-tandem, and tandem positions. The percentage of the variance in performance explained by strength alone was always lower than 20%. CONCLUSIONS In this population, which does not include the strongest older women, there is a departure from linearity in the relationship between muscular strength and some measures of lower extremity performance.
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Affiliation(s)
- L Ferrucci
- Geriatric Department, I Fraticini, National Research Institute (INRCA), Florence, Italy
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27
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Tappen RM, Roach KE, Buchner D, Barry C, Edelstein J. Reliability of physical performance measures in nursing home residents with Alzheimer's disease. J Gerontol A Biol Sci Med Sci 1997; 52:M52-5. [PMID: 9008669 PMCID: PMC1965283 DOI: 10.1093/gerona/52a.1.m52] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.4] [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] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Investigation of the effects of exercise on frail, institutionalized individuals with dementia has been impeded by concerns about the reliability of physical performance measures when used in this population. METHODS The physical performance of 33 institutionalized subjects with Alzheimer's disease was measured during both the morning and afternoon of day 1 by rater 1 and during both the morning and afternoon of day 2, one week later, by rater 1 and rater 2. Intraclass correlation coefficients (ICCs) were calculated to examine the inter- and intrarater reliability of "sit to stand," "25-foot walk," and "the distance walked in 6 minutes" and walking speed over 25 feet and for 6 minutes. An analysis of variance was performed to determine the components of variance for each test. RESULTS ICCs for "distance walked in 6 minutes" ranged from .80 to .99 with 77% of the variance explained by inter-subject difference. The ICCs for "time to walk 25 feet" ranged from .57 to .97 with 25% of the variance explained by inter-subject differences. In contrast, the "sit to stand" measure produced ICCs ranging from -.07 to .85 with only 7% of the variance explained by inter-subject differences in this impaired population. CONCLUSION Our results support the contention that some physical performance measures can be used to test individuals in the later stages of Alzheimer's disease given appropriate modification. Although subjects with Alzheimer's disease may have difficulty following commands and/or require physical assistance, this does not prohibit the reliable assessment of physical performance if measurements are made over longer (6-minute walk) rather than shorter periods (25-foot walk).
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Affiliation(s)
- R M Tappen
- College of Nursing, Florida Atlantic University, Boca Raton, USA
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28
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Pate RR, Pratt M, Blair SN, Haskell WL, Macera CA, Bouchard C, Buchner D, Ettinger W, Heath GW, King AC. Physical activity and public health. A recommendation from the Centers for Disease Control and Prevention and the American College of Sports Medicine. JAMA 1995. [PMID: 7823386 DOI: 10.1001/jama.1995.03520290054029] [Citation(s) in RCA: 3249] [Impact Index Per Article: 112.0] [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: 12/25/2022]
Abstract
OBJECTIVE To encourage increased participation in physical activity among Americans of all ages by issuing a public health recommendation on the types and amounts of physical activity needed for health promotion and disease prevention. PARTICIPANTS A planning committee of five scientists was established by the Centers for Disease Control and Prevention and the American College of Sports Medicine to organize a workshop. This committee selected 15 other workshop discussants on the basis of their research expertise in issues related to the health implications of physical activity. Several relevant professional or scientific organizations and federal agencies also were represented. EVIDENCE The panel of experts reviewed the pertinent physiological, epidemiologic, and clinical evidence, including primary research articles and recent review articles. CONSENSUS PROCESS Major issues related to physical activity and health were outlined, and selected members of the expert panel drafted sections of the paper from this outline. A draft manuscript was prepared by the planning committee and circulated to the full panel in advance of the 2-day workshop. During the workshop, each section of the manuscript was reviewed by the expert panel. Primary attention was given to achieving group consensus concerning the recommended types and amounts of physical activity. A concise "public health message" was developed to express the recommendations of the panel. During the ensuing months, the consensus statement was further reviewed and revised and was formally endorsed by both the Centers for Disease Control and Prevention and the American College of Sports Medicine. CONCLUSION Every US adult should accumulate 30 minutes or more of moderate-intensity physical activity on most, preferably all, days of the week.
