1
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Rauch E, Amendt T, Lopez Krol A, Lang FB, Linse V, Hohmann M, Keim AC, Kreutzer S, Kawengian K, Buchholz M, Duschner P, Grauer S, Schnierle B, Ruhl A, Burtscher I, Dehnert S, Kuria C, Kupke A, Paul S, Liehr T, Lechner M, Schnare M, Kaufmann A, Huber M, Winkler TH, Bauer S, Yu P. T-bet + B cells are activated by and control endogenous retroviruses through TLR-dependent mechanisms. Nat Commun 2024; 15:1229. [PMID: 38336876 PMCID: PMC10858178 DOI: 10.1038/s41467-024-45201-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
Endogenous retroviruses (ERVs) are an integral part of the mammalian genome. The role of immune control of ERVs in general is poorly defined as is their function as anti-cancer immune targets or drivers of autoimmune disease. Here, we generate mouse-strains where Moloney-Murine Leukemia Virus tagged with GFP (ERV-GFP) infected the mouse germline. This enables us to analyze the role of genetic, epigenetic and cell intrinsic restriction factors in ERV activation and control. We identify an autoreactive B cell response against the neo-self/ERV antigen GFP as a key mechanism of ERV control. Hallmarks of this response are spontaneous ERV-GFP+ germinal center formation, elevated serum IFN-γ levels and a dependency on Age-associated B cells (ABCs) a subclass of T-bet+ memory B cells. Impairment of IgM B cell receptor-signal in nucleic-acid sensing TLR-deficient mice contributes to defective ERV control. Although ERVs are a part of the genome they break immune tolerance, induce immune surveillance against ERV-derived self-antigens and shape the host immune response.
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Affiliation(s)
- Eileen Rauch
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
- CSL Behring Innovation GmbH, Emil-von-Behring-Str. 76, 35041, Marburg, Germany
| | - Timm Amendt
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
- The Francis Crick Institute, NW1 1AT, London, UK
| | | | - Fabian B Lang
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Vincent Linse
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Michelle Hohmann
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
- Apollo Ventures Holding GmbH, 20457, Hamburg, Germany
| | - Ann-Christin Keim
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Susanne Kreutzer
- Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Kevin Kawengian
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Malte Buchholz
- Department of Gastroenterology, Endocrinology and Metabolism, and Core Facility Small Animal Multispectral and Ultrasound Imaging, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Philipp Duschner
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Saskia Grauer
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Barbara Schnierle
- Department of Virology, Paul-Ehrlich-Institut, 63225, Langen, Germany
| | - Andreas Ruhl
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
- Department of Infection Biology, University Hospital Erlangen, 91054, Erlangen, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Sonja Dehnert
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Chege Kuria
- Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Alexandra Kupke
- Institute of Virology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Stephanie Paul
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, 07747, Jena, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Markus Schnare
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Andreas Kaufmann
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Magdalena Huber
- Institute of Sytems Immunology, Center for Tumor and Immunobiology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Thomas H Winkler
- Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Stefan Bauer
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Philipp Yu
- Institute of Immunology, Philipps-Universität Marburg, 35043, Marburg, Germany.
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2
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Moradi S, Guenther S, Soori S, Sharifi-Zarchi A, Kuenne C, Khoddami V, Tavakol P, Kreutzer S, Braun T, Baharvand H. Time-resolved Small-RNA Sequencing Identifies MicroRNAs Critical for Formation of Embryonic Stem Cells from the Inner Cell Mass of Mouse Embryos. Stem Cell Rev Rep 2023; 19:2361-2377. [PMID: 37402099 DOI: 10.1007/s12015-023-10582-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
Cells of the inner cell mass (ICM) acquire a unique ability for unlimited self-renewal during transition into embryonic stem cells (ESCs) in vitro, while preserving their natural multi-lineage differentiation potential. Several different pathways have been identified to play roles in ESC formation but the function of non-coding RNAs in this process is poorly understood. Here, we describe several microRNAs (miRNAs) that are crucial for efficient generation of mouse ESCs from ICMs. Using small-RNA sequencing, we characterize dynamic changes in miRNA expression profiles during outgrowth of ICMs in a high-resolution, time-course dependent manner. We report several waves of miRNA transcription during ESC formation, to which miRNAs from the imprinted Dlk1-Dio3 locus contribute extensively. In silico analyses followed by functional investigations reveal that Dlk1-Dio3 locus-embedded miRNAs (miR-541-5p, miR-410-3p, and miR-381-3p), miR-183-5p, and miR-302b-3p promote, while miR-212-5p and let-7d-3p inhibit ESC formation. Collectively, these findings offer new mechanistic insights into the role of miRNAs during ESC derivation.
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Affiliation(s)
- Sharif Moradi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Stefan Guenther
- Department of Cardiac Development and Remodelling, Max-Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231, Bad Nauheim, Germany
| | - Samira Soori
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ali Sharifi-Zarchi
- Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Carsten Kuenne
- Department of Cardiac Development and Remodelling, Max-Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231, Bad Nauheim, Germany
| | - Vahid Khoddami
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Pouya Tavakol
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Susanne Kreutzer
- Department of Cardiac Development and Remodelling, Max-Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231, Bad Nauheim, Germany
| | - Thomas Braun
- Department of Cardiac Development and Remodelling, Max-Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231, Bad Nauheim, Germany.
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran.
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3
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Hiltbrunner S, Cords L, Kasser S, Freiberger SN, Kreutzer S, Toussaint NC, Grob L, Opitz I, Messerli M, Zoche M, Soltermann A, Rechsteiner M, van den Broek M, Bodenmiller B, Curioni-Fontecedro A. Acquired resistance to anti-PD1 therapy in patients with NSCLC associates with immunosuppressive T cell phenotype. Nat Commun 2023; 14:5154. [PMID: 37620318 PMCID: PMC10449840 DOI: 10.1038/s41467-023-40745-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Immune checkpoint inhibitor treatment has the potential to prolong survival in non-small cell lung cancer (NSCLC), however, some of the patients develop resistance following initial response. Here, we analyze the immune phenotype of matching tumor samples from a cohort of NSCLC patients showing good initial response to immune checkpoint inhibitors, followed by acquired resistance at later time points. By using imaging mass cytometry and whole exome and RNA sequencing, we detect two patterns of resistance¨: One group of patients is characterized by reduced numbers of tumor-infiltrating CD8+ T cells and reduced expression of PD-L1 after development of resistance, whereas the other group shows high CD8+ T cell infiltration and high expression of PD-L1 in addition to markedly elevated expression of other immune-inhibitory molecules. In two cases, we detect downregulation of type I and II IFN pathways following progression to resistance, which could lead to an impaired anti-tumor immune response. This study thus captures the development of immune checkpoint inhibitor resistance as it progresses and deepens our mechanistic understanding of immunotherapy response in NSCLC.
