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Cui L, Yang B, Xiao S, Gao J, Baud A, Graham D, McBride M, Dominiczak A, Schafer S, Aumatell RL, Mont C, Teruel AF, Hübner N, Flint J, Mott R, Huang L. Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing. Genome Biol 2023; 24:215. [PMID: 37773188 PMCID: PMC10540365 DOI: 10.1186/s13059-023-03060-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Dominance and other non-additive genetic effects arise from the interaction between alleles, and historically these phenomena play a major role in quantitative genetics. However, most genome-wide association studies (GWAS) assume alleles act additively. RESULTS We systematically investigate both dominance-here representing any non-additive within-locus interaction-and additivity across 574 physiological and gene expression traits in three mammalian stocks: F2 intercross pigs, rat heterogeneous stock, and mice heterogeneous stock. Dominance accounts for about one quarter of heritable variance across all physiological traits in all species. Hematological and immunological traits exhibit the highest dominance variance, possibly reflecting balancing selection in response to pathogens. Although most quantitative trait loci (QTLs) are detectable as additive QTLs, we identify 154, 64, and 62 novel dominance QTLs in pigs, rats, and mice respectively that are undetectable as additive QTLs. Similarly, even though most cis-acting expression QTLs are additive, gene expression exhibits a large fraction of dominance variance, and trans-acting eQTLs are enriched for dominance. Genes causal for dominance physiological QTLs are less likely to be physically linked to their QTLs but instead act via trans-acting dominance eQTLs. In addition, thousands of eQTLs are associated with alternatively spliced isoforms with complex additive and dominant architectures in heterogeneous stock rats, suggesting a possible mechanism for dominance. CONCLUSIONS Although heritability is predominantly additive, many mammalian genetic effects are dominant and likely arise through distinct mechanisms. It is therefore advantageous to consider both additive and dominance effects in GWAS to improve power and uncover causality.
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Affiliation(s)
- Leilei Cui
- National Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China
- School of Life Sciences, Nanchang University, Nanchang, China
| | - Bin Yang
- National Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Shijun Xiao
- National Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Jun Gao
- National Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Amelie Baud
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Delyth Graham
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, G12 8TA, UK
| | - Martin McBride
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, G12 8TA, UK
| | - Anna Dominiczak
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, G12 8TA, UK
| | - Sebastian Schafer
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Regina Lopez Aumatell
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Carme Mont
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Albert Fernandez Teruel
- Departamento de Psiquiatría y Medicