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Tkalec Ž, Antignac JP, Bandow N, Béen FM, Belova L, Bessems J, Le Bizec B, Brack W, Cano-Sancho G, Chaker J, Covaci A, Creusot N, David A, Debrauwer L, Dervilly G, Duca RC, Fessard V, Grimalt JO, Guerin T, Habchi B, Hecht H, Hollender J, Jamin EL, Klánová J, Kosjek T, Krauss M, Lamoree M, Lavison-Bompard G, Meijer J, Moeller R, Mol H, Mompelat S, Van Nieuwenhuyse A, Oberacher H, Parinet J, Van Poucke C, Roškar R, Togola A, Trontelj J, Price EJ. Innovative analytical methodologies for characterizing chemical exposure with a view to next-generation risk assessment. Environ Int 2024; 186:108585. [PMID: 38521044 DOI: 10.1016/j.envint.2024.108585] [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: 08/18/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
The chemical burden on the environment and human population is increasing. Consequently, regulatory risk assessment must keep pace to manage, reduce, and prevent adverse impacts on human and environmental health associated with hazardous chemicals. Surveillance of chemicals of known, emerging, or potential future concern, entering the environment-food-human continuum is needed to document the reality of risks posed by chemicals on ecosystem and human health from a one health perspective, feed into early warning systems and support public policies for exposure mitigation provisions and safe and sustainable by design strategies. The use of less-conventional sampling strategies and integration of full-scan, high-resolution mass spectrometry and effect-directed analysis in environmental and human monitoring programmes have the potential to enhance the screening and identification of a wider range of chemicals of known, emerging or potential future concern. Here, we outline the key needs and recommendations identified within the European Partnership for Assessment of Risks from Chemicals (PARC) project for leveraging these innovative methodologies to support the development of next-generation chemical risk assessment.
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Affiliation(s)
- Žiga Tkalec
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia.
| | | | - Nicole Bandow
- German Environment Agency, Laboratory for Water Analysis, Colditzstraße 34, 12099 Berlin, Germany.
| | - Frederic M Béen
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; KWR Water Research Institute, Nieuwegein, The Netherlands.
| | - Lidia Belova
- Toxicological Center, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Jos Bessems
- Flemish Institute for Technological Research (VITO), Mol, Belgium.
| | | | - Werner Brack
- Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Effect-Directed Analysis, Permoserstraße 15, 04318 Leipzig, Germany; Goethe University Frankfurt, Department of Evolutionary Ecology and Environmental Toxicology, Max-von-Laue-Strasse 13, 60438 Frankfurt, Germany.
| | | | - Jade Chaker
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
| | - Adrian Covaci
- Toxicological Center, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Nicolas Creusot
- INRAE, French National Research Institute For Agriculture, Food & Environment, UR1454 EABX, Bordeaux Metabolome, MetaboHub, Gazinet Cestas, France.
| | - Arthur David
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France.
| | | | - Radu Corneliu Duca
- Unit Environmental Hygiene and Human Biological Monitoring, Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg; Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit of Leuven (KU Leuven), 3000 Leuven, Belgium.
| | - Valérie Fessard
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory of Fougères, Toxicology of Contaminants Unit, 35306 Fougères, France.
| | - Joan O Grimalt
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Catalonia, Spain.
| | - Thierry Guerin
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Strategy and Programs Department, F-94701 Maisons-Alfort, France.
| | - Baninia Habchi
- INRS, Département Toxicologie et Biométrologie Laboratoire Biométrologie 1, rue du Morvan - CS 60027 - 54519, Vandoeuvre Cedex, France.
| | - Helge Hecht
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
| | - Juliane Hollender
- Swiss Federal Institute of Aquatic Science and Technology - Eawag, 8600 Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland.
| | - Emilien L Jamin
- Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France.
| | - Jana Klánová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
| | - Tina Kosjek
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia.
| | - Martin Krauss
- Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Effect-Directed Analysis, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Marja Lamoree
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Gwenaelle Lavison-Bompard
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Pesticides and Marine Biotoxins Unit, F-94701 Maisons-Alfort, France.
| | - Jeroen Meijer
- Vrije Universiteit Amsterdam, Amsterdam Institute for Life and Environment (A-LIFE), Section Chemistry for Environment and Health, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Ruth Moeller
- Unit Medical Expertise and Data Intelligence, Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg.
| | - Hans Mol
- Wageningen Food Safety Research - Part of Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands.
| | - Sophie Mompelat
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory of Fougères, Toxicology of Contaminants Unit, 35306 Fougères, France.
| | - An Van Nieuwenhuyse
- Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit of Leuven (KU Leuven), 3000 Leuven, Belgium; Department of Health Protection, Laboratoire National de Santé (LNS), 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg.
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Insbruck, 6020 Innsbruck, Austria.
| | - Julien Parinet
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Pesticides and Marine Biotoxins Unit, F-94701 Maisons-Alfort, France.
| | - Christof Van Poucke
- Flanders Research Institute for Agriculture, Fisheries And Food (ILVO), Brusselsesteenweg 370, 9090 Melle, Belgium.
| | - Robert Roškar
- University of Ljubljana, Faculty of Pharmacy, Slovenia.
| | - Anne Togola
- BRGM, 3 avenue Claude Guillemin, 45060 Orléans, France.
| | | | - Elliott J Price
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
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2
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Zhao Y, Meijer J, Walker DI, Kim J, Portengen L, Jones DP, Saberi Hosnijeh F, Vlaanderen J, Vermeulen R. Dioxin(-like)-Related Biological Effects through Integrated Chemical-wide and Metabolome-wide Analyses. Environ Sci Technol 2024; 58:258-268. [PMID: 38149779 PMCID: PMC10785760 DOI: 10.1021/acs.est.3c07588] [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] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/28/2023]
Abstract
Dioxin(-like) exposures are linked to adverse health effects, including cancer. However, metabolic alterations induced by these chemicals remain largely unknown. Beyond known dioxin(-like) compounds, we leveraged a chemical-wide approach to assess chlorinated co-exposures and parent compound products [termed dioxin(-like)-related compounds] among 137 occupational workers. Endogenous metabolites were profiled by untargeted metabolomics, namely, reversed-phase chromatography with negative electrospray ionization (C18-negative) and hydrophilic interaction liquid chromatography with positive electrospray ionization (HILIC-positive). We performed a metabolome-wide association study to select dioxin(-like) associated metabolic features using a 20% false discovery rate threshold. Metabolic features were then characterized by pathway enrichment analyses. There are no significant features associated with polychlorinated dibenzo-p-dioxins (PCDDs), a subgroup of known dioxin(-like) compounds. However, 3,110 C18-negative and 2,894 HILIC-positive features were associated with at least one of the PCDD-related compounds. Abundant metabolic changes were also observed for polychlorinated dibenzofuran-related and polychlorinated biphenyl-related compounds. These metabolic features were primarily enriched in pathways of amino acids, lipid and fatty acids, carbohydrates, cofactors, and nucleotides. Our study highlights the potential of chemical-wide analysis for comprehensive exposure assessment beyond targeted chemicals. Coupled with advanced endogenous metabolomics, this approach allows for an in-depth exploration of metabolic alterations induced by environmental chemicals.
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Affiliation(s)
- Yujia Zhao
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
| | - Jeroen Meijer
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
- Department
Environment & Health, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
| | - Douglas I. Walker
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Juni Kim
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Lützen Portengen
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
| | - Dean P. Jones
- Division
of Pulmonary, Allergy, Critical Care and Sleep Medicine, School of
Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Fatemeh Saberi Hosnijeh
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
| | - Jelle Vlaanderen
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
| | - Roel Vermeulen
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
- Julius
Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht 3584 CX, The Netherlands
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van Dijk B, Buffard P, Farr AD, Giersdorf F, Meijer J, Dutilh BE, Rainey PB. Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome. ISME Commun 2023; 3:90. [PMID: 37640834 PMCID: PMC10462680 DOI: 10.1038/s43705-023-00294-w] [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] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.
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Affiliation(s)
- Bram van Dijk
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
| | - Pauline Buffard
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Andrew D Farr
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Franz Giersdorf
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL CNRS, Paris, France.
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4
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Alberga JM, Meijer J, Raghoebar GM, Langendijk JA, Korfage A, Steenbakkers RJHM, Meijer TWH, Reintsema H, Vissink A, Witjes MJH. Planned dose of intensity modulated proton beam therapy versus volumetric modulated arch therapy to tooth-bearing regions. Oral Oncol 2023; 140:106392. [PMID: 37084567 DOI: 10.1016/j.oraloncology.2023.106392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/23/2023]
Abstract
BACKGROUND Intensity modulated proton beam therapy (IMPT) for head and neck cancer offers dosimetric benefits for the organs at risk when compared to photon-based volumetric modulated arch therapy (VMAT). However, limited data exists about the potential benefits of IMPT for tooth-bearing regions. The aim of this study was to compare the IMPT and VMAT radiation dosimetrics of the tooth-bearing regions in head and neck cancer patients. Also, we aimed to identify prognostic factors for a cumulative radiation dose of ≥40 Gy on the tooth-bearing areas, which is considered the threshold dose for prophylactic dental extractions. METHODS A total of 121 head and neck cancer patients were included in this retrospective analysis of prospectively collected data. We compared the average Dmean values of IMPT versus VMAT of multiple tooth-bearing regions in the same patients. Multivariate logistic regression analysis was performed for receiving a cumulative radiation dose of ≥40 Gy to the tooth-bearing regions (primary endpoint) in both VMAT and IMPT. RESULTS A lower Dmean was seen after applying IMPT to the tooth-bearing tumour regions (p < 0.001). Regarding VMAT, oral cavity tumours, T3-T4 tumours, molar regions in the mandible, and regions ipsilateral to the tumour were risk factors for receiving a cumulative radiation dose of ≥40 Gy. CONCLUSIONS IMPT significantly reduces the radiation dose to the tooth-bearing regions.
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Affiliation(s)
- J M Alberga
- Department of Oral and Maxillofacial Surgery, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
| | - J Meijer
- Department of Oral and Maxillofacial Surgery, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - G M Raghoebar
- Department of Oral and Maxillofacial Surgery, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - J A Langendijk
- Department of Radiotherapy, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - A Korfage
- Department of Oral and Maxillofacial Surgery, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - R J H M Steenbakkers
- Department of Radiotherapy, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - T W H Meijer
- Department of Radiotherapy, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - H Reintsema
- Department of Oral and Maxillofacial Surgery, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - A Vissink
- Department of Oral and Maxillofacial Surgery, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - M J H Witjes
- Department of Oral and Maxillofacial Surgery, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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Jonkers TJH, Keizers PHJ, Béen F, Meijer J, Houtman CJ, Al Gharib I, Molenaar D, Hamers T, Lamoree MH. Identifying antimicrobials and their metabolites in wastewater and surface water with effect-directed analysis. Chemosphere 2023; 320:138093. [PMID: 36758810 DOI: 10.1016/j.chemosphere.2023.138093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 12/12/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
This study aimed to identify antimicrobial contaminants in the aquatic environment with effect-directed analysis. Wastewater influent, effluent, and surface water (up- and downstream of the discharge location) were sampled at two study sites. The samples were enriched, subjected to high-resolution fractionation, and the resulting 80 fractions were tested in an antibiotics bioassay. The resulting bioactive fractions guided the suspect and nontargeted identification strategy in the high-resolution mass spectrometry data that was recorded in parallel. Chemical features were annotated with reference databases, assessed on annotation quality, and assigned identification confidence levels. To identify antibiotic metabolites, Phase I metabolites were predicted in silico for over 500 antibiotics and included as a suspect list. Predicted retention times and fragmentation patterns reduced the number of annotations to consider for confirmation testing. Overall, the bioactivity of three fractions could be explained by the identified antibiotics (clarithromycin and azithromycin) and an antibiotic metabolite (14-OH(R) clarithromycin), explaining 78% of the bioactivity measured at one study site. The applied identification strategy successfully identified antibiotic metabolites in the aquatic environment, emphasizing the need to include the toxic effects of bioactive metabolites in environmental risk assessments.