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Affiliation(s)
- Stefanie Hiltbrunner
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, 8091, Switzerland
- Comprehensive Cancer Center Zurich, University Hospital Zurich, Zurich, 8091, Switzerland
- University of Zurich, Zurich, Switzerland
- University of Fribourg, Faculty of Science and Medicine, Fribourg, 1700, Switzerland
| | - Lena Cords
- University of Zurich, Zurich, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, 8049, Switzerland
- Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Sabrina Kasser
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, 8091, Switzerland
- University of Zurich, Zurich, Switzerland
| | - Sandra N Freiberger
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Center Zurich, ETH and University of Zurich, Zurich, 8057, Switzerland
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich, 8952, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Linda Grob
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich, 8952, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Isabelle Opitz
- Department of Thoracic Surgery, University Hospital Zurich, Zurich, 8091, Switzerland
| | - Michael Messerli
- University of Zurich, Zurich, Switzerland
- Department of Nuclear Medicine, University Hospital Zurich, Zurich, 8091, Switzerland
| | - Martin Zoche
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Alex Soltermann
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Zurich, Switzerland
- Pathologie Länggasse, Ittigen, 3063, Switzerland
| | - Markus Rechsteiner
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Maries van den Broek
- University of Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, 8057, Switzerland
| | - Bernd Bodenmiller
- University of Zurich, Zurich, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, 8049, Switzerland
| | - Alessandra Curioni-Fontecedro
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, 8091, Switzerland.
- Comprehensive Cancer Center Zurich, University Hospital Zurich, Zurich, 8091, Switzerland.
- University of Zurich, Zurich, Switzerland.
- University of Fribourg, Faculty of Science and Medicine, Fribourg, 1700, Switzerland.
- Clinic of Oncology, Cantonal Hospital Fribourg, Fribourg, 1752, Switzerland.
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4
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Silva NM, Kreutzer S, Souleles A, Triantaphyllou S, Kotsakis K, Urem-Kotsou D, Halstead P, Efstratiou N, Kotsos S, Karamitrou-Mentessidi G, Adaktylou F, Chondroyianni-Metoki A, Pappa M, Ziota C, Sampson A, Papathanasiou A, Vitelli K, Cullen T, Kyparissi-Apostolika N, Lanz AZ, Peters J, Rio J, Wegmann D, Burger J, Currat M, Papageorgopoulou C. Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis. Sci Rep 2022; 12:13474. [PMID: 35931723 PMCID: PMC9356035 DOI: 10.1038/s41598-022-16745-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Abstract
The aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolithic and 319 modern sequences. To test for population continuity through time in Greece, we use an original structured population continuity test that simulates DNA from different periods by explicitly considering the spatial and temporal dynamics of populations. We explore specific scenarios of the mode and tempo of the European Neolithic expansion along the Danubian axis applying spatially explicit simulations coupled with Approximate Bayesian Computation. We observe a striking genetic homogeneity for the maternal line throughout the Neolithic in Greece whereas population continuity is rejected between the Neolithic and present-day Greeks. Along the Danubian expansion axis, our best-fitting scenario supports a substantial decrease in mobility and an increasing local hunter-gatherer contribution to the gene-pool of farmers following the initial rapid Neolithic expansion. Οur original simulation approach models key demographic parameters rather than inferring them from fragmentary data leading to a better understanding of this important process in European prehistory.
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Affiliation(s)
- Nuno M Silva
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Susanne Kreutzer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University of Mainz, 55099, Mainz, Germany.,Functional Genomics Center Zurich/GEML, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Angelos Souleles
- Laboratory of Physical Anthropology, Department of History & Ethnology, Democritus University of Thrace, 69100, Komotini, Greece
| | - Sevasti Triantaphyllou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Kostas Kotsakis
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dushka Urem-Kotsou
- Department of History & Ethnology, Democritus University of Thrace, 69100, Komotini, Greece
| | - Paul Halstead
- Emeritus, Department of Archaeology, University of Sheffield, Sheffield, S1 3NJ, UK
| | - Nikos Efstratiou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Stavros Kotsos
- Ephorate of Antiquities of Thessaloniki City, Hellenic Ministry of Culture and Sports, 54003, Thessaloniki, Greece
| | | | - Fotini Adaktylou
- Ephorate of Antiquities of Chalcidice and Mount Athos, Hellenic Ministry of Culture and Sports, 63100, Poligiros Chalcidice, Greece
| | | | - Maria Pappa
- Ephorate of Antiquities of Thessaloniki Region, Hellenic Ministry of Culture and Sports, 54646, Thessaloniki, Greece
| | - Christina Ziota
- Ephorate of Antiquities of Florina, Hellenic Ministry of Culture and Sports, 53100, Florina, Greece
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of Aegean, 85132, Rhodes, Greece
| | - Anastasia Papathanasiou
- Ephorate of Paleoanthropology and Speleology, Hellenic Ministry of Culture and Sports, 11636, Athens, Greece
| | - Karen Vitelli
- Prof. Emerita, Department of Anthropology, Franchthi Cave Project, Indiana University Bloomington, Bloomington, USA
| | - Tracey Cullen
- American School of Classical Studies at Athens, Princeton, NJ, USA
| | - Nina Kyparissi-Apostolika
- Ephor Emerita of the Ephorate of Paleoanthropology and Speleology, Hellenic Ministry of Culture and Sports, 11636, Athens, Greece
| | - Andrea Zeeb Lanz
- General Direction for Cultural Heritage of Rhineland-Palatinate, Speyer, Germany
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, Munich, Germany.,SNSB, State Collection of Palaeoanatomy Munich, Munich, Germany
| | - Jérémy Rio
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1700, Fribourg, Switzerland
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University of Mainz, 55099, Mainz, Germany.,Functional Genomics Center Zurich/GEML, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Mathias Currat
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland.
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History & Ethnology, Democritus University of Thrace, 69100, Komotini, Greece.
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5
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Böck D, Rothgangl T, Villiger L, Schmidheini L, Matsushita M, Mathis N, Ioannidi E, Rimann N, Grisch-Chan HM, Kreutzer S, Kontarakis Z, Kopf M, Thöny B, Schwank G. In vivo prime editing of a metabolic liver disease in mice. Sci Transl Med 2022; 14:eabl9238. [PMID: 35294257 PMCID: PMC7614134 DOI: 10.1126/scitranslmed.abl9238] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Prime editing is a highly versatile CRISPR-based genome editing technology that works without DNA double-strand break formation. Despite rapid technological advances, in vivo application for the treatment of genetic diseases remains challenging. Here, we developed a size-reduced SpCas9 prime editor (PE) lacking the RNaseH domain (PE2ΔRnH) and an intein-split construct (PE2 p.1153) for adeno-associated virus-mediated delivery into the liver. Editing efficiencies reached 15% at the Dnmt1 locus and were further elevated to 58% by delivering unsplit PE2ΔRnH via human adenoviral vector 5 (AdV). To provide proof of concept for correcting a genetic liver disease, we used the AdV approach for repairing the disease-causing Pahenu2 mutation in a mouse model of phenylketonuria (PKU) via prime editing. Average correction efficiencies of 11.1% (up to 17.4%) in neonates led to therapeutic reduction of blood phenylalanine, without inducing detectable off-target mutations or prolonged liver inflammation. Although the current in vivo prime editing approach for PKU has limitations for clinical application due to the requirement of high vector doses (7 × 1014 vg/kg) and the induction of immune responses to the vector and the PE, further development of the technology may lead to curative therapies for PKU and other genetic liver diseases.