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Affiliation(s)
- R R Pate
- Department of Exercise Science, University of South Carolina School of Public Health, Columbia 29208
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29
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Pate RR, Pratt M, Blair SN, Haskell WL, Macera CA, Bouchard C, Buchner D, Ettinger W, Heath GW, King AC. Physical activity and public health. A recommendation from the Centers for Disease Control and Prevention and the American College of Sports Medicine. JAMA 1995; 273:402-7. [PMID: 7823386 DOI: 10.1001/jama.273.5.402] [Citation(s) in RCA: 1667] [Impact Index Per Article: 57.5] [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: 01/27/2023]
Abstract
OBJECTIVE To encourage increased participation in physical activity among Americans of all ages by issuing a public health recommendation on the types and amounts of physical activity needed for health promotion and disease prevention. PARTICIPANTS A planning committee of five scientists was established by the Centers for Disease Control and Prevention and the American College of Sports Medicine to organize a workshop. This committee selected 15 other workshop discussants on the basis of their research expertise in issues related to the health implications of physical activity. Several relevant professional or scientific organizations and federal agencies also were represented. EVIDENCE The panel of experts reviewed the pertinent physiological, epidemiologic, and clinical evidence, including primary research articles and recent review articles. CONSENSUS PROCESS Major issues related to physical activity and health were outlined, and selected members of the expert panel drafted sections of the paper from this outline. A draft manuscript was prepared by the planning committee and circulated to the full panel in advance of the 2-day workshop. During the workshop, each section of the manuscript was reviewed by the expert panel. Primary attention was given to achieving group consensus concerning the recommended types and amounts of physical activity. A concise "public health message" was developed to express the recommendations of the panel. During the ensuing months, the consensus statement was further reviewed and revised and was formally endorsed by both the Centers for Disease Control and Prevention and the American College of Sports Medicine. CONCLUSION Every US adult should accumulate 30 minutes or more of moderate-intensity physical activity on most, preferably all, days of the week.
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Affiliation(s)
- R R Pate
- Department of Exercise Science, University of South Carolina School of Public Health, Columbia 29208
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30
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Abstract
Randomized phase III clinical trials provide important information on the efficacy of new pharmaceutical agents for cancer patients. Policy makers are showing increased interest in both economic and clinical data on new agents in order to approve pharmaceuticals for widespread use, and clinical trials have been viewed as the proper setting to evaluate these outcomes for new agents. With the recent approval of new pharmaceutical agents that have high costs, early assessments of economic benefit have taken on larger importance to physicians and patients. The integration of economic and clinical analysis in phase III clinical trials raises methodological and practical issues related to study design, collection of data on resource utilization, and generalizability of data to other settings. In this paper, we review these issues and discuss their relationship to clinical trials for new pharmaceutical products.
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Affiliation(s)
- C L Bennett
- Division of Health Services Research and Development, Durham Veterans Administration, North Carolina
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31
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Ko GN, Zhang LD, Yan WW, Zhang MD, Buchner D, Xia ZY, Wyatt RJ, Jeste DV. The Shanghai 800: prevalence of tardive dyskinesia in a Chinese psychiatric hospital. Am J Psychiatry 1989; 146:387-9. [PMID: 2563929 DOI: 10.1176/ajp.146.3.387] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [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: 01/01/2023]
Abstract
The authors found that 73 (8.4%) of 866 patients with chronic schizophrenia in the Shanghai Psychiatric Hospital who had been treated with neuroleptics had tardive dyskinesia. This low prevalence rate is possibly ascribable to the use of relatively low doses of neuroleptics.
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Affiliation(s)
- G N Ko
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle
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Abstract
Adverse drug reactions causing cognitive impairment are an important problem in the elderly. Thirty-five patients with adverse drug reaction were identified among more than 300 patients evaluated for cognitive impairment and compared with patients without adverse drug reaction. Sedative hypnotic agents, especially long-acting benzodiazepines, were the commonest drugs associated with cognitive impairment in this population. The number of drugs used, use of sedative hypnotics and antihypertensives, and falling were strongly associated with adverse reactions in logistic regression analyses. The relative odds of an adverse reaction associated with cognitive impairment increased as the number of prescription drugs increased, exceeding 9.0 for patients taking four or more prescription drugs. Adverse drug reactions are an important source of excess morbidity in patients with dementia or suspected dementia. Strategies that could minimize this problem include a high index of suspicion, drug-free trials in suspected cases, and careful monitoring of drug therapy.
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