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Affiliation(s)
- Tim J H Jonkers
- Department of Environment & Health, Faculty of Science, Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands.
| | - Peter H J Keizers
- National Institute for Public Health and the Environment RIVM, A. van Leeuwenhoeklaan 9, 3721MA, Bilthoven, the Netherlands.
| | - Frederic Béen
- Department of Environment & Health, Faculty of Science, Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands; KWR Water Research Institute, Groningenhaven 7, 3430 BB, Nieuwegein, the Netherlands.
| | - Jeroen Meijer
- Department of Environment & Health, Faculty of Science, Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Utrecht University, Yalelaan 2, 3584 CM, Utrecht, the Netherlands.
| | - Corine J Houtman
- The Water Laboratory, J.W. Lucasweg 2, 2031 BE, Haarlem, the Netherlands.
| | - Imane Al Gharib
- Systems Biology Lab, Faculty of Science, Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Douwe Molenaar
- Systems Biology Lab, Faculty of Science, Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands.
| | - Timo Hamers
- Department of Environment & Health, Faculty of Science, Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands.
| | - Marja H Lamoree
- Department of Environment & Health, Faculty of Science, Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands.
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6
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Figueiredo DM, Lô S, Krop E, Meijer J, Beeltje H, Lamoree MH, Vermeulen R. Do cats mirror their owner? Paired exposure assessment using silicone bands to measure residential PAH exposure. Environ Res 2023; 222:115412. [PMID: 36736760 DOI: 10.1016/j.envres.2023.115412] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 12/20/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
It has been suggested that domestic animals can serve as sentinels for human exposures. In this study our objectives were to demonstrate that i) silicone collars can be used to measure environmental exposures of (domestic) animals, and that ii) domestic animals can be used as sentinels for human residential exposure. For this, we simultaneously measured polycyclic aromatic hydrocarbons (PAHs) using silicone bands worn by 30 pet cats (collar) and their owner (wristband). Collars and wristbands were worn for 7 days and analyzed via targeted Gas Chromatography-Mass Spectrometry (GC-MS). Demographics and daily routines were collected for humans and cats. Out of 16 PAHs, 9 were frequently detected (>50% of samples) in both wristbands and collars, of which Phenanthrene and Fluorene were detected in all samples. Concentrations of wristbands and collars were moderately correlated for these 9 PAHs (Median Spearman's r = 0.51 (range 0.16-0.68)). Determinants of PAH concentrations of cats and humans showed considerable overlap, with vacuum cleaning resulting in higher exposures and frequent changing of bed sheets in lower exposures. This study adds proof-of-principle data for the use of silicone collars to measure (domestic) animal exposure and shows that cats can be used as sentinels for human residential exposure.
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Affiliation(s)
- Daniel M Figueiredo
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Yalelaan 2, 3584 CM, Utrecht, the Netherlands.
| | - Serigne Lô
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Yalelaan 2, 3584 CM, Utrecht, the Netherlands
| | - Esmeralda Krop
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Yalelaan 2, 3584 CM, Utrecht, the Netherlands
| | - Jeroen Meijer
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Yalelaan 2, 3584 CM, Utrecht, the Netherlands; Department of Environment & Health, Faculty of Science, Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Henry Beeltje
- TNO Environmeral Modelling, Sensing & Analysis, Princetonlaan 8, 3584 CB, Utrecht, the Netherlands; AQUON, De Blomboogerd 12, 4003 BX, Tiel, the Netherlands
| | - Marja H Lamoree
- Department of Environment & Health, Faculty of Science, Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Yalelaan 2, 3584 CM, Utrecht, the Netherlands
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Wortel MT, Agashe D, Bailey SF, Bank C, Bisschop K, Blankers T, Cairns J, Colizzi ES, Cusseddu D, Desai MM, van Dijk B, Egas M, Ellers J, Groot AT, Heckel DG, Johnson ML, Kraaijeveld K, Krug J, Laan L, Lässig M, Lind PA, Meijer J, Noble LM, Okasha S, Rainey PB, Rozen DE, Shitut S, Tans SJ, Tenaillon O, Teotónio H, de Visser JAGM, Visser ME, Vroomans RMA, Werner GDA, Wertheim B, Pennings PS. Towards evolutionary predictions: Current promises and challenges. Evol Appl 2023; 16:3-21. [PMID: 36699126 PMCID: PMC9850016 DOI: 10.1111/eva.13513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.
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Affiliation(s)
- Meike T. Wortel
- Swammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - Deepa Agashe
- National Centre for Biological SciencesBangaloreIndia
| | | | - Claudia Bank
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
- Gulbenkian Science InstituteOeirasPortugal
| | - Karen Bisschop
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
- Origins CenterGroningenThe Netherlands
- Laboratory of Aquatic Biology, KU Leuven KulakKortrijkBelgium
| | - Thomas Blankers
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
- Origins CenterGroningenThe Netherlands
| | | | - Enrico Sandro Colizzi
- Origins CenterGroningenThe Netherlands
- Mathematical InstituteLeiden UniversityLeidenThe Netherlands
| | | | | | - Bram van Dijk
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Martijn Egas
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Jacintha Ellers
- Department of Ecological ScienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Astrid T. Groot
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | | | | | - Ken Kraaijeveld
- Leiden Centre for Applied BioscienceUniversity of Applied Sciences LeidenLeidenThe Netherlands
| | - Joachim Krug
- Institute for Biological PhysicsUniversity of CologneCologneGermany
| | - Liedewij Laan
- Department of Bionanoscience, Kavli Institute of NanoscienceTU DelftDelftThe Netherlands
| | - Michael Lässig
- Institute for Biological PhysicsUniversity of CologneCologneGermany
| | - Peter A. Lind
- Department Molecular BiologyUmeå UniversityUmeåSweden
| | - Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Luke M. Noble
- Institute de Biologie, École Normale Supérieure, CNRS, InsermParisFrance
| | | | - Paul B. Rainey
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Laboratoire Biophysique et Évolution, CBI, ESPCI Paris, Université PSL, CNRSParisFrance
| | - Daniel E. Rozen
- Institute of Biology, Leiden UniversityLeidenThe Netherlands
| | - Shraddha Shitut
- Origins CenterGroningenThe Netherlands
- Institute of Biology, Leiden UniversityLeidenThe Netherlands
| | | | | | | | | | - Marcel E. Visser
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Renske M. A. Vroomans
- Origins CenterGroningenThe Netherlands
- Informatics InstituteUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Bregje Wertheim
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
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8
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Mohammed Taha H, Aalizadeh R, Alygizakis N, Antignac JP, Arp HPH, Bade R, Baker N, Belova L, Bijlsma L, Bolton EE, Brack W, Celma A, Chen WL, Cheng T, Chirsir P, Čirka Ľ, D’Agostino LA, Djoumbou Feunang Y, Dulio V, Fischer S, Gago-Ferrero P, Galani A, Geueke B, Głowacka N, Glüge J, Groh K, Grosse S, Haglund P, Hakkinen PJ, Hale SE, Hernandez F, Janssen EML, Jonkers T, Kiefer K, Kirchner M, Koschorreck J, Krauss M, Krier J, Lamoree MH, Letzel M, Letzel T, Li Q, Little J, Liu Y, Lunderberg DM, Martin JW, McEachran AD, McLean JA, Meier C, Meijer J, Menger F, Merino C, Muncke J, Muschket M, Neumann M, Neveu V, Ng K, Oberacher H, O’Brien J, Oswald P, Oswaldova M, Picache JA, Postigo C, Ramirez N, Reemtsma T, Renaud J, Rostkowski P, Rüdel H, Salek RM, Samanipour S, Scheringer M, Schliebner I, Schulz W, Schulze T, Sengl M, Shoemaker BA, Sims K, Singer H, Singh RR, Sumarah M, Thiessen PA, Thomas KV, Torres S, Trier X, van Wezel AP, Vermeulen RCH, Vlaanderen JJ, von der Ohe PC, Wang Z, Williams AJ, Willighagen EL, Wishart DS, Zhang J, Thomaidis NS, Hollender J, Slobodnik J, Schymanski EL. The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry. Environ Sci Eur 2022; 34:104. [PMID: 36284750 PMCID: PMC9587084 DOI: 10.1186/s12302-022-00680-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
Background The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for "suspect screening" lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA's CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101). Conclusions The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the "one substance, one assessment" approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/). Supplementary Information The online version contains supplementary material available at 10.1186/s12302-022-00680-6.