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Affiliation(s)
- Desirée Böck
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Tanja Rothgangl
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Lukas Villiger
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland,Correspondence to: Lukas Villiger () and Gerald Schwank ()
| | - Lukas Schmidheini
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland,Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Mai Matsushita
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Nicolas Mathis
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Eleonora Ioannidi
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Nicole Rimann
- Division of Metabolism and Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
| | - Hiu Man Grisch-Chan
- Division of Metabolism and Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
| | - Susanne Kreutzer
- Genome Engineering and Measurement Laboratory (GEML), ETH Zurich, 8093 Zurich, Switzerland,Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland
| | - Zacharias Kontarakis
- Genome Engineering and Measurement Laboratory (GEML), ETH Zurich, 8093 Zurich, Switzerland,Functional Genomics Center Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland
| | - Manfred Kopf
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Beat Thöny
- Division of Metabolism and Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland,Zurich Center for Integrative Human Physiology, 8006 Zurich, Switzerland,Neuroscience Center Zurich, 8057 Zurich, Switzerland
| | - Gerald Schwank
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland,Correspondence to: Lukas Villiger () and Gerald Schwank ()
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6
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Gerhard N, Thurnheer T, Kreutzer S, Gmür RD, Attin T, Russo G, Karygianni L. Necrotizing Gingivitis: Microbial Diversity and Quantification of Protein Secretion in Necrotizing Gingivitis. Antibiotics (Basel) 2021; 10:antibiotics10101197. [PMID: 34680779 PMCID: PMC8532655 DOI: 10.3390/antibiotics10101197] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/18/2022] Open
Abstract
Necrotizing gingivitis (NG) is a necrotizing periodontal disease that differs from chronic gingivitis (CG). To date, both the microbiological causes and the involved host cytokine response of NG still remain unclear. Here, we investigated corresponding interdental plaque and serum samples from two groups of Chinese patients with CG (n = 21) or NG (n = 21). The microbiota were studied by 16S rRNA Illumina MiSeq sequencing of the microbial metagenome and by assessing quantitatively the abundance of the phylum Bacteroidetes, the genus Prevotella and the species T. forsythia, P. endodontalis, and P. gingivalis using fluorescence in situ hybridization (FISH). With respect to the associated host response, the levels of 30 inflammatory mediators were quantified by multiplex immunoassay analysis. Differential microbial abundance analysis of the two disease groups revealed at the phylum level that Proteobacteria accounted for 67% of the differentially abundant organisms, followed by organisms of Firmicutes (21%) and Actinobacteria (9%). At the species level, significant differences in abundance were seen for 75 species of which 58 species were significantly more abundant in CG patients. Notably, the FISH analysis revealed that Bacteroidetes was the most prevalent phylum in NG. The multiplex cytokine assay showed significant quantitative differences between the disease groups for eight analytes (GM–CSF, G–CSF, IFN–α, IL–4, IL–13, TNF–α, MIG, and HGF). The G–CSF was found to be the most significantly increased inflammatory protein marker in NG. The next-generation sequencing (NGS) data supported the understanding of NG as a multi-microbial infection with distinct differences to CG in regard to the microbial composition.
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Affiliation(s)
- Nicolas Gerhard
- Clinic for Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland; (N.G.); (T.T.); (R.D.G.); (T.A.)
| | - Thomas Thurnheer
- Clinic for Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland; (N.G.); (T.T.); (R.D.G.); (T.A.)
| | - Susanne Kreutzer
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, 8057 Zurich, Switzerland; (S.K.); (G.R.)
| | - Rudolf Dominik Gmür
- Clinic for Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland; (N.G.); (T.T.); (R.D.G.); (T.A.)
| | - Thomas Attin
- Clinic for Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland; (N.G.); (T.T.); (R.D.G.); (T.A.)
| | - Giancarlo Russo
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, 8057 Zurich, Switzerland; (S.K.); (G.R.)
| | - Lamprini Karygianni
- Clinic for Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland; (N.G.); (T.T.); (R.D.G.); (T.A.)
- Correspondence: ; Tel.: +0041-44-634-3275
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7
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Rothgangl T, Dennis MK, Lin PJC, Oka R, Witzigmann D, Villiger L, Qi W, Hruzova M, Kissling L, Lenggenhager D, Borrelli C, Egli S, Frey N, Bakker N, Walker JA, Kadina AP, Victorov DV, Pacesa M, Kreutzer S, Kontarakis Z, Moor A, Jinek M, Weissman D, Stoffel M, van Boxtel R, Holden K, Pardi N, Thöny B, Häberle J, Tam YK, Semple SC, Schwank G. In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels. Nat Biotechnol 2021; 39:949-957. [PMID: 34012094 PMCID: PMC8352781 DOI: 10.1038/s41587-021-00933-4] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/23/2021] [Indexed: 02/02/2023]
Abstract
Most known pathogenic point mutations in humans are C•G to T•A substitutions, which can be directly repaired by adenine base editors (ABEs). In this study, we investigated the efficacy and safety of ABEs in the livers of mice and cynomolgus macaques for the reduction of blood low-density lipoprotein (LDL) levels. Lipid nanoparticle-based delivery of mRNA encoding an ABE and a single-guide RNA targeting PCSK9, a negative regulator of LDL, induced up to 67% editing (on average, 61%) in mice and up to 34% editing (on average, 26%) in macaques. Plasma PCSK9 and LDL levels were stably reduced by 95% and 58% in mice and by 32% and 14% in macaques, respectively. ABE mRNA was cleared rapidly, and no off-target mutations in genomic DNA were found. Re-dosing in macaques did not increase editing, possibly owing to the detected humoral immune response to ABE upon treatment. These findings support further investigation of ABEs to treat patients with monogenic liver diseases.