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Affiliation(s)
- Hiba Mohammed Taha
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Reza Aalizadeh
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Nikiforos Alygizakis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
| | | | - Hans Peter H. Arp
- Norwegian Geotechnical Institute (NGI), Ullevål Stadion, P.O. Box 3930, 0806 Oslo, Norway
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Richard Bade
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, QLD 4102 Australia
| | | | - Lidia Belova
- Toxicological Centre, University of Antwerp, Antwerp, Belgium
| | - Lubertus Bijlsma
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Castelló, Spain
| | - Evan E. Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Werner Brack
- UFZ, Helmholtz Centre for Environmental Research, Leipzig, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt Am Main, Germany
| | - Alberto Celma
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Castelló, Spain
- Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Wen-Ling Chen
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, 17 Xuzhou Rd., Zhongzheng Dist., Taipei, Taiwan
| | - Tiejun Cheng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Parviel Chirsir
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Ľuboš Čirka
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
- Faculty of Chemical and Food Technology, Institute of Information Engineering, Automation, and Mathematics, Slovak University of Technology in Bratislava (STU), Radlinského 9, 812 37 Bratislava, Slovak Republic
| | - Lisa A. D’Agostino
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, 10691 Stockholm, Sweden
| | | | - Valeria Dulio
- INERIS, National Institute for Environment and Industrial Risks, Verneuil en Halatte, France
| | - Stellan Fischer
- Swedish Chemicals Agency (KEMI), P.O. Box 2, 172 13 Sundbyberg, Sweden
| | - Pablo Gago-Ferrero
- Institute of Environmental Assessment and Water Research-Severo Ochoa Excellence Center (IDAEA), Spanish Council of Scientific Research (CSIC), Barcelona, Spain
| | - Aikaterini Galani
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Birgit Geueke
- Food Packaging Forum Foundation, Staffelstrasse 10, 8045 Zurich, Switzerland
| | - Natalia Głowacka
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
| | - Juliane Glüge
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Ksenia Groh
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Sylvia Grosse
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Peter Haglund
- Department of Chemistry, Chemical Biological Centre (KBC), Umeå University, Linnaeus Väg 6, 901 87 Umeå, Sweden
| | - Pertti J. Hakkinen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Sarah E. Hale
- Norwegian Geotechnical Institute (NGI), Ullevål Stadion, P.O. Box 3930, 0806 Oslo, Norway
| | - Felix Hernandez
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Castelló, Spain
| | - Elisabeth M.-L. Janssen
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Tim Jonkers
- Department Environment and Health, Amsterdam Institute for Life and Environment, Vrije Universiteit, Amsterdam, The Netherlands
| | - Karin Kiefer
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Michal Kirchner
- Water Research Institute (WRI), Nábr. Arm. Gen. L. Svobodu 5, 81249 Bratislava, Slovak Republic
| | - Jan Koschorreck
- German Environment Agency (UBA), Wörlitzer Platz 1, Dessau-Roßlau, Germany
| | - Martin Krauss
- UFZ, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jessy Krier
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Marja H. Lamoree
- Department Environment and Health, Amsterdam Institute for Life and Environment, Vrije Universiteit, Amsterdam, The Netherlands
| | - Marion Letzel
- Bavarian Environment Agency, 86179 Augsburg, Germany
| | - Thomas Letzel
- Analytisches Forschungsinstitut Für Non-Target Screening GmbH (AFIN-TS), Am Mittleren Moos 48, 86167 Augsburg, Germany
| | - Qingliang Li
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - James Little
- Mass Spec Interpretation Services, 3612 Hemlock Park Drive, Kingsport, TN 37663 USA
| | - Yanna Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (SKLECE, RCEES, CAS), No. 18 Shuangqing Road, Haidian District, Beijing, 100086 China
| | - David M. Lunderberg
- Hope College, Holland, MI 49422 USA
- University of California, Berkeley, CA USA
| | - Jonathan W. Martin
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, 10691 Stockholm, Sweden
| | - Andrew D. McEachran
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd, Santa Clara, CA 95051 USA
| | - John A. McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235 USA
| | - Christiane Meier
- German Environment Agency (UBA), Wörlitzer Platz 1, Dessau-Roßlau, Germany
| | - Jeroen Meijer
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Frank Menger
- Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Carla Merino
- University Rovira i Virgili, Tarragona, Spain
- Biosfer Teslab, Reus, Spain
| | - Jane Muncke
- Food Packaging Forum Foundation, Staffelstrasse 10, 8045 Zurich, Switzerland
| | | | - Michael Neumann
- German Environment Agency (UBA), Wörlitzer Platz 1, Dessau-Roßlau, Germany
| | - Vanessa Neveu
- Nutrition and Metabolism Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Kelsey Ng
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
- RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Muellerstrasse 44, Innsbruck, Austria
| | - Jake O’Brien
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, QLD 4102 Australia
| | - Peter Oswald
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
| | - Martina Oswaldova
- Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic
| | - Jaqueline A. Picache
- Department of Chemistry, Center for Innovative Technology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235 USA
| | - Cristina Postigo
- Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- Technologies for Water Management and Treatment Research Group, Department of Civil Engineering, University of Granada, Campus de Fuentenueva S/N, 18071 Granada, Spain
| | - Noelia Ramirez
- University Rovira i Virgili, Tarragona, Spain
- Institute of Health Research Pere Virgili, Tarragona, Spain
| | | | - Justin Renaud
- Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | | | - Heinz Rüdel
- Fraunhofer Institute for Molecular Biology and Applied Ecology (Fraunhofer IME), Schmallenberg, Germany
| | - Reza M. Salek
- Nutrition and Metabolism Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Saer Samanipour
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, Amsterdam, 1090 GD The Netherlands
| | - Martin Scheringer
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
- RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
| | - Ivo Schliebner
- German Environment Agency (UBA), Wörlitzer Platz 1, Dessau-Roßlau, Germany
| | - Wolfgang Schulz
- Laboratory for Operation Control and Research, Zweckverband Landeswasserversorgung, Am Spitzigen Berg 1, 89129 Langenau, Germany
| | - Tobias Schulze
- UFZ, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Manfred Sengl
- Bavarian Environment Agency, 86179 Augsburg, Germany
| | - Benjamin A. Shoemaker
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Kerry Sims
- Environment Agency, Horizon House, Deanery Road, Bristol, BS1 5AH UK
| | - Heinz Singer
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Randolph R. Singh
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
- Chemical Contamination of Marine Ecosystems (CCEM) Unit, Institut Français de Recherche pour l’Exploitation de la Mer (IFREMER), Rue de l’Ile d’Yeu, BP 21105, 44311 Cedex 3, Nantes France
| | - Mark Sumarah
- Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Paul A. Thiessen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Kevin V. Thomas
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, QLD 4102 Australia
| | | | - Xenia Trier
- Section for Environmental Chemistry and Physics, Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Annemarie P. van Wezel
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Roel C. H. Vermeulen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Jelle J. Vlaanderen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | | | - Zhanyun Wang
- Technology and Society Laboratory, Empa-Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Antony J. Williams
- Computational Chemistry and Cheminformatics Branch (CCCB), Chemical Characterization and Exposure Division (CCED), Center for Computational Toxicology and Exposure (CCTE), United States Environmental Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711 USA
| | - Egon L. Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | | | - Jian Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Nikolaos S. Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Juliane Hollender
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | | | - Emma L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
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9
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Jonkers TJ, Meijer J, Vlaanderen JJ, Vermeulen RCH, Houtman CJ, Hamers T, Lamoree MH. High-Performance Data Processing Workflow Incorporating Effect-Directed Analysis for Feature Prioritization in Suspect and Nontarget Screening. Environ Sci Technol 2022; 56:1639-1651. [PMID: 35050604 PMCID: PMC8812114 DOI: 10.1021/acs.est.1c04168] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Effect-directed analysis (EDA) aims at the detection of bioactive chemicals of emerging concern (CECs) by combining toxicity testing and high-resolution mass spectrometry (HRMS). However, consolidation of toxicological and chemical analysis techniques to identify bioactive CECs remains challenging and laborious. In this study, we incorporate state-of-the-art identification approaches in EDA and propose a robust workflow for the high-throughput screening of CECs in environmental and human samples. Three different sample types were extracted and chemically analyzed using a single high-performance liquid chromatography HRMS method. Chemical features were annotated by suspect screening with several reference databases. Annotation quality was assessed using an automated scoring system. In parallel, the extracts were fractionated into 80 micro-fractions each covering a couple of seconds from the chromatogram run and tested for bioactivity in two bioassays. The EDA workflow prioritized and identified chemical features related to bioactive fractions with varying levels of confidence. Confidence levels were improved with the in silico software tools MetFrag and the retention time indices platform. The toxicological and chemical data quality was comparable between the use of single and multiple technical replicates. The proposed workflow incorporating EDA for feature prioritization in suspect and nontarget screening paves the way for the routine identification of CECs in a high-throughput manner.
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Affiliation(s)
- Tim J.
H. Jonkers
- Department
of Environment & Health, Faculty of Science, Amsterdam Institute
of Molecular and Life Sciences, Vrije Universiteit
Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Jeroen Meijer
- Department
of Environment & Health, Faculty of Science, Amsterdam Institute
of Molecular and Life Sciences, Vrije Universiteit
Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Institute
for Risk Assessment Sciences (IRAS), Utrecht
University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Jelle J. Vlaanderen
- Institute
for Risk Assessment Sciences (IRAS), Utrecht
University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Roel C. H. Vermeulen
- Institute
for Risk Assessment Sciences (IRAS), Utrecht
University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Corine J. Houtman
- The
Water Laboratory, J.W. Lucasweg 2, 2031 BE Haarlem, The Netherlands
| | - Timo Hamers
- Department
of Environment & Health, Faculty of Science, Amsterdam Institute
of Molecular and Life Sciences, Vrije Universiteit
Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Marja H. Lamoree
- Department
of Environment & Health, Faculty of Science, Amsterdam Institute
of Molecular and Life Sciences, Vrije Universiteit
Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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10
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Meijer J, Lamoree M, Hamers T, Antignac JP, Hutinet S, Debrauwer L, Covaci A, Huber C, Krauss M, Walker DI, Schymanski EL, Vermeulen R, Vlaanderen J. An annotation database for chemicals of emerging concern in exposome research. Environ Int 2021; 152:106511. [PMID: 33773387 DOI: 10.1016/j.envint.2021.106511] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/03/2021] [Accepted: 03/06/2021] [Indexed: 05/18/2023]
Abstract
BACKGROUND Chemicals of Emerging Concern (CECs) include a very wide group of chemicals that are suspected to be responsible for adverse effects on health, but for which very limited information is available. Chromatographic techniques coupled with high-resolution mass spectrometry (HRMS) can be used for non-targeted screening and detection of CECs, by using comprehensive annotation databases. Establishing a database focused on the annotation of CECs in human samples will provide new insight into the distribution and extent of exposures to a wide range of CECs in humans. OBJECTIVES This study describes an approach for the aggregation and curation of an annotation database (CECscreen) for the identification of CECs in human biological samples. METHODS The approach consists of three main parts. First, CECs compound lists from various sources were aggregated and duplications and inorganic compounds were removed. Subsequently, the list was curated by standardization of structures to create "MS-ready" and "QSAR-ready" SMILES, as well as calculation of exact masses (monoisotopic and adducts) and molecular formulas. The second step included the simulation of Phase I metabolites. The third and final step included the calculation of QSAR predictions related to physicochemical properties, environmental fate, toxicity and Absorption, Distribution, Metabolism, Excretion (ADME) processes and the retrieval of information from the US EPA CompTox Chemicals Dashboard. RESULTS All CECscreen database and property files are publicly available (DOI: https://doi.org/10.5281/zenodo.3956586). In total, 145,284 entries were aggregated from various CECs data sources. After elimination of duplicates and curation, the pipeline produced 70,397 unique "MS-ready" structures and 66,071 unique QSAR-ready structures, corresponding with 69,526 CAS numbers. Simulation of Phase I metabolites resulted in 306,279 unique metabolites. QSAR predictions could be performed for 64,684 of the QSAR-ready structures, whereas information was retrieved from the CompTox Chemicals Dashboard for 59,739 CAS numbers out of 69,526 inquiries. CECscreen is incorporated in the in silico fragmentation approach MetFrag. DISCUSSION The CECscreen database can be used to prioritize annotation of CECs measured in non-targeted HRMS, facilitating the large-scale detection of CECs in human samples for exposome research. Large-scale detection of CECs can be further improved by integrating the present database with resources that contain CECs (metabolites) and meta-data measurements, further expansion towards in silico and experimental (e.g., MassBank) generation of MS/MS spectra, and development of bioinformatics approaches capable of using correlation patterns in the measured chemical features.
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Affiliation(s)
- Jeroen Meijer
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands; Department Environment & Health, Vrije Universiteit, Amsterdam, the Netherlands
| | - Marja Lamoree
- Department Environment & Health, Vrije Universiteit, Amsterdam, the Netherlands
| | - Timo Hamers
- Department Environment & Health, Vrije Universiteit, Amsterdam, the Netherlands
| | | | | | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, Toulouse, France; Metatoul-AXIOM Platform, National Infrastructure for Metabolomics and Fluxomics: MetaboHUB, Toxalim, INRAE, Toulouse, France
| | - Adrian Covaci
- Toxicological Center, University of Antwerp, Belgium
| | - Carolin Huber
- Department Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin Krauss
- Department Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Jelle Vlaanderen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands.
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11
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Hébert V, Bastos S, Drenovska K, Meijer J, Ingen-Housz-Oro S, Bedane C, Lunardon L, Debarbieux S, Jedlickova H, Caux F, Chaby G, D'Incan M, Feliciani C, Boulard C, Schumacher N, Schmidt E, Roussel A, Richard MA, Gottlieb J, Ferranti V, Guérin O, Bénichou J, Joly P. International multicentre observational study to assess the efficacy and safety of a 0·5 mg kg -1 per day starting dose of oral corticosteroids to treat bullous pemphigoid. Br J Dermatol 2021; 185:1232-1239. [PMID: 34173243 DOI: 10.1111/bjd.20593] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND European guidelines propose a 0·5 mg kg-1 per day dose of oral prednisone as initial treatment for bullous pemphigoid (BP). We assessed the safety and efficacy of this regimen depending on BP extent and general condition of the patients. METHODS In a prospective international study, we consecutively included all patients diagnosed with BP. Patients received a 0·5 mg kg-1 per day dose of prednisone, which was then gradually tapered 15 days after disease control, with the aim of stopping prednisone or maintaining minimal treatment (0·1 mg kg-1 per day) within 6 months after the start of treatment. The two coprimary endpoints were control of disease activity at day 21 and 1-year overall survival. Disease severity was assessed according to the Bullous Pemphigoid Disease Area Index (BPDAI) score. RESULTS In total, 198 patients were included between 2015 and 2017. The final analysis comprised 190 patients with a mean age of 80·9 (SD 9·1) years. Control of disease activity was achieved at day 21 in 119 patients [62·6%, 95% confidence interval (CI) 55·3-69.5]; 18 of 24 patients (75%, 95% CI 53·3-90·2), 75 of 110 patients (68·8%, 95% CI 59·2-77·3) and 26 of 56 patients (46.4%, 95% CI 33·0-60·3) had mild, moderate and severe BP, respectively (P = 0·0218). A total of 30 patients died during the study. The overall Kaplan-Meier 1-year survival was 82·6% (95% CI 76·3-87·4) corresponding to 90·9%, 83·0% and 80·0% rates in patients with mild, moderate and severe BP, respectively (P = 0·5). Thresholds of 49 points for BPDAI score and 70 points for Karnofsky score yielded maximal Youden index values with respect to disease control at day 21 and 1-year survival, respectively. CONCLUSIONS A 0·5 mg kg-1 per day dose of prednisone is a valuable therapeutic option in patients with mild or moderate BP whose general condition allows them to be autonomous.