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Affiliation(s)
- Tanja Rothgangl
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | | | | | - Rurika Oka
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Dominik Witzigmann
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Lukas Villiger
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Martina Hruzova
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Lucas Kissling
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Daniela Lenggenhager
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Sabina Egli
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Nina Frey
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Noëlle Bakker
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | | | | | | | - Martin Pacesa
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
- Genome Engineering and Measurement Laboratory, ETH Zurich, Zurich, Switzerland
| | - Zacharias Kontarakis
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
- Genome Engineering and Measurement Laboratory, ETH Zurich, Zurich, Switzerland
| | - Andreas Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Markus Stoffel
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Ruben van Boxtel
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | | | - Norbert Pardi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beat Thöny
- Division of Metabolism and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, Zurich, Switzerland
- Neuroscience Center Zurich, Zurich, Switzerland
| | - Johannes Häberle
- Division of Metabolism and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ying K Tam
- Acuitas Therapeutics Inc., Vancouver, BC, Canada
| | | | - Gerald Schwank
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland.
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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8
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Salzmann AP, Arora N, Russo G, Kreutzer S, Snipen L, Haas C. Assessing time dependent changes in microbial composition of biological crime scene traces using microbial RNA markers. Forensic Sci Int Genet 2021; 53:102537. [PMID: 34090061 DOI: 10.1016/j.fsigen.2021.102537] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 01/16/2023]
Abstract
Current body fluid identification methods do not reveal any information about the time since deposition (TsD) of biological traces, even though determining the age of traces could be crucial for the investigative process. To determine the utility of microbial RNA markers for TsD estimation, we examined RNA sequencing data from five forensically relevant body fluids (blood, menstrual blood, saliva, semen, and vaginal secretion) over seven time points, ranging from fresh to 1.5 years. One set of samples was stored indoors while another was exposed to outdoor conditions. In outdoor samples, we observed a consistent compositional shift, occurring after 4 weeks: this shift was characterized by an overall increase in non-human eukaryotic RNA and an overall decrease in prokaryotic RNA. In depth analyses showed a high fraction of tree, grass and fungal signatures, which are characteristic for the environment the samples were exposed to. When examining the prokaryotic fraction in more detail, three bacterial phyla were found to exhibit the largest changes in abundance, namely Actinobacteria, Proteobacteria and Firmicutes. More detailed analyses at the order level were done using a Lasso regression analysis to find a predictive subset of bacterial taxa. We found 26 bacterial orders to be indicative of sample age. Indoor samples did not reveal such a clear compositional change at the domain level: eukaryotic and prokaryotic abundance remained relatively stable across the assessed time period. Nonetheless, a Lasso regression analysis identified 32 bacterial orders exhibiting clear changes over time, enabling the prediction of TsD. For both indoor and outdoor samples, a larger number (around 60%) of the bacterial orders identified as indicative of TsD are part of the Actinobacteria, Proteobacteria and Firmicutes. In summary, we found that the observed changes across time are not primarily due to changes associated with body fluid specific bacteria but mostly due to accumulation of bacteria from the environment. Orders of these environmental bacteria could be evaluated for TsD prediction, considering the location and environment of the crime scene. However, further studies are needed to verify these findings, determine the applicability across samples, replicates, donors, and other variables, and also to further assess the effect of different seasons and locations on the samples.
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Affiliation(s)
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Giancarlo Russo
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Lars Snipen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
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9
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Salzmann AP, Russo G, Kreutzer S, Haas C. Degradation of human mRNA transcripts over time as an indicator of the time since deposition (TsD) in biological crime scene traces. Forensic Sci Int Genet 2021; 53:102524. [PMID: 34015741 DOI: 10.1016/j.fsigen.2021.102524] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022]
Abstract
Knowledge about the age of a stain, also termed as time since deposition (TsD), would provide law-enforcing authorities with valuable information for the prosecution of criminal offenses. Yet, there is no reliable method for the inference / assessment of TsD available. The aim of this study was to gain further insight into the RNA degradation pattern of forensically relevant body fluids and to find candidate markers for TsD estimation. Blood, menstrual blood, saliva, semen and vaginal secretion samples were exposed to indoor (dark, room temperature) and outdoor (exposed to sun, wind, etc. but protected from rain) conditions for up to 1.5 years. Based on expression and degradation analyses, we were able to identify body fluid specific signatures and RNA degradation patterns. The indoor samples showed a marked drop in RNA integrity after 6 months, while the outdoor samples were difficult to interpret and therefore excluded for some of the analyses. Up to 4 weeks, indoor samples showed more stable and less degrading transcripts than outdoor samples. Stable transcripts tended to be significantly shorter than degrading ones or transcripts, which are neither degrading nor stable. We reinforced the body fluid specific and the housekeeping gene nature of previously reported markers. With an unbiased approach, we selected stable and degrading genes for each body fluid in the short term and assessed their integrity during extended storage. We identified several stable and degrading gene transcripts, which could be tested in a targeted assay to assess the TsD interval e.g. by analyzing the ratio of degrading vs stable transcripts. In conclusion, we were able to detect RNA degradation patterns in samples being aged up to 1.5 years and identified several candidate markers, which could be evaluated for TsD estimation.
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Affiliation(s)
| | - Giancarlo Russo
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
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10
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Healy ME, Boege Y, Hodder MC, Böhm F, Malehmir M, Scherr AL, Jetzer J, Chan LK, Parrotta R, Jacobs K, Clerbaux LA, Kreutzer S, Campbell A, Gilchrist E, Gilroy K, Rodewald AK, Honcharova-Biletska H, Schimmer R, Vélez K, Büeler S, Cammareri P, Kalna G, Wenning AS, McCoy KD, Gomez de Agüero M, Schulze-Bergkamen H, Klose CSN, Unger K, Macpherson AJ, Moor AE, Köhler B, Sansom OJ, Heikenwälder M, Weber A. MCL1 Is Required for Maintenance of Intestinal Homeostasis and Prevention of Carcinogenesis in Mice. Gastroenterology 2020; 159:183-199. [PMID: 32179094 PMCID: PMC7397524 DOI: 10.1053/j.gastro.2020.03.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 02/25/2020] [Accepted: 03/10/2020] [Indexed: 02/01/2023]
Abstract
BACKGROUND & AIMS Intestinal epithelial homeostasis depends on a tightly regulated balance between intestinal epithelial cell (IEC) death and proliferation. While the disruption of several IEC death regulating factors result in intestinal inflammation, the loss of the anti-apoptotic BCL2 family members BCL2 and BCL2L1 has no effect on intestinal homeostasis in mice. We investigated the functions of the antiapoptotic protein MCL1, another member of the BCL2 family, in intestinal homeostasis in mice. METHODS We generated mice with IEC-specific disruption of Mcl1 (Mcl1ΔIEC mice) or tamoxifen-inducible IEC-specific disruption of Mcl1 (i-Mcl1ΔIEC mice); these mice and mice with full-length Mcl1 (controls) were raised under normal or germ-free conditions. Mice were analyzed by endoscopy and for intestinal epithelial barrier permeability. Intestinal tissues were analyzed by histology, in situ hybridization, proliferation assays, and immunoblots. Levels of calprotectin, a marker of intestinal inflammation, were measured in intestinal tissues and feces. RESULTS Mcl1ΔIEC mice spontaneously developed apoptotic enterocolopathy, characterized by increased IEC apoptosis, hyperproliferative crypts, epithelial barrier dysfunction, and chronic inflammation. Loss of MCL1 retained intestinal crypts in a hyperproliferated state and prevented the differentiation of intestinal stem cells. Proliferation of intestinal stem cells in MCL1-deficient mice required WNT signaling and was associated with DNA damage accumulation. By 1 year of age, Mcl1ΔIEC mice developed intestinal tumors with morphologic and genetic features of human adenomas and carcinomas. Germ-free housing of Mcl1ΔIEC mice reduced markers of microbiota-induced intestinal inflammation but not tumor development. CONCLUSION The antiapoptotic protein MCL1, a member of the BCL2 family, is required for maintenance of intestinal homeostasis and prevention of carcinogenesis in mice. Loss of MCL1 results in development of intestinal carcinomas, even under germ-free conditions, and therefore does not involve microbe-induced chronic inflammation. Mcl1ΔIEC mice might be used to study apoptotic enterocolopathy and inflammatory bowel diseases.
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Affiliation(s)
- Marc E Healy
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Yannick Boege
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Michael C Hodder
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, UK.
| | - Friederike Böhm
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Mohsen Malehmir
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Anna-Lena Scherr
- National Center for Tumor Diseases, Department of Medical Oncology and Heidelberg University Hospital, Internal Medicine VI, Heidelberg, Germany
| | - Jasna Jetzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Lap Kwan Chan
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Rossella Parrotta
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Kurt Jacobs
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Laure-Alix Clerbaux
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Susanne Kreutzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Andrew Campbell
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, Glasgow, UK
| | - Ella Gilchrist
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, Glasgow, UK
| | - Kathryn Gilroy
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, Glasgow, UK
| | - Ann-Katrin Rodewald
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | | | - Roman Schimmer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Karelia Vélez
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Simone Büeler
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Patrizia Cammareri
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, Glasgow, UK
| | - Gabriela Kalna
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, Glasgow, UK
| | - Anna S Wenning
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
| | - Kathy D McCoy
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland; Department of Physiology and Pharmacology and Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mercedes Gomez de Agüero
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
| | - Henning Schulze-Bergkamen
- National Center for Tumor Diseases, Department of Medical Oncology and Heidelberg University Hospital, Internal Medicine VI, Heidelberg, Germany
| | - Christoph S N Klose
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, Germany
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg Germany
| | - Andrew J Macpherson
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
| | - Andreas E Moor
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Bruno Köhler
- National Center for Tumor Diseases, Department of Medical Oncology and Heidelberg University Hospital, Internal Medicine VI, Heidelberg, Germany
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, UK.
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, Deutsches Krebs-Forschungszentrum (DKFZ), Heidelberg, Germany.
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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11
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Kontopoulos I, Penkman K, Mullin VE, Winkelbach L, Unterländer M, Scheu A, Kreutzer S, Hansen HB, Margaryan A, Teasdale MD, Gehlen B, Street M, Lynnerup N, Liritzis I, Sampson A, Papageorgopoulou C, Allentoft ME, Burger J, Bradley DG, Collins MJ. Screening archaeological bone for palaeogenetic and palaeoproteomic studies. PLoS One 2020; 15:e0235146. [PMID: 32584871 PMCID: PMC7316274 DOI: 10.1371/journal.pone.0235146] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/09/2020] [Indexed: 11/18/2022] Open
Abstract
The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals’ size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.
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Affiliation(s)
- Ioannis Kontopoulos
- Department of Archaeology, BioArCh, University of York, York, United Kingdom
- * E-mail:
| | - Kirsty Penkman
- Department of Chemistry, BioArCh, University of York, York, United Kingdom
| | - Victoria E. Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Martina Unterländer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
- German Federal Criminal Police Office, Wiesbaden, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Henrik B. Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew D. Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Birgit Gehlen
- Collaborative Research Centre, project D4, Cologne University, Cologne, Germany
| | - Martin Street
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM Leibniz Research Institute for Archaeology, Neuwied, Germany
| | - Niels Lynnerup
- Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ioannis Liritzis
- Laboratory of Archaeometry, Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
- Center on Yellow River Civilization of Henan Province, Key Research Institute of Yellow River Civilization and Sustainable Development and Collaborative Innovation, Henan University, Kaifeng, China
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
| | - Morten E. Allentoft
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Matthew J. Collins
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
- Centre for Evogenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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12
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Bialas P, Welsch K, Gronwald B, Gottschling S, Kreutzer S, Haber M, Volk T. [The effects of setting a standard in the acute pain therapy on a ward : Parameters for patient and provider satisfaction and cost structure (STANDAKU)]. Schmerz 2018; 32:449-455. [PMID: 30306308 DOI: 10.1007/s00482-018-0330-6] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND There is neither a "gold standard" nor commonly approved therapy goals in postoperative pain therapy. In a multi-center study, more than 80% of all patients treated stated that they suffered from postoperative pain. Moreover, patients evaluated the pain therapy as significantly worse than other medical or nursing practices. Therefore, there is a need for optimization in therapy for acute pain. OBJECTIVES The goal of our project was to figure out if the introduction of a "pain treatment standard" would increase the satisfaction of patients, physicians, and nurses, and reduce the costs of pain-related medicine. MATERIALS AND METHODS Overall, 2769 patients and 285 providers (202 nurses and 83 physicians) were polled. The medication costs in ten areas of the ward were evaluated and compared. The providers were offered a training course on the "pain standard" and it was officially introduced onto the wards. After some time, the satisfaction of patients and providers and the use of medicine were recorded again. RESULTS AND DISCUSSION The maximum pain values declared by the patients significantly decreased after the introduction of the "pain standard." The satisfaction with pain therapy significantly increased for the patients and for the providers. The reported minimum pain values of the patients did not change significantly. The costs of pain medicine slightly increased. In general, there was a positive effect of introducing a "pain standard" for patients and providers.