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Affiliation(s)
- V Hébert
- Department of Dermatology, Rouen University Hospital, Center for Autoimmune Bullous Diseases, and INSERM U1234, Normandie University, Rouen, France
| | - S Bastos
- Department of Dermatology, Rouen University Hospital, Center for Autoimmune Bullous Diseases, and INSERM U1234, Normandie University, Rouen, France
| | - K Drenovska
- Department of Dermatology, Medical University of Sofia, Sofia, Bulgaria
| | - J Meijer
- Center for Blistering Diseases, Department of Dermatology, University Medical Center Groningen, Groningen, the Netherlands
| | - S Ingen-Housz-Oro
- Department of Dermatology, Henri Mondor University Hospital, (AP-HP), Creteil, France
| | - C Bedane
- Department of Dermatology, Limoges University Hospital, Limoges, France
| | - L Lunardon
- Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - S Debarbieux
- Department of Dermatology, Hospices Civils de Lyon, Lyon, France
| | - H Jedlickova
- Department of Dermatology, St. Anne's Faculty Hospital, Brno, Czech Republic
| | - F Caux
- Department of Dermatology, Avicenne Hospital, University Paris 13, Bobigny, France
| | - G Chaby
- Department of Dermatology, Amiens University Hospital, Amiens, France
| | - M D'Incan
- Department of Dermatology, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - C Feliciani
- Section of Dermatology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - C Boulard
- Department of Dermatology, Monod General Hospital, le Havre, France
| | - N Schumacher
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - E Schmidt
- Department of Dermatology, University of Lübeck, Lübeck, Germany.,Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - A Roussel
- Department of Dermatology, Orleans Hospital, Orléans, France
| | - M A Richard
- Department of Dermatology, Hôpital la Timone, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - J Gottlieb
- Department of Dermatology, Saint Louis Hospital, (AP-HP), Paris, France
| | - V Ferranti
- Department of Biostatistics, Rouen University Hospital, Rouen, France
| | - O Guérin
- Department of Biostatistics, Rouen University Hospital, Rouen, France
| | - J Bénichou
- Department of Biostatistics, Rouen University Hospital, Rouen, France
| | - P Joly
- Department of Dermatology, Rouen University Hospital, Center for Autoimmune Bullous Diseases, and INSERM U1234, Normandie University, Rouen, France
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12
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Durand A, Baron Y, Redjem W, Herzig T, Benali A, Pezzagna S, Meijer J, Kuznetsov AY, Gérard JM, Robert-Philip I, Abbarchi M, Jacques V, Cassabois G, Dréau A. Broad Diversity of Near-Infrared Single-Photon Emitters in Silicon. Phys Rev Lett 2021; 126:083602. [PMID: 33709758 DOI: 10.1103/physrevlett.126.083602] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/21/2021] [Indexed: 05/28/2023]
Abstract
We report the detection of individual emitters in silicon belonging to seven different families of optically active point defects. These fluorescent centers are created by carbon implantation of a commercial silicon-on-insulator wafer usually employed for integrated photonics. Single photon emission is demonstrated over the 1.1-1.55 μm range, spanning the O and C telecom bands. We analyze their photoluminescence spectra, dipolar emissions, and optical relaxation dynamics at 10 K. For a specific family, we show a constant emission intensity at saturation from 10 K to temperatures well above the 77 K liquid nitrogen temperature. Given the advanced control over nanofabrication and integration in silicon, these individual artificial atoms are promising systems to investigate for Si-based quantum technologies.
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Affiliation(s)
- A Durand
- Laboratoire Charles Coulomb, Université de Montpellier and CNRS, 34095 Montpellier, France
| | - Y Baron
- Laboratoire Charles Coulomb, Université de Montpellier and CNRS, 34095 Montpellier, France
| | - W Redjem
- Laboratoire Charles Coulomb, Université de Montpellier and CNRS, 34095 Montpellier, France
| | - T Herzig
- Division of Applied Quantum Systems, Felix-Bloch Institute for Solid-State Physics, University Leipzig, Linnéestraße 5, 04103 Leipzig, Germany
| | - A Benali
- CNRS, Aix-Marseille Université, Centrale Marseille, IM2NP, UMR 7334, Campus de St. Jérôme, 13397 Marseille, France
| | - S Pezzagna
- Division of Applied Quantum Systems, Felix-Bloch Institute for Solid-State Physics, University Leipzig, Linnéestraße 5, 04103 Leipzig, Germany
| | - J Meijer
- Division of Applied Quantum Systems, Felix-Bloch Institute for Solid-State Physics, University Leipzig, Linnéestraße 5, 04103 Leipzig, Germany
| | - A Yu Kuznetsov
- Department of Physics, University of Oslo, NO-0316 Oslo, Norway
| | - J-M Gérard
- Department of Physics, IRIG-PHELIQS, Univ. Grenoble Alpes and CEA, F-38000 Grenoble, France
| | - I Robert-Philip
- Laboratoire Charles Coulomb, Université de Montpellier and CNRS, 34095 Montpellier, France
| | - M Abbarchi
- CNRS, Aix-Marseille Université, Centrale Marseille, IM2NP, UMR 7334, Campus de St. Jérôme, 13397 Marseille, France
| | - V Jacques
- Laboratoire Charles Coulomb, Université de Montpellier and CNRS, 34095 Montpellier, France
| | - G Cassabois
- Laboratoire Charles Coulomb, Université de Montpellier and CNRS, 34095 Montpellier, France
| | - A Dréau
- Laboratoire Charles Coulomb, Université de Montpellier and CNRS, 34095 Montpellier, France
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13
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Ditalia Tchernij S, Lühmann T, Corte E, Sardi F, Picollo F, Traina P, Brajković M, Crnjac A, Pezzagna S, Pastuović Ž, Degiovanni IP, Moreva E, Aprà P, Olivero P, Siketić Z, Meijer J, Genovese M, Forneris J. Fluorine-based color centers in diamond. Sci Rep 2020; 10:21537. [PMID: 33298995 PMCID: PMC7726554 DOI: 10.1038/s41598-020-78436-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/31/2020] [Accepted: 11/05/2020] [Indexed: 11/22/2022] Open
Abstract
We report on the creation and characterization of the luminescence properties of high-purity diamond substrates upon F ion implantation and subsequent thermal annealing. Their room-temperature photoluminescence emission consists of a weak emission line at 558 nm and of intense bands in the 600–750 nm spectral range. Characterization at liquid He temperature reveals the presence of a structured set of lines in the 600–670 nm spectral range. We discuss the dependence of the emission properties of F-related optical centers on different experimental parameters such as the operating temperature and the excitation wavelength. The correlation of the emission intensity with F implantation fluence, and the exclusive observation of the afore-mentioned spectral features in F-implanted and annealed samples provides a strong indication that the observed emission features are related to a stable F-containing defective complex in the diamond lattice.
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Affiliation(s)
- S Ditalia Tchernij
- Physics Department, University of Torino, 10125, Turin, Italy.,Istituto Nazionale Di Fisica Nucleare (INFN), Sezione Di Torino, 10125, Turin, Italy.,Istituto Nazionale Di Ricerca Metrologica (INRiM), 10135, Turin, Italy
| | - T Lühmann
- Applied Quantum Systems, Felix-Bloch Institute for Solid-State Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - E Corte
- Physics Department, University of Torino, 10125, Turin, Italy.,Istituto Nazionale Di Fisica Nucleare (INFN), Sezione Di Torino, 10125, Turin, Italy
| | - F Sardi
- Physics Department, University of Torino, 10125, Turin, Italy
| | - F Picollo
- Physics Department, University of Torino, 10125, Turin, Italy.,Istituto Nazionale Di Fisica Nucleare (INFN), Sezione Di Torino, 10125, Turin, Italy
| | - P Traina
- Istituto Nazionale Di Ricerca Metrologica (INRiM), 10135, Turin, Italy
| | - M Brajković
- Laboratory for Ion Beam Interactions, Ruđer Bošković Institute, 10000, Zagreb, Croatia
| | - A Crnjac
- Laboratory for Ion Beam Interactions, Ruđer Bošković Institute, 10000, Zagreb, Croatia
| | - S Pezzagna
- Applied Quantum Systems, Felix-Bloch Institute for Solid-State Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Ž Pastuović
- Centre for Accelerator Science, Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW, 2234, Australia
| | - I P Degiovanni
- Istituto Nazionale Di Fisica Nucleare (INFN), Sezione Di Torino, 10125, Turin, Italy.,Istituto Nazionale Di Ricerca Metrologica (INRiM), 10135, Turin, Italy
| | - E Moreva
- Istituto Nazionale Di Ricerca Metrologica (INRiM), 10135, Turin, Italy
| | - P Aprà
- Physics Department, University of Torino, 10125, Turin, Italy.,Istituto Nazionale Di Fisica Nucleare (INFN), Sezione Di Torino, 10125, Turin, Italy
| | - P Olivero
- Physics Department, University of Torino, 10125, Turin, Italy.,Istituto Nazionale Di Fisica Nucleare (INFN), Sezione Di Torino, 10125, Turin, Italy.,Istituto Nazionale Di Ricerca Metrologica (INRiM), 10135, Turin, Italy
| | - Z Siketić
- Laboratory for Ion Beam Interactions, Ruđer Bošković Institute, 10000, Zagreb, Croatia
| | - J Meijer
- Applied Quantum Systems, Felix-Bloch Institute for Solid-State Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - M Genovese
- Istituto Nazionale Di Fisica Nucleare (INFN), Sezione Di Torino, 10125, Turin, Italy.,Istituto Nazionale Di Ricerca Metrologica (INRiM), 10135, Turin, Italy
| | - J Forneris
- Physics Department, University of Torino, 10125, Turin, Italy. .,Istituto Nazionale Di Fisica Nucleare (INFN), Sezione Di Torino, 10125, Turin, Italy. .,Istituto Nazionale Di Ricerca Metrologica (INRiM), 10135, Turin, Italy.
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14
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Botsch L, Raatz N, Pezzagna S, Staacke R, John R, Abel B, Esquinazi PD, Meijer J, Diziain S. Vectorial calibration of superconducting magnets with a quantum magnetic sensor. Rev Sci Instrum 2020; 91:125003. [PMID: 33379962 DOI: 10.1063/5.0023597] [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] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Cryogenic vector magnet systems make it possible to study the anisotropic magnetic properties of materials without mechanically rotating the sample but by electrically tilting and turning the magnetic field. Vector magnetic fields generated inside superconducting vector magnets are generally measured with three Hall sensors. These three probes must be calibrated over a range of temperatures, and the temperature-dependent calibrations cannot be easily carried out inside an already magnetized superconducting magnet because of remaining magnetic fields. A single magnetometer based on an ensemble of nitrogen vacancy (NV) centers in diamond is proposed to overcome these limitations. The quenching of the photoluminescence intensity emitted by NV centers can determine the field in the remanent state of the solenoids and allows an easy and fast canceling of the residual magnetic field. Once the field is reset to zero, the calibration of this magnetometer can be performed in situ by a single measurement of an optically detected magnetic resonance spectrum. Thereby, these magnetometers do not require any additional temperature-dependent calibrations outside the magnet and offer the possibility to measure vector magnetic fields in three dimensions with a single sensor. Its axial alignment is given by the crystal structure of the diamond host, which increases the accuracy of the field orientation measured with this sensor, compared to the classical arrangement of three Hall sensors. It is foreseeable that the magnetometer described here has the potential to be applied in various fields in the future, such as the characterization of ferromagnetic core solenoids or other magnetic arrangements.