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Affiliation(s)
- P Bialas
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum des Saarlandes und Medizinische Fakultät, Universität des Saarlandes, Kirrbergerstraße 1, 66421, Homburg/Saar, Deutschland.
| | - K Welsch
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum des Saarlandes und Medizinische Fakultät, Universität des Saarlandes, Kirrbergerstraße 1, 66421, Homburg/Saar, Deutschland
| | - B Gronwald
- Zentrum für Palliativmedizin und Kinderschmerztherapie, Universitätsklinikum des Saarlandes und Medizinische Fakultät Universität des Saarlandes, Homburg/Saar, 66421, Kirrbergerstraße 1, Deutschland
| | - S Gottschling
- Zentrum für Palliativmedizin und Kinderschmerztherapie, Universitätsklinikum des Saarlandes und Medizinische Fakultät Universität des Saarlandes, Homburg/Saar, 66421, Kirrbergerstraße 1, Deutschland
| | - S Kreutzer
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum des Saarlandes und Medizinische Fakultät, Universität des Saarlandes, Kirrbergerstraße 1, 66421, Homburg/Saar, Deutschland
| | - M Haber
- Apotheke des Universitätsklinikums des Saarlandes und Medizinische Fakultät, Universität des Saarlandes, Homburg/Saar, Deutschland
| | - T Volk
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum des Saarlandes und Medizinische Fakultät, Universität des Saarlandes, Kirrbergerstraße 1, 66421, Homburg/Saar, Deutschland
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13
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Silva NM, Rio J, Kreutzer S, Papageorgopoulou C, Currat M. Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations. Evol Appl 2018; 11:1642-1655. [PMID: 30344633 PMCID: PMC6183456 DOI: 10.1111/eva.12655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 05/23/2018] [Accepted: 05/27/2018] [Indexed: 11/28/2022] Open
Abstract
The retrieval of ancient DNA from osteological material provides direct evidence of human genetic diversity in the past. Ancient DNA samples are often used to investigate whether there was population continuity in the settlement history of an area. Methods based on the serial coalescent algorithm have been developed to test whether the population continuity hypothesis can be statistically rejected by analysing DNA samples from the same region but of different ages. Rejection of this hypothesis is indicative of a large genetic shift, possibly due to immigration occurring between two sampling times. However, this approach is only able to reject a model of full continuity model (a total absence of genetic input from outside), but admixture between local and immigrant populations may lead to partial continuity. We have recently developed a method to test for population continuity that explicitly considers the spatial and temporal dynamics of populations. Here, we extended this approach to estimate the proportion of genetic continuity between two populations, using ancient genetic samples. We applied our original approach to the question of the Neolithic transition in Central Europe. Our results confirmed the rejection of full continuity, but our approach represents an important step forward by estimating the relative contribution of immigrant farmers and of local hunter-gatherers to the final Central European Neolithic genetic pool. Furthermore, we show that a substantial proportion of genes brought by the farmers in this region were assimilated from other hunter-gatherer populations along the way from Anatolia, which was not detectable by previous continuity tests. Our approach is also able to jointly estimate demographic parameters, as we show here by finding both low density and low migration rate for pre-Neolithic hunter-gatherers. It provides a useful tool for the analysis of the numerous ancient DNA data sets that are currently being produced for many different species.
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Affiliation(s)
- Nuno Miguel Silva
- AGP LabDepartment of Genetics & Evolution – Anthropology UnitUniversity of GenevaGenevaSwitzerland
| | - Jeremy Rio
- AGP LabDepartment of Genetics & Evolution – Anthropology UnitUniversity of GenevaGenevaSwitzerland
| | - Susanne Kreutzer
- Palaeogenetics GroupInstitute of AnthropologyJohannes Gutenberg UniversityMainzGermany
| | - Christina Papageorgopoulou
- Laboratory of Physical AnthropologyDepartment of History & EthnologyDemocritus University of ThraceKomotiniGreece
| | - Mathias Currat
- AGP LabDepartment of Genetics & Evolution – Anthropology UnitUniversity of GenevaGenevaSwitzerland
- Institute of Genetics and Genomics in Geneva (IGE3)GenevaSwitzerland
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14
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Bassinet C, Kreutzer S, Mercier N, Clairand I. Violet stimulated luminescence signal from electronic components for radiation accident dosimetry. RADIAT MEAS 2017. [DOI: 10.1016/j.radmeas.2017.04.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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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15
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Suchomel H, Kreutzer S, Jörg M, Brodbeck S, Pieczarka M, Betzold S, Dietrich CP, Sęk G, Schneider C, Höfling S. Room temperature strong coupling in a semiconductor microcavity with embedded AlGaAs quantum wells designed for polariton lasing. Opt Express 2017; 25:24816-24826. [PMID: 29041294 DOI: 10.1364/oe.25.024816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
We report a systematic study of the temperature and excitation density behavior of an AlAs/AlGaAs, vertically emitting microcavity with embedded ternary Al0.20Ga0.80As/AlAs quantum wells in the strong coupling regime. Temperature-dependent photoluminescence measurements of the bare quantum wells indicate a crossover from the type-II indirect to the type-I direct transition. The resulting mixing of quantum well and barrier ground states in the conduction band leads to an estimated exciton binding energy systematically exceeding 25 meV. The formation of exciton-polaritons is evidenced in our quantum well microcavity via reflection measurements with Rabi splittings ranging from (13.93 ± 0.15) meV at low temperature (30 K) to (8.58 ± 0.40) meV at room temperature (300 K). Furthermore, the feasibility of polariton laser operation is demonstrated under non-resonant optical excitation conditions at 20 K and emission around 1.835 eV.
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16
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Lenggenhager D, Gouttenoire J, Malehmir M, Bawohl M, Honcharova-Biletska H, Kreutzer S, Semela D, Neuweiler J, Hürlimann S, Aepli P, Fraga M, Sahli R, Terracciano L, Rubbia-Brandt L, Müllhaupt B, Sempoux C, Moradpour D, Weber A. Visualization of hepatitis E virus RNA and proteins in the human liver. J Hepatol 2017; 67:471-479. [PMID: 28412294 DOI: 10.1016/j.jhep.2017.04.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 03/31/2017] [Accepted: 04/04/2017] [Indexed: 12/28/2022]
Abstract
BACKGROUND & AIMS Although hepatitis E constitutes a substantial disease burden worldwide, surprisingly little is known about the localization of hepatitis E virus (HEV) in the human liver. We therefore aimed to visualize HEV RNA and proteins in situ. METHODS A panel of 12 different antibodies against HEV open reading frame (ORF) 1-3 proteins was evaluated for immunohistochemistry (IHC) and two probes for in situ hybridization (ISH) in formalin-fixed, paraffin-embedded (FFPE) HuH7 cells transfected with HEV ORF1-3 expression vectors. IHC (and partly ISH) were then applied to Hep293TT cells replicating infectious HEV and liver specimens from patients with hepatitis E (n=20) and controls (n=134). RESULTS Whereas ORF1-3 proteins were all detectable in transfected, HEV protein-expressing cells, only ORF2 and 3 proteins were traceable in cells replicating infectious HEV. Only the ORF2-encoded capsid protein was also unequivocally detectable in liver specimens from patients with hepatitis E. IHC for ORF2 protein revealed a patchy expression in individual or grouped hepatocytes, generally stronger in chronic compared to acute hepatitis. Besides cytoplasmic and canalicular, ORF2 protein also displayed a hitherto unknown nuclear localization. Positivity for ORF2 protein in defined areas correlated with HEV RNA detection by ISH. IHC was specific and comparably sensitive as PCR for HEV RNA. CONCLUSIONS ORF2 protein can be reliably visualized in the liver of patients with hepatitis E, allowing for sensitive and specific detection of HEV in FFPE samples. Its variable subcellular distribution in individual hepatocytes of the same liver suggests a redistribution of ORF2 protein during infection and interaction with nuclear components. LAY SUMMARY The open reading frame (ORF) 2 protein can be used to visualize the hepatitis E virus (HEV) in the human liver. This enabled us to discover a hitherto unknown localization of the HEV ORF2 protein in the nucleus of hepatocytes and to develop a test for rapid histopathologic diagnosis of hepatitis E, the most common cause of acute hepatitis worldwide.