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Affiliation(s)
- L Botsch
- Division of Superconductivity and Magnetism, Felix Bloch Institute for Solid State Physics, University of Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
| | - N Raatz
- Division of Applied Quantum Systems, Felix Bloch Institute for Solid State Physics, University of Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
| | - S Pezzagna
- Division of Applied Quantum Systems, Felix Bloch Institute for Solid State Physics, University of Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
| | - R Staacke
- Division of Applied Quantum Systems, Felix Bloch Institute for Solid State Physics, University of Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
| | - R John
- Division of Applied Quantum Systems, Felix Bloch Institute for Solid State Physics, University of Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
| | - B Abel
- Leibniz Institute of Surface Engineering (IOM), Permoserstrasse15, D-04318 Leipzig, Germany
| | - P D Esquinazi
- Division of Superconductivity and Magnetism, Felix Bloch Institute for Solid State Physics, University of Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
| | - J Meijer
- Division of Applied Quantum Systems, Felix Bloch Institute for Solid State Physics, University of Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
| | - S Diziain
- Division of Superconductivity and Magnetism, Felix Bloch Institute for Solid State Physics, University of Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
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15
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Meijer J, van Dijk B, Hogeweg P. Contingent evolution of alternative metabolic network topologies determines whether cross-feeding evolves. Commun Biol 2020; 3:401. [PMID: 32728180 PMCID: PMC7391776 DOI: 10.1038/s42003-020-1107-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 06/19/2020] [Indexed: 12/13/2022] Open
Abstract
Metabolic exchange is widespread in natural microbial communities and an important driver of ecosystem structure and diversity, yet it remains unclear what determines whether microbes evolve division of labor or maintain metabolic autonomy. Here we use a mechanistic model to study how metabolic strategies evolve in a constant, one resource environment, when metabolic networks are allowed to freely evolve. We find that initially identical ancestral communities of digital organisms follow different evolutionary trajectories, as some communities become dominated by a single, autonomous lineage, while others are formed by stably coexisting lineages that cross-feed on essential building blocks. Our results show how without presupposed cellular trade-offs or external drivers such as temporal niches, diverse metabolic strategies spontaneously emerge from the interplay between ecology, spatial structure, and metabolic constraints that arise during the evolution of metabolic networks. Thus, in the long term, whether microbes remain autonomous or evolve metabolic division of labour is an evolutionary contingency.
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Affiliation(s)
- Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
| | - Bram van Dijk
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
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16
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Pourchet M, Debrauwer L, Klanova J, Price EJ, Covaci A, Caballero-Casero N, Oberacher H, Lamoree M, Damont A, Fenaille F, Vlaanderen J, Meijer J, Krauss M, Sarigiannis D, Barouki R, Le Bizec B, Antignac JP. Suspect and non-targeted screening of chemicals of emerging concern for human biomonitoring, environmental health studies and support to risk assessment: From promises to challenges and harmonisation issues. Environ Int 2020; 139:105545. [PMID: 32361063 DOI: 10.1016/j.envint.2020.105545] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [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: 10/14/2019] [Revised: 02/02/2020] [Accepted: 02/02/2020] [Indexed: 05/07/2023]
Abstract
Large-scale suspect and non-targeted screening approaches based on high-resolution mass spectrometry (HRMS) are today available for chemical profiling and holistic characterisation of biological samples. These advanced techniques allow the simultaneous detection of a large number of chemical features, including markers of human chemical exposure. Such markers are of interest for biomonitoring, environmental health studies and support to risk assessment. Furthermore, these screening approaches have the promising capability to detect chemicals of emerging concern (CECs), document the extent of human chemical exposure, generate new research hypotheses and provide early warning support to policy. Whilst of growing importance in the environment and food safety areas, respectively, CECs remain poorly addressed in the field of human biomonitoring. This shortfall is due to several scientific and methodological reasons, including a global lack of harmonisation. In this context, the main aim of this paper is to present an overview of the basic principles, promises and challenges of suspect and non-targeted screening approaches applied to human samples as this specific field introduce major specificities compared to other fields. Focused on liquid chromatography coupled to HRMS-based data acquisition methods, this overview addresses all steps of these new analytical workflows. Beyond this general picture, the main activities carried out on this topic within the particular framework of the European Human Biomonitoring initiative (project HBM4EU, 2017-2021) are described, with an emphasis on harmonisation measures.
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Affiliation(s)
| | - Laurent Debrauwer
- TOXALIM (Research Centre in Food Toxicology), Toulouse University, INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University, 31027 Toulouse, France; Metatoul-AXIOM Platform, National Infrastructure for Metabolomics and Fluxomics: MetaboHUB, Toxalim, INRAE, F-31027 Toulouse, France
| | - Jana Klanova
- RECETOX Centre, Masaryk University, Brno, Czech Republic
| | - Elliott J Price
- RECETOX Centre, Masaryk University, Brno, Czech Republic; Faculty of Sports Studies, Masaryk University, Brno, Czech Republic
| | - Adrian Covaci
- Toxicological Center, University of Antwerp, Belgium
| | | | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Austria
| | - Marja Lamoree
- Vrije Universiteit, Department Environment & Health, Amsterdam, the Netherlands
| | - Annelaure Damont
- Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, Gif-sur-Yvette, France
| | - François Fenaille
- Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, Gif-sur-Yvette, France
| | - Jelle Vlaanderen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Jeroen Meijer
- Vrije Universiteit, Department Environment & Health, Amsterdam, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Martin Krauss
- UFZ, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Denis Sarigiannis
- HERACLES Research Center on the Exposome and Health, Aristotle University of Thessaloniki, Greece
| | - Robert Barouki
- Unité UMR-S 1124 Inserm-Université Paris Descartes "Toxicologie Pharmacologie et Signalisation Cellulaire", Paris, France
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17
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Bastos S, Hebert V, Vassileva S, Patsatsi A, Meijer J, Quéreux G, Bedane C, Prost-Squarcioni C, Debardieux S, Oro S, Chaby G, D’Incan M, Litrowski N, Boulard C, Lunardon L, Kiritsi D, Jedlickova H, Feliciani C, Roussel A, Kottler D, Plantin P, Richard MA, Friedrichsen L, Abasq C, Duvert Lehembre S, Gottlieb J, Zebrowska A, Hofmann S, Joly P. Efficacité et tolérance de la prednisone à 0,5 mg/kg/j en traitement initial de la pemphigoïde bulleuse. Ann Dermatol Venereol 2019. [DOI: 10.1016/j.annder.2019.09.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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van Dijk B, Meijer J, Cuypers TD, Hogeweg P. Trusting the hand that feeds: microbes evolve to anticipate a serial transfer protocol as individuals or collectives. BMC Evol Biol 2019; 19:201. [PMID: 31684861 PMCID: PMC6829849 DOI: 10.1186/s12862-019-1512-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/12/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Experimental evolution of microbes often involves a serial transfer protocol, where microbes are repeatedly diluted by transfer to a fresh medium, starting a new growth cycle. This has revealed that evolution can be remarkably reproducible, where microbes show parallel adaptations both on the level of the phenotype as well as the genotype. However, these studies also reveal a strong potential for divergent evolution, leading to diversity both between and within replicate populations. We here study how in silico evolved Virtual Microbe "wild types" (WTs) adapt to a serial transfer protocol to investigate generic evolutionary adaptations, and how these adaptations can be manifested by a variety of different mechanisms. RESULTS We show that all WTs evolve to anticipate the regularity of the serial transfer protocol by adopting a fine-tuned balance of growth and survival. This anticipation is done by evolving either a high yield mode, or a high growth rate mode. We find that both modes of anticipation can be achieved by individual lineages and by collectives of microbes. Moreover, these different outcomes can be achieved with or without regulation, although the individual-based anticipation without regulation is less well adapted in the high growth rate mode. CONCLUSIONS All our in silico WTs evolve to trust the hand that feeds by evolving to anticipate the periodicity of a serial transfer protocol, but can do so by evolving two distinct growth strategies. Furthermore, both these growth strategies can be accomplished by gene regulation, a variety of different polymorphisms, and combinations thereof. Our work reveals that, even under controlled conditions like those in the lab, it may not be possible to predict individual evolutionary trajectories, but repeated experiments may well result in only a limited number of possible outcomes.
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Affiliation(s)
- Bram van Dijk
- Theoretical Biology, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Jeroen Meijer
- Theoretical Biology, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Thomas D. Cuypers
- Theoretical Biology, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Paulien Hogeweg
- Theoretical Biology, Utrecht University, Padualaan 8, Utrecht, The Netherlands
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19
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Lamberts A, Kotnik N, Diercks G, Meijer J, Di Zenzo G, Pas H, Raap U, Jonkman M, Horvath B. 078 IgE in skin and serum of nonbullous and bullous pemphigoid patients. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.07.081] [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: 11/15/2022]
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20
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Prevot G, Stevens J, Leguay A, Brier T, Meijer J, Aguilaniu B. OPALE accompagnement des patients traités pour une fibrose pulmonaire idiopathique. Rev Mal Respir 2019. [DOI: 10.1016/j.rmr.2018.10.298] [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: 10/27/2022]
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21
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Staal YCM, Meijer J, van der Kris RJC, de Bruijn AC, Boersma AY, Gremmer ER, Zwart EP, Beekhof PK, Slob W, van der Ven LTM. Head skeleton malformations in zebrafish (Danio rerio) to assess adverse effects of mixtures of compounds. Arch Toxicol 2018; 92:3549-3564. [PMID: 30288550 PMCID: PMC6290702 DOI: 10.1007/s00204-018-2320-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/26/2018] [Indexed: 11/22/2022]
Abstract
The EU-EuroMix project adopted the strategy of the European Food Safety Authority (EFSA) for cumulative risk assessment, which limits the number of chemicals to consider in a mixture to those that induce a specific toxicological phenotype. These so-called cumulative assessment groups (CAGs) are refined at several levels, including the target organ and specific phenotype. Here, we explore the zebrafish embryo as a test model for quantitative evaluation in one such CAG, skeletal malformations, through exposure to test compounds 0-120 hpf and alcian blue cartilage staining at 120 hpf, focusing on the head skeleton. Reference compounds cyproconazole, flusilazole, metam, and thiram induced distinctive phenotypes in the head skeleton between the triazoles and dithiocarbamates. Of many evaluated parameters, the Meckel's-palatoquadrate (M-PQ) angle was selected for further assessment, based on the best combination of a small confidence interval, an intermediate maximal effect size and a gentle slope of the dose-response curve with cyproconazole and metam. Additional test compounds included in the CAG skeletal malformations database were tested for M-PQ effects, and this set was supplemented with compounds associated with craniofacial malformations or cleft palate to accommodate otherwise organized databases. This additional set included hexaconazole, all-trans-retinoic acid, AM580, CD3254, maneb, pyrimethanil, imidacloprid, pirimiphos-methyl, 2,4-dinitrophenol, 5-fluorouracil, 17alpha-ethynylestradiol (EE2), ethanol, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), PCB 126, methylmercury, boric acid, and MEHP. Most of these compounds produced a dose-response for M-PQ effects. Application of the assay in mixture testing was provided by combined exposure to cyproconazole and TCDD through the isobole method, supporting that in this case the combined effect can be modeled through concentration addition.
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Affiliation(s)
- Yvonne C. M. Staal
- RIVM: National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, PO Box 1, 3721 MA Bilthoven, The Netherlands
| | - Jeroen Meijer
- RIVM: National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, PO Box 1, 3721 MA Bilthoven, The Netherlands
| | - Remco J. C. van der Kris
- RIVM: National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, PO Box 1, 3721 MA Bilthoven, The Netherlands
| | - Annamaria C. de Bruijn
- RIVM: National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, PO Box 1, 3721 MA Bilthoven, The Netherlands
| | - Anke Y. Boersma
- RIVM: National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, PO Box 1, 3721 MA Bilthoven, The Netherlands
| | - Eric R. Gremmer
- RIVM: National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, PO Box 1, 3721 MA Bilthoven, The Netherlands
| | - Edwin P. Zwart
- RIVM: National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, PO Box 1, 3721 MA Bilthoven, The Netherlands
| | - Piet K. Beekhof
- RIVM: National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, PO Box 1, 3721 MA Bilthoven, The Netherlands
| | - Wout Slob
- RIVM: National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, PO Box 1, 3721 MA Bilthoven, The Netherlands
| | - Leo T. M. van der Ven
- RIVM: National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, PO Box 1, 3721 MA Bilthoven, The Netherlands
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Abd El-Daim IA, Bejai S, Fridborg I, Meijer J. Identifying potential molecular factors involved in Bacillus amyloliquefaciens 5113 mediated abiotic stress tolerance in wheat. Plant Biol (Stuttg) 2018; 20:271-279. [PMID: 29247572 DOI: 10.1111/plb.12680] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 07/09/2017] [Accepted: 12/09/2017] [Indexed: 05/28/2023]
Abstract
Abiotic stressors are main limiting factors for agricultural production around the world. Plant growth-promoting bacteria have been successfully used to improve abiotic stress tolerance in several crops including wheat. However, the molecular changes involved in the improvement of stress management are poorly understood. The present investigation addressed some molecular factors involved in bacterially induced plant abiotic stress responses by identifying differentially expressed genes in wheat (Triticum aestivum) seedlings treated with the beneficial bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5113 prior to challenge with abiotic stress conditions such as heat, cold or drought. cDNA-AFLP analysis revealed differential expression of more than 200 transcript-derived fragments (TDFs) in wheat leaves. Expression of selected TDFs was confirmed using RT-PCR. DNA sequencing of 31 differentially expressed TDFs revealed significant homology with both known and unknown genes in database searches. Virus-induced gene silencing of two abscisic acid-related TDFs showed different effects upon heat and drought stress. We conclude that treatment with B. amyloliquefaciens 5113 caused molecular modifications in wheat in order to induce tolerance against heat, cold and drought stress. Bacillus treatment provides systemic effects that involve metabolic and regulatory functions supporting both growth and stress management.
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Affiliation(s)
- I A Abd El-Daim
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
- Department of Microbiology, Soils, Water and Environment Research Institute, Agricultural Research Centre, Giza, Egypt
| | - S Bejai
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
| | - I Fridborg
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
| | - J Meijer
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
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Krause B, Meyer T, Sieg H, Kästner C, Reichardt P, Tentschert J, Jungnickel H, Estrela-Lopis I, Burel A, Chevance S, Gauffre F, Jalili P, Meijer J, Böhmert L, Braeuning A, Thünemann AF, Emmerling F, Fessard V, Laux P, Lampen A, Luch A. Characterization of aluminum, aluminum oxide and titanium dioxide nanomaterials using a combination of methods for particle surface and size analysis. RSC Adv 2018; 8:14377-14388. [PMID: 35540747 PMCID: PMC9079890 DOI: 10.1039/c8ra00205c] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/22/2018] [Indexed: 12/22/2022] Open
Abstract
The application of appropriate analytical techniques is essential for nanomaterial (NM) characterization. In this study, we compared different analytical techniques for NM analysis. Regarding possible adverse health effects, ionic and particulate NM effects have to be taken into account. As NMs behave quite differently in physiological media, special attention was paid to techniques which are able to determine the biosolubility and complexation behavior of NMs. Representative NMs of similar size were selected: aluminum (Al0) and aluminum oxide (Al2O3), to compare the behavior of metal and metal oxides. In addition, titanium dioxide (TiO2) was investigated. Characterization techniques such as dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA) were evaluated with respect to their suitability for fast characterization of nanoparticle dispersions regarding a particle's hydrodynamic diameter and size distribution. By application of inductively coupled plasma mass spectrometry in the single particle mode (SP-ICP-MS), individual nanoparticles were quantified and characterized regarding their size. SP-ICP-MS measurements were correlated with the information gained using other characterization techniques, i.e. transmission electron microscopy (TEM) and small angle X-ray scattering (SAXS). The particle surface as an important descriptor of NMs was analyzed by X-ray diffraction (XRD). NM impurities and their co-localization with biomolecules were determined by ion beam microscopy (IBM) and confocal Raman microscopy (CRM). We conclude advantages and disadvantages of the different techniques applied and suggest options for their complementation. Thus, this paper may serve as a practical guide to particle characterization techniques. The application of appropriate analytical techniques is essential for nanomaterial (NM) characterization.![]()
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Meijer J, de Lang E, Diercks G, Pas H, Jonkman M. 381 Minimal requirements for diagnosis of cutaneous pemphigoid. Comparative study of direct immunofluorescence, serology and clinical features in 316 patients. J Invest Dermatol 2016. [DOI: 10.1016/j.jid.2016.06.401] [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: 10/21/2022]
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Li S, Zamaratskaia G, Roos S, Båth K, Meijer J, Borch E, Johansson M. Inter-relationships between the metrics of instrumental meat color and microbial growth during aerobic storage of beef at 4°C. ACTA AGR SCAND A-AN 2015. [DOI: 10.1080/09064702.2015.1072579] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Lorite I, Zandalazini C, Esquinazi P, Spemann D, Friedländer S, Pöppl A, Michalsky T, Grundmann M, Vogt J, Meijer J, Heluani SP, Ohldag H, Adeagbo WA, Nayak SK, Hergert W, Ernst A, Hoffmann M. Study of the negative magneto-resistance of single proton-implanted lithium-doped ZnO microwires. J Phys Condens Matter 2015; 27:256002. [PMID: 26043764 DOI: 10.1088/0953-8984/27/25/256002] [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] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The magneto-transport properties of single proton-implanted ZnO and of Li(7%)-doped ZnO microwires have been studied. The as-grown microwires were highly insulating and not magnetic. After proton implantation the Li(7%) doped ZnO microwires showed a non-monotonous behavior of the negative magneto-resistance (MR) at temperature above 150 K. This is in contrast to the monotonous NMR observed below 50 K for proton-implanted ZnO. The observed difference in the transport properties of the wires is related to the amount of stable Zn vacancies created at the near surface region by the proton implantation and Li doping. The magnetic field dependence of the resistance might be explained by the formation of a magnetic/non-magnetic heterostructure in the wire after proton implantation.
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Affiliation(s)
- I Lorite
- Institut für Experimentelle Physik II, University of Leipzig, Linnéstraße 5, D-04103 Leipzig, Germany
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Meijer J, Nakajima Y, Zhang C, Meinsma R, Ito T, Van Kuilenburg ABP. Publisher's note. Identification of a novel synonymous mutation in the human β-ureidopropionase gene UPB1 affecting pre-mRNA splicing. Nucleosides Nucleotides Nucleic Acids 2015; 33:639-45. [PMID: 24940676 DOI: 10.1080/15257770.2014.913907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
β-Ureidopropionase is the third enzyme of the pyrimidine degradation pathway and it catalyzes the conversion of N-carbamyl-β-alanine and N-carbamyl-β-aminoisobutyric acid to β-alanine and β-aminoisobutyric acid, respectively, and ammonia and CO2. To date, only 16 genetically confirmed patients with a complete ß-ureidopropionase deficiency have been reported. Here, we report the clinical, biochemical, and molecular analysis of a newly identified patient with β-ureidopropionase deficiency. Mutation analysis of the UPB1 gene showed that the patient was compound heterozygous for a novel synonymous mutation c.93C>T (p.Gly31Gly) in exon 1 and a previously described missense mutation c.977G>A (p.Arg326Gln) in exon 9. The in silico predicted effect of the synonymous mutation p.Gly31Gly on pre-mRNA splicing was investigated using a minigene approach. Wild-type and the mutated minigene constructs, containing the entire exon 1, intron 1, and exon 2 of UPB1, yielded different splicing products after expression in HEK293 cells. The c.93C>T (p.Gly31Gly) mutation resulted in altered pre-mRNA splicing of the UPB1 minigene construct and a deletion of the last 13 nucleotides of exon 1. This deletion (r.92 104delGCAAGGAACTCAG) results in a frame shift and the generation of a premature stop codon (p.Lys32SerfsX31). Using a minigene approach, we have thus identified the first synonymous mutation in the UPB1 gene, creating a cryptic splice-donor site affecting pre-mRNA splicing.
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Romach Y, Müller C, Unden T, Rogers LJ, Isoda T, Itoh KM, Markham M, Stacey A, Meijer J, Pezzagna S, Naydenov B, McGuinness LP, Bar-Gill N, Jelezko F. Spectroscopy of surface-induced noise using shallow spins in diamond. Phys Rev Lett 2015; 114:017601. [PMID: 25615501 DOI: 10.1103/physrevlett.114.017601] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Indexed: 06/04/2023]
Abstract
We report on the noise spectrum experienced by few nanometer deep nitrogen-vacancy centers in diamond as a function of depth, surface coating, magnetic field and temperature. Analysis reveals a double-Lorentzian noise spectrum consistent with a surface electronic spin bath in the low frequency regime, along with a faster noise source attributed to surface-modified phononic coupling. These results shed new light on the mechanisms responsible for surface noise affecting shallow spins at semiconductor interfaces, and suggests possible directions for further studies. We demonstrate dynamical decoupling from the surface noise, paving the way to applications ranging from nanoscale NMR to quantum networks.
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Affiliation(s)
- Y Romach
- The Racah Institute of Physics, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - C Müller
- Institute for Quantum Optics and Center for Integrated Quantum Science and Technology, University of Ulm, D-89081 Ulm, Germany
| | - T Unden
- Institute for Quantum Optics and Center for Integrated Quantum Science and Technology, University of Ulm, D-89081 Ulm, Germany
| | - L J Rogers
- Institute for Quantum Optics and Center for Integrated Quantum Science and Technology, University of Ulm, D-89081 Ulm, Germany
| | - T Isoda
- School of Fundamental Science and Technology, Keio University, Yokohama 223-8522 Japan
| | - K M Itoh
- School of Fundamental Science and Technology, Keio University, Yokohama 223-8522 Japan
| | - M Markham
- Element Six, Ltd, Kings Ride Park, Ascot SL5 8BP, United Kingdom
| | - A Stacey
- Element Six, Ltd, Kings Ride Park, Ascot SL5 8BP, United Kingdom
| | - J Meijer
- Institute for Experimental Physics II, Linnéstraße 5, University of Leipzig, 04103 Leipzig, Germany
| | - S Pezzagna
- Institute for Experimental Physics II, Linnéstraße 5, University of Leipzig, 04103 Leipzig, Germany
| | - B Naydenov
- Institute for Quantum Optics and Center for Integrated Quantum Science and Technology, University of Ulm, D-89081 Ulm, Germany
| | - L P McGuinness
- Institute for Quantum Optics and Center for Integrated Quantum Science and Technology, University of Ulm, D-89081 Ulm, Germany
| | - N Bar-Gill
- The Racah Institute of Physics, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Department of Applied Physics, Rachel and Selim School of Engineering, Hebrew University, Jerusalem 91904, Israel
| | - F Jelezko
- Institute for Quantum Optics and Center for Integrated Quantum Science and Technology, University of Ulm, D-89081 Ulm, Germany
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Affiliation(s)
| | - T. Rosskopf
- Department of Physics, ETH Zurich, Otto Stern Weg 1, 8093 Zurich, Switzerland
| | - J. M. Boss
- Department of Physics, ETH Zurich, Otto Stern Weg 1, 8093 Zurich, Switzerland
| | - S. Pezzagna
- Institute for Experimental Physics II, Department of Nuclear Solid State Physics, Universität Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
| | - J. Meijer
- Institute for Experimental Physics II, Department of Nuclear Solid State Physics, Universität Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
| | - C. L. Degen
- Department of Physics, ETH Zurich, Otto Stern Weg 1, 8093 Zurich, Switzerland
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Abstract
Extending magnetic resonance imaging to the atomic scale has been a long-standing aspiration, driven by the prospect of directly mapping atomic positions in molecules with three-dimensional spatial resolution. We report detection of individual, isolated proton spins by a nitrogen-vacancy (NV) center in a diamond chip covered by an inorganic salt. The single-proton identity was confirmed by the Zeeman effect and by a quantum coherent rotation of the weakly coupled nuclear spin. Using the hyperfine field of the NV center as an imaging gradient, we determined proton-NV distances of less than 1 nm.