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Affiliation(s)
- Daniela Lenggenhager
- Department of Pathology and Molecular Pathology, University Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Jérôme Gouttenoire
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Mohsen Malehmir
- Department of Pathology and Molecular Pathology, University Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Marion Bawohl
- Department of Pathology and Molecular Pathology, University Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Hanna Honcharova-Biletska
- Department of Pathology and Molecular Pathology, University Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Susanne Kreutzer
- Department of Pathology and Molecular Pathology, University Zurich and University Hospital Zurich, Zurich, Switzerland
| | - David Semela
- Division of Gastroenterology and Hepatology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Jörg Neuweiler
- Institute of Pathology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Sandra Hürlimann
- Institute of Pathology, Cantonal Hospital Lucerne, Lucerne, Switzerland
| | - Patrick Aepli
- Gastroenterology and Hepatology Unit, Cantonal Hospital Lucerne, Lucerne, Switzerland
| | - Montserrat Fraga
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Roland Sahli
- Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Luigi Terracciano
- Department of Pathology, University Hospital Basel, Basel, Switzerland
| | - Laura Rubbia-Brandt
- Service de Pathologie Clinique Geneva University Hospitals Faculté de Médecine Geneva, Switzerland
| | - Beat Müllhaupt
- Clinics of Hepatology and Gastroenterology, University and University Hospital Zurich, Zurich, Switzerland
| | - Christine Sempoux
- Institut Universitaire de Pathologie, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Darius Moradpour
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University Zurich and University Hospital Zurich, Zurich, Switzerland.
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17
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Broushaki F, Thomas MG, Link V, López S, van Dorp L, Kirsanow K, Hofmanová Z, Diekmann Y, Cassidy LM, Díez-Del-Molino D, Kousathanas A, Sell C, Robson HK, Martiniano R, Blöcher J, Scheu A, Kreutzer S, Bollongino R, Bobo D, Davudi H, Munoz O, Currat M, Abdi K, Biglari F, Craig OE, Bradley DG, Shennan S, Veeramah K, Mashkour M, Wegmann D, Hellenthal G, Burger J. Early Neolithic genomes from the eastern Fertile Crescent. Science 2016; 353:499-503. [PMID: 27417496 DOI: 10.1126/science.aaf7943] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/05/2016] [Indexed: 01/06/2023]
Abstract
We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.
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Affiliation(s)
- Farnaz Broushaki
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Vivian Link
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Saioa López
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Karola Kirsanow
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Zuzana Hofmanová
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Yoan Diekmann
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - David Díez-Del-Molino
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - Athanasios Kousathanas
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
| | - Christian Sell
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Harry K Robson
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Rui Martiniano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jens Blöcher
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Ruth Bollongino
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Dean Bobo
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Hossein Davudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran
| | - Olivia Munoz
- UMR 7041 ArScAn -VEPMO, Maison de l'Archéologie et de l'Ethnologie, 21 allée de l'Université, 92023 Nanterre, France
| | - Mathias Currat
- Department of Genetics & Evolution-Anthropology Unit, University of Geneva, 1211 Geneva, Switzerland
| | - Kamyar Abdi
- Samuel Jordan Center for Persian Studies and Culture, University of California-lrvine, Irvine, CA 92697-3370, USA
| | - Fereidoun Biglari
- Paleolithic Department, National Museum of Iran, 113617111, Tehran, Iran
| | - Oliver E Craig
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Stephen Shennan
- Institute of Archaeology, University College London, London WC1H 0PY, UK
| | - Krishna Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Marjan Mashkour
- CNRS/MNHN/SUs - UMR 7209, Archéozoologie et Archéobotanique, Sociétés, Pratiques et Environnements, Département Ecologie et Gestion de la Biodiversité, 55 rue Buffon, 75005 Paris, France
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Joachim Burger
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
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18
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Richter D, Mittelstraß D, Kreutzer S, Pintaske R, Dornich K, Fuchs M. A new fully integrated X-ray irradiator system for dosimetric research. Appl Radiat Isot 2016; 112:122-30. [PMID: 27041090 DOI: 10.1016/j.apradiso.2016.03.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/11/2016] [Accepted: 03/19/2016] [Indexed: 10/22/2022]
Abstract
A fully housed X-ray irradiator was developed for use within lexsyg or Magnettech desktop equipment. The importance of hardening of the low energy photon radiation is discussed, its performance and feasibility is empirically shown and sustained by basic numerical simulations. Results of the latter for various materials are given for different X-ray source settings in order to provide estimates on the required setup for the irradiation of different geometries and materials. A Si-photodiode provides real-time monitoring of the X-ray-irradiator designed for use in dosimetric dating and other dosimetric application where irradiation of small samples or dosemeters is required.
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Affiliation(s)
- D Richter
- Freiberg Instruments GmbH, Delfterstr. 6, 09599 Freiberg, Germany; Institute of Ecology, Subject Area Landscape Change, Leuphana University, Lüneburg, Germany; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - D Mittelstraß
- Freiberg Instruments GmbH, Delfterstr. 6, 09599 Freiberg, Germany; Department of Geography, Justus-Liebig-University, Gießen, Germany; Department of Physics, Technische Universität Dresden, 01062 Dresden, Germany
| | - S Kreutzer
- Department of Geography, Justus-Liebig-University, Gießen, Germany; IRAMAT-CRP2A, Université Bordeaux Montaigne, Pessac Cedex, France
| | - R Pintaske
- Pintaske CONSULTING, Neunzehnhainer Strasse 2, 09514 Lengefeld, Germany
| | - K Dornich
- Freiberg Instruments GmbH, Delfterstr. 6, 09599 Freiberg, Germany
| | - M Fuchs
- Department of Geography, Justus-Liebig-University, Gießen, Germany
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19
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Kreutzer S. [Nurses traveling afar]. Pflege Z 2014; 67:756-758. [PMID: 25632595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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20
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Kreutzer S. "Hollywood nurses" in West Germany: biographies, self-images, and experiences of academically trained nurses after 1945. Nurs Hist Rev 2013; 21:33-54. [PMID: 23901626 DOI: 10.1891/1062-8061.21.33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The School of Nursing at Heidelberg University was founded in 1953 on the initiative of the Rockefeller Foundation to generate new, scientifically trained nursing elite to advance the professionalization of nursing in West Germany. The "American" concept met massive resistance. Its "superior nursing training" was seen as creating "Hollywood nurses"-a threat to the traditional Christian understanding of good, caring nursing. Intense social conflicts also caused problems with other groups of nurses. The school nevertheless played a very important role as a "cadre academy" in the history of professionalization. Many of the first German professors in the nursing sciences trained or underwent further training in Heidelberg.