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Affiliation(s)
- M Loretz
- Department of Physics, ETH Zurich, Otto Stern Weg 1, 8093 Zurich, Switzerland
| | - T Rosskopf
- Department of Physics, ETH Zurich, Otto Stern Weg 1, 8093 Zurich, Switzerland
| | - J M Boss
- Department of Physics, ETH Zurich, Otto Stern Weg 1, 8093 Zurich, Switzerland
| | - S Pezzagna
- Institute for Experimental Physics II, Department of Nuclear Solid State Physics, Universität Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
| | - J Meijer
- Institute for Experimental Physics II, Department of Nuclear Solid State Physics, Universität Leipzig, Linnéstrasse 5, D-04103 Leipzig, Germany
| | - C L Degen
- Department of Physics, ETH Zurich, Otto Stern Weg 1, 8093 Zurich, Switzerland.
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Hiltermann T, Pore M, Meijer J, Timens W, De Bock G, Groen H, Kruijt F. Overall Survival in Small Cell Lung Cancer Detected with Epithelial, Mesenchymal and Stem Cell Biomarkers. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu355.6] [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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Müller C, Kong X, Cai JM, Melentijević K, Stacey A, Markham M, Twitchen D, Isoya J, Pezzagna S, Meijer J, Du JF, Plenio MB, Naydenov B, McGuinness LP, Jelezko F. Nuclear magnetic resonance spectroscopy with single spin sensitivity. Nat Commun 2014; 5:4703. [PMID: 25146503 PMCID: PMC4143926 DOI: 10.1038/ncomms5703] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [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: 01/22/2014] [Accepted: 07/15/2014] [Indexed: 12/17/2022] Open
Abstract
Nuclear magnetic resonance spectroscopy and magnetic resonance imaging at the ultimate sensitivity limit of single molecules or single nuclear spins requires fundamentally new detection strategies. The strong coupling regime, when interaction between sensor and sample spins dominates all other interactions, is one such strategy. In this regime, classically forbidden detection of completely unpolarized nuclei is allowed, going beyond statistical fluctuations in magnetization. Here we realize strong coupling between an atomic (nitrogen-vacancy) sensor and sample nuclei to perform nuclear magnetic resonance on four (29)Si spins. We exploit the field gradient created by the diamond atomic sensor, in concert with compressed sensing, to realize imaging protocols, enabling individual nuclei to be located with Angstrom precision. The achieved signal-to-noise ratio under ambient conditions allows single nuclear spin sensitivity to be achieved within seconds.
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Affiliation(s)
- C Müller
- 1] Institute for Quantum Optics, Albert-Einstein Allee 11, University of Ulm, Ulm D-89081, Germany [2] Center for Integrated Quantum Science and Technology, University of Ulm, Ulm D-89081 Germany [3]
| | - X Kong
- 1] Institute for Quantum Optics, Albert-Einstein Allee 11, University of Ulm, Ulm D-89081, Germany [2] Department of Modern Physics, Hefei National Laboratory for Physics Sciences at Microscale, University of Science and Technology of China, Hefei 230026, China [3] Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China [4]
| | - J-M Cai
- 1] Center for Integrated Quantum Science and Technology, University of Ulm, Ulm D-89081 Germany [2] Institute for Theoretical Physics, Albert-Einstein Allee 11, University of Ulm, Ulm D-89081, Germany
| | - K Melentijević
- 1] Institute for Quantum Optics, Albert-Einstein Allee 11, University of Ulm, Ulm D-89081, Germany [2] Center for Integrated Quantum Science and Technology, University of Ulm, Ulm D-89081 Germany
| | - A Stacey
- Element Six, Ltd., Ascot, Berkshire SL5 8BP, UK
| | - M Markham
- Element Six, Ltd., Ascot, Berkshire SL5 8BP, UK
| | - D Twitchen
- Element Six, Ltd., Ascot, Berkshire SL5 8BP, UK
| | - J Isoya
- Research Center for Knowledge Communities, University of Tsukuba, 1-2 Kasuga, Tsukuba, Ibaraki 305-8550, Japan
| | - S Pezzagna
- Experimental Physics II, University Leipzig, Linnéstr. 5, 03401 Leipzig, Germany
| | - J Meijer
- Experimental Physics II, University Leipzig, Linnéstr. 5, 03401 Leipzig, Germany
| | - J F Du
- 1] Department of Modern Physics, Hefei National Laboratory for Physics Sciences at Microscale, University of Science and Technology of China, Hefei 230026, China [2] Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - M B Plenio
- 1] Center for Integrated Quantum Science and Technology, University of Ulm, Ulm D-89081 Germany [2] Institute for Theoretical Physics, Albert-Einstein Allee 11, University of Ulm, Ulm D-89081, Germany
| | - B Naydenov
- 1] Institute for Quantum Optics, Albert-Einstein Allee 11, University of Ulm, Ulm D-89081, Germany [2] Center for Integrated Quantum Science and Technology, University of Ulm, Ulm D-89081 Germany
| | - L P McGuinness
- 1] Institute for Quantum Optics, Albert-Einstein Allee 11, University of Ulm, Ulm D-89081, Germany [2] Center for Integrated Quantum Science and Technology, University of Ulm, Ulm D-89081 Germany
| | - F Jelezko
- 1] Institute for Quantum Optics, Albert-Einstein Allee 11, University of Ulm, Ulm D-89081, Germany [2] Center for Integrated Quantum Science and Technology, University of Ulm, Ulm D-89081 Germany
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van Wanrooij RLJ, Müller DMJ, Neefjes-Borst EA, Meijer J, Koudstaal LG, Heideman DAM, Bontkes HJ, von Blomberg BME, Bouma G, Mulder CJJ. Optimal strategies to identify aberrant intra-epithelial lymphocytes in refractory coeliac disease. J Clin Immunol 2014; 34:828-35. [PMID: 25062848 DOI: 10.1007/s10875-014-0075-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 07/02/2014] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Different strategies have been developed to identify those refractory celiac disease (RCD) patients who are at risk to develop an enteropathy associated T-cell lymphoma (EATL). Flow cytometric analysis of intra-epithelial lymphocytes (IEL) with an aberrant phenotype is considered the golden standard but is not widely available. Immunohistochemistry (IHC) and T-cell receptor (TCR) rearrangement studies are commonly available but may lack sensitivity and specificity. Here, we compared the three different methods in the workup of patients suspected for RCD. METHODS Duodenal biopsies from control patient (n = 5), RCD patients with moderately increased aberrant IEL populations (20-50 %: n = 14), and RCD patients with high numbers of aberrant IEL (>50 %: n = 5) as determined by flow cytometry were analysed by IHC and TCR-γ chain rearrangement analysis. Three pathologists scored the slides independently. RESULTS Sensitivity of IHC and TCR-γ rearrangement analysis in RCD patients with high numbers of aberrant IELs was 100 and 71 %, respectively. RCD patients with aberrant cells between 25 and 50 % however, were missed by IHC and TCR in 50 and 57 % of cases, respectively. In addition, inter-rater reliability analysis of the IHC scoring revealed coder-pair Kappa coefficients between 0.28 and 0.85. CONCLUSION Immunohistochemistry and to a lesser extent TCR-γ clonality analysis are sensitive in identifying patients with high numbers of aberrant IEL populations, yet miss half of RCD patients with moderately increased numbers. In addition, IHC has a high inter-observer variability. Therefore, patients suspected for RCD should undergo flow cytometric analysis of the duodenum.
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Affiliation(s)
- R L J van Wanrooij
- Department of Gastroenterology and Hepatology, VU University Medical Center, PO Box 7057, 1007 MB, Amsterdam, The Netherlands,
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Meijer J, Nakajima Y, Zhang C, Meinsma R, Ito T, Van Kuilenburg ABP. Identification of a novel synonymous mutation in the human β -Ureidopropionase Gene UPB1 affecting pre-mRNA splicing. Nucleosides Nucleotides Nucleic Acids 2014; 32:639-45. [PMID: 24328561 DOI: 10.1080/15257770.2013.847189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
β-Ureidopropionase is the third enzyme of the pyrimidine degradation pathway and it catalyzes the conversion of N-carbamyl-β-alanine and N-carbamyl-β-aminoisobutyric acid to β-alanine and β-aminoisobutyric acid, respectively, and ammonia and CO2. To date, only 16 genetically confirmed patients with a complete ß-ureidopropionase deficiency have been reported. Here, we report the clinical, biochemical, and molecular analysis of a newly identified patient with β-ureidopropionase deficiency. Mutation analysis of the UPB1 gene showed that the patient was compound heterozygous for a novel synonymous mutation c.93C >T (p.Gly31Gly) in exon 1 and a previously described missense mutation c.977G >A (p.Arg326Gln) in exon 9. The in silico predicted effect of the synonymous mutation p.Gly31Gly on pre-mRNA splicing was investigated using a minigene approach. Wild-type and the mutated minigene constructs, containing the entire exon 1, intron 1, and exon 2 of UPB1, yielded different splicing products after expression in HEK293 cells. The c.93C >T (p.Gly31Gly) mutation resulted in altered pre-mRNA splicing of the UPB1 minigene construct and a deletion of the last 13 nucleotides of exon 1. This deletion (r.92_104delGCAAGGAACTCAG) results in a frame shift and the generation of a premature stop codon (p.Lys32SerfsX31). Using a minigene approach, we have thus identified the first synonymous mutation in the UPB1 gene, creating a cryptic splice-donor site affecting pre-mRNA splicing.
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Affiliation(s)
- J Meijer
- a Laboratory of Genetic Metabolic Diseases , Academic Medical Center , Amsterdam , The Netherlands
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van de Schans SAM, Strobbe L, van der Holst IM, Meijer J, Mattijssen V, de Kievit IM, Mandigers C, Raemaekers J, Aben KKH, van Krieken JH. Diagnosing and classifying malignant lymphomas is improved by referring cases to a panel of expert pathologists. J Hematop 2013. [DOI: 10.1007/s12308-013-0196-6] [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: 11/30/2022] Open
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Gross E, Meul C, Raab S, Propping C, Avril S, Aubele M, Gkazepis A, Schuster T, Grebenchtchikov N, Schmitt M, Kiechle M, Meijer J, Vijzelaar R, Meindl A, van Kuilenburg ABP. Somatic copy number changes in DPYD are associated with lower risk of recurrence in triple-negative breast cancers. Br J Cancer 2013; 109:2347-55. [PMID: 24104963 PMCID: PMC3817342 DOI: 10.1038/bjc.2013.621] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 05/16/2013] [Revised: 09/06/2013] [Accepted: 09/15/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Genomic rearrangements at the fragile site FRA1E may disrupt the dihydropyrimidine dehydrogenase gene (DPYD) which is involved in 5-fluorouracil (5-FU) catabolism. In triple-negative breast cancer (TNBC), a subtype of breast cancer frequently deficient in DNA repair, we have investigated the susceptibility to acquire copy number variations (CNVs) in DPYD and evaluated their impact on standard adjuvant treatment. METHODS DPYD CNVs were analysed in 106 TNBC tumour specimens using multiplex ligation-dependent probe amplification (MLPA) analysis. Dihydropyrimidine dehydrogenase (DPD) expression was determined by immunohistochemistry in 146 tumour tissues. RESULTS In TNBC, we detected 43 (41%) tumour specimens with genomic deletions and/or duplications within DPYD which were associated with higher histological grade (P=0.006) and with rearrangements in the DNA repair gene BRCA1 (P=0.007). Immunohistochemical analysis revealed low, moderate and high DPD expression in 64%, 29% and 7% of all TNBCs, and in 40%, 53% and 7% of TNBCs with DPYD CNVs, respectively. Irrespective of DPD protein levels, the presence of CNVs was significantly related to longer time to progression in patients who had received 5-FU- and/or anthracycline-based polychemotherapy (hazard ratio=0.26 (95% CI: 0.07-0.91), log-rank P=0.023; adjusted for tumour stage: P=0.037). CONCLUSION Genomic rearrangements in DPYD, rather than aberrant DPD protein levels, reflect a distinct tumour profile associated with prolonged time to progression upon first-line chemotherapy in TNBC.