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Affiliation(s)
- Susanne Kreutzer
- Department for Humanities/Nursing Science, University of Osnabriick. Germany
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21
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Kreutzer S. [Historical practice of Christian accompaniment in dying. "With us no one died alone"]. Pflege Z 2013; 66:47-49. [PMID: 23394057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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22
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Kreutzer S. [History of routine nursing after 1945. From vocation to professional career]. Pflege Z 2012; 65:436-438. [PMID: 22893948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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23
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Kreutzer S. [Rationalization of Protestant nursing. A comparison of Deaconess Motherhouses in West Germany and the United States, 1945-1970]. Medizinhist J 2012; 47:221-243. [PMID: 23802347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protestant Deaconess Motherhouses emerged as a German nursing organization in the nineteenth century to be later exported to many other countries including the United States. The motherhouse principle could not be simply transferred without being adapted to the situation prevailing in each of those countries. The essay investigates the conception and transformation of Protestant nursing by comparing a West German and American deaconess motherhouse each in their particular context. It shows that the deaconesses in the United States developed their own, more scientifically oriented understanding of nursing and were therefore more open to the rationalization of nursing than their West German counterpart.
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Affiliation(s)
- Susanne Kreutzer
- Fachhochschule Münster, Fachbereich Pflege und Gesundheit, Münster.
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24
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Kreutzer S. [After the war: US Americans influence the professionalization of nursing. A new nursing elite is created. The "Hollywood Nurses"]. Pflege Z 2011; 64:688-690. [PMID: 22097410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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25
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Kreutzer S. [The community nurse - work and everyday life 1945 to 1970. "It was not just about time..."]. Pflege Z 2011; 64:173-175. [PMID: 21462473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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26
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Bauch C, Kreutzer S, Becker PH. Breeding experience affects condition: blood metabolite levels over the course of incubation in a seabird. J Comp Physiol B 2010; 180:835-45. [DOI: 10.1007/s00360-010-0453-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 02/05/2010] [Accepted: 02/09/2010] [Indexed: 10/19/2022]
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Abstract
In Lutheran Germany, parish nursing traditionally constituted the deaconesses' principal work. As "Christian mothers of the parish" they were charged with a wide spectrum of tasks, including nursing, social service, and pastoral care. At the center of the Christian understanding of nursing was the idea of nursing body and soul as a unity. This article analyzes the conception and transformation of Protestant parish nursing in the nineteenth and twentieth centuries in Germany and the United States, which developed very differently. In West Germany, parish nursing proved surprisingly resistant to modernization even in the face of upheavals of the 1960s, and in some places this traditional model survived as late as the 1980s and 1990s. In the United States, by contrast, an understanding of nursing rooted in the division of labor between care for body and care for soul had come to prevail by the 1920s and '30s, pushing out the German model of the parish deaconess altogether.
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Affiliation(s)
- Susanne Kreutzer
- Department for Humanities/Nursing Science, University of Osnabrück, Berlin, Germany
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28
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Kreutzer S. "Before, we were always there--now, everything is separate": on nursing reforms in Western Germany. Nurs Hist Rev 2008; 16:180-200. [PMID: 18595347 DOI: 10.1891/1062-8061.16.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Susanne Kreutzer
- Institute of Sociology, Leibniz University of Hanover, Berlin, Germany
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29
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Kreutzer S. [Learning by doing? The restructuring of nursing education after 1945]. Med Ges Gesch 2007; 25:155-80. [PMID: 17645004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
This study deals with the reform of nursing education on a day-to-day level and exemplifies the dramatic change in the image of nursing in the 1960s, when the erstwhile religious calling was transformed into a modern-day female profession. The analysis is based on interviews with two different groups of nurses who were educated between the 1930s and 1960s. The first group is composed of the deaconesses of a Protestant mother-house in Hannover (Henriettenstiftung). The second group is formed by nurses who were noted for their important role in the professionalisation of nursing in West Germany. The methodology of this study draws on the experiences of the practice of oral history which reflects the actual context of the narratives, the problem of commemoration and the relationship between individual and collective memory. Nursing education, as late as the 1950s, was based on practical experience. The nursing students were responsible for a certain number of patients from the very first day of their training. Comparison of the different narratives shows that such an experience-based training principle was bound to a specific, family-like concept of nursing which was supported by the sisterhoods. This traditional system of nursing education changed essentially in the 1960s when knowledge based on experience lost a great deal of its meaning, while a theory-based training took preference. Furthermore, the regulation and fragmentation of nursing education increased significantly. The outcome was that continuity in caring for patients decreased dramatically in the 1960s and it became much more difficult to learn how to observe the sick and to demand confidence in dealing with patients. The reform of nursing education also had far-reaching consequences for the construction of everyday life in the wards as the students had previously undertaken a major part of the work.
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Ullrich D, Kreutzer S. [Comparison of gold-plated silver- and silver oxide-impregnated silastic tympanostomy tubes: a randomized, prospective clinical trial]. Laryngorhinootologie 2006; 85:501-5. [PMID: 16612753 DOI: 10.1055/s-2006-925206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
UNLABELLED The insertion of tympanostomy tubes is the most common surgical procedure in the world. A major complication of chronic intubation is infectious otorrhea. The present study compares the rate of infectious otorrhea and survival rate of gold-plated silver tubes (GPR) vs. Silver Oxide-Impregnated Silastic Tubes (SPR). STUDY DESIGN The prospective, randomized clincial trial was conducted with 116 children (59 female, 57 male) aged between 16 and 127 months (median: 51 months). Bilateral insertion of ventilation tubes was performed with SPR on one side and GPR on the other side in all children. The resulting data were compared using 2-tailed Wilcoxon-test. RESULTS Out of 116 children, 11 left the study, 26 children finished the study by extrusion of both tubes, 32 children lost one tube and 47 children lost no tube. Total follow-up of GPR and SPR amounted to 703 and 949 months, respectively. Mean survival rate of SPR and GPR was 9.9 +/- 4.6 and 7.0 +/- 3.4 months, respectively (p < 0.001). During the first postoperative week, 13% of children suffered from otorrhea; after the first postoperative week until extrusion of the tubes, otorrhea was observed in 55% of children. The ratio otorrhea/months amounted to 0.046 and 0.05 in SPR and GPR, respectively (p: n. s.). CONCLUSIONS Survival rate of SPR is significantly longer than compared to GPR. No differences in the otorrhea rate of SPR vs. GPR are detectable. The longer survival rate of SPR seems to be independent of the rate of infectious otorrhea but depends probably on other effects of biocompatibility.
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