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Affiliation(s)
- E Gross
- Department of Gynecology and Obstetrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
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Staudacher T, Shi F, Pezzagna S, Meijer J, Du J, Meriles CA, Reinhard F, Wrachtrup J. Nuclear magnetic resonance spectroscopy on a (5-nanometer)3 sample volume. Science 2013; 339:561-3. [PMID: 23372009 DOI: 10.1126/science.1231675] [Citation(s) in RCA: 261] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Application of nuclear magnetic resonance (NMR) spectroscopy to nanoscale samples has remained an elusive goal, achieved only with great experimental effort at subkelvin temperatures. We demonstrated detection of NMR signals from a (5-nanometer)(3) voxel of various fluid and solid organic samples under ambient conditions. We used an atomic-size magnetic field sensor, a single nitrogen-vacancy defect center, embedded ~7 nanometers under the surface of a bulk diamond to record NMR spectra of various samples placed on the diamond surface. Its detection volume consisted of only 10(4) nuclear spins with a net magnetization of only 10(2) statistically polarized spins.
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Affiliation(s)
- T Staudacher
- 3rd Physics Institute and Research Center SCoPE, University of Stuttgart, 70569 Stuttgart, Germany
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Dekker N, Meijer J, Koeter M, van den Brink W, van Beveren N, Kahn RS, Linszen DH, van Os J, Wiersma D, Bruggeman R, Cahn W, de Haan L, Krabbendam L, Myin-Germeys I. Age at onset of non-affective psychosis in relation to cannabis use, other drug use and gender. Psychol Med 2012; 42:1903-1911. [PMID: 22452790 DOI: 10.1017/s0033291712000062] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [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: 11/05/2022]
Abstract
BACKGROUND Cannabis use is associated with an earlier age at onset of psychotic illness. The aim of the present study was to examine whether this association is confounded by gender or other substance use in a large cohort of patients with a non-affective psychotic disorder. METHOD In 785 patients with a non-affective psychotic disorder, regression analysis was used to investigate the independent effects of gender, cannabis use and other drug use on age at onset of first psychosis. RESULTS Age at onset was 1.8 years earlier in cannabis users compared to non-users, controlling for gender and other possible confounders. Use of other drugs did not have an additional effect on age at onset when cannabis use was taken into account. In 63.5% of cannabis-using patients, age at most intense cannabis use preceded the age at onset of first psychosis. In males, the mean age at onset was 1.3 years lower than in females, controlling for cannabis use and other confounders. CONCLUSIONS Cannabis use and gender are independently associated with an earlier onset of psychotic illness. Our findings also suggest that cannabis use may precipitate psychosis. More research is needed to clarify the neurobiological factors that make people vulnerable to this precipitating effect of cannabis.
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Affiliation(s)
- N Dekker
- Department of Psychiatry, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
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Kolesov R, Xia K, Reuter R, Stöhr R, Zappe A, Meijer J, Hemmer PR, Wrachtrup J. Optical detection of a single rare-earth ion in a crystal. Nat Commun 2012; 3:1029. [PMID: 22929786 PMCID: PMC3432461 DOI: 10.1038/ncomms2034] [Citation(s) in RCA: 188] [Impact Index Per Article: 15.7] [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: 05/11/2012] [Accepted: 07/30/2012] [Indexed: 11/17/2022] Open
Abstract
Rare-earth-doped laser materials show strong prospects for quantum information storage and processing, as well as for biological imaging, due to their high-Q 4f↔4f optical transitions. However, the inability to optically detect single rare-earth dopants has prevented these materials from reaching their full potential. Here we detect a single photostable Pr(3+) ion in yttrium aluminium garnet nanocrystals with high contrast photon antibunching by using optical upconversion of the excited state population of the 4f↔4f optical transition into ultraviolet fluorescence. We also demonstrate on-demand creation of Pr(3+) ions in a bulk yttrium aluminium garnet crystal by patterned ion implantation. Finally, we show generation of local nanophotonic structures and cell death due to photochemical effects caused by upconverted ultraviolet fluorescence of praseodymium-doped yttrium aluminium garnet in the surrounding environment. Our study demonstrates versatile use of rare-earth atomic-size ultraviolet emitters for nanoengineering and biotechnological applications.
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Affiliation(s)
- R Kolesov
- 3. Physikalisches Institut, Universität Stuttgart and Stuttgart Research Center of Photonic Engineering (SCoPE), Pfaffenwaldring 57, D-70569 Stuttgart, Germany.
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Meijer J, Simons CJP, Quee PJ, Verweij K. Cognitive alterations in patients with non-affective psychotic disorder and their unaffected siblings and parents. Acta Psychiatr Scand 2012; 125:66-76. [PMID: 22013907 DOI: 10.1111/j.1600-0447.2011.01777.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The purpose of this study was to examine a range of cognitive measures as candidate phenotypic liability markers for psychosis in a uniquely large sample of patients with psychosis, their unaffected relatives and control subjects. METHOD Patients with non-affective psychosis (n = 1093), their unaffected siblings (n = 1044), parents (n = 911), and controls (n = 587) completed a comprehensive cognitive test battery. Cognitive functioning was compared using tests of verbal learning and memory, attention/vigilance, working memory, processing speed, reasoning and problem solving, acquired knowledge, and social cognition. Age- and gender-adjusted z-scores were compared between groups using mixed-model analyses of covariance. Clinically relevant impairment (-1 and -2 SD from control mean) was compared between subject groups. RESULTS Patients performed significantly worse than controls in all cognitive domains (z-range -0.26 to -1.34). Siblings and parents showed alterations for immediate verbal learning, processing speed, reasoning and problem solving, acquired knowledge, and working memory (z-range -0.22 to -0.98). Parents showed additional alterations for social cognition. Prevalence of clinically relevant impairment in relatives ranged from 50% (-1 SD criterion) to 10% (-2 SD criterion). CONCLUSION Cognitive functioning is a candidate intermediate phenotype given significant small to large alterations in patients and intermediate alterations in first-degree relatives.
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Affiliation(s)
- J Meijer
- Department of Psychiatry, Academic Medical Centre University of Amsterdam, The Netherlands
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Bongers K, von Rosenstiel I, Schats W, Meijer J. Language as key in the implementation of Integrative Medicine. Eur J Integr Med 2010. [DOI: 10.1016/j.eujim.2010.09.191] [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: 10/18/2022]
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Meijer J. Accelerate change in healthcare by focusing on primary care and connecting Integrative Medicine with sustainability. Eur J Integr Med 2010. [DOI: 10.1016/j.eujim.2010.09.061] [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: 11/24/2022]
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von Rosenstiel I, Bongers K, Schats W, Rutten G, Meijer J. Building national bridges in the Dutch Integrative Medicine field. Eur J Integr Med 2010. [DOI: 10.1016/j.eujim.2010.09.127] [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: 11/25/2022]
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Schats W, von Rosenstiel I, Bongers K, Meijer J. Teamwork in evidence-based integrative medicine: Doctors and librarians. Eur J Integr Med 2010. [DOI: 10.1016/j.eujim.2010.09.106] [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: 10/18/2022]
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van Kuilenburg ABP, Zoetekouw L, Meijer J, Kuijpers TW. Identification of purine nucleoside phosphorylase deficiency in dried blood spots by a non-radiochemical assay using reversed-phase high-performance liquid chromatography. Nucleosides Nucleotides Nucleic Acids 2010; 29:466-70. [PMID: 20544539 DOI: 10.1080/15257771003741455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Purine nucleoside phosphorylase (PNP) deficiency results in severe T cell dysfunction and hypouricemia. An assay to measure PNP activity in dried blood spots was developed using reversed-phase HPLC. The assay was linear with reaction times between 5 and 12.5 minutes, and protein concentrations ranging from 0.4 to 1.8 mg/ml. The intra-assay CV and the inter-assay CV for the complete assay was <3.6%. The PNP activity in a control blood spot, stored at 4 degrees C, remained stable for at least one year. In a patient suffering from a PNP deficiency, the residual PNP activity was only 0.3% compared to that observed in controls (1431 +/- 238 nmol/mg/h, n = 114). The PNP activity (483 +/- 35 nmol/mg/h, n = 3) in heterozygotes for the c.614A > C mutation (p.E205A) in the PNP gene was 34% compared to controls. Thus, the analysis of the PNP activity in blood spots can readily detect patients with a PNP deficiency.
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Affiliation(s)
- A B P van Kuilenburg
- Academic Medical Center, Emma Children's Hospital, Laboratory Genetic Metabolic Diseases, Amsterdam, the Netherlands.
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van Kuilenburg ABP, Zoetekouw L, Meijer J, Kuijpers TW. Determination of adenosine deaminase activity in dried blood spots by a nonradiochemical assay using reversed-phase high-performance liquid chromatography. Nucleosides Nucleotides Nucleic Acids 2010; 29:461-5. [PMID: 20544538 DOI: 10.1080/15257771003741406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Adenosine deaminase (ADA) deficiency is a rare metabolic disease causing severe combined immunodeficiency (SCID). An assay to determine ADA activity in dried blood spots was developed using reversed-phase HPLC. The assay was linear with reaction times up to at least 4 hours, and protein concentrations up to at least 2.2 mg/ml. The intra-assay CV and the inter-assay CV for the complete assay was 3.5 and 8.4%, respectively. The ADA activity in a control blood spot, stored at 4 degrees C, remained stable for at least one year. Only a slightly decreased ADA activity (35 +/- 13 nmol/mg/h, n = 4) was observed in heterozygotes for a c.704G > A mutation in the ADA gene when compared to that observed in controls (41 +/- 13 nmol/mg/h, n = 108). In addition, increased ADA activity as found in a rare form of congenital anemia can be assessed, as observed in a bloodspot from a patient diagnosed with Diamond Blackfan anemia (ADA activity 150 nmol/mg/h).
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Affiliation(s)
- A B P van Kuilenburg
- Academic Medical Center, Emma Children's Hospital, Laboratory Genetic Metabolic Diseases, Amsterdam, the Netherlands.
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van Kuilenburg ABP, Meijer J, Gökcay G, Baykal T, Rubio-Gozalbo ME, Mul ANPM, de Die-Smulders CEM, Weber P, Mori AC, Bierau J, Fowler B, Macke K, Sass JO, Meinsma R, Hennermann JB, Miny P, Zoetekouw L, Roelofsen J, Vijzelaar R, Nicolai J, Hennekam RCM. Dihydropyrimidine dehydrogenase deficiency caused by a novel genomic deletion c.505_513del of DPYD. Nucleosides Nucleotides Nucleic Acids 2010; 29:509-14. [PMID: 20544545 DOI: 10.1080/15257771003730227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Dihydropyrimidine dehydrogenase (DPD) deficiency is an autosomal recessive disorder of the pyrimidine degradation pathway. In a patient presenting with convulsions, psychomotor retardation and Reye like syndrome, strongly elevated levels of uracil and thymine were detected in urine. No DPD activity could be detected in peripheral blood mononuclear cells. Analysis of the gene encoding DPD (DPYD) showed that the patient was homozygous for a novel c.505_513del (p.169_171del) mutation in exon 6 of DPYD.
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Meijer J, Vermeer P. A convenient synthesis of 1- alkynes from methoxyallene and Grignard reagents in the presence of copper(I) halides. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19740930702] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Verboom W, Schoufs M, Meijer J, Verkruijsse HD, Brandsma L. Convenient methods for the preparation of di(1-alkynyl) sulfides, sulfoxides and sulfones, and application of the sulfoxides and sulfones in the formation of novel heterocyclic systems. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19780970907] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Oostveen EA, Elsevier CJ, Meijer J, Vermeer P. The regiochemistry of organocopper-induced substitution of 2,4-pentadiynyl methanesulfinates. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19821011102] [Citation(s) in RCA: 2] [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: 11/06/2022]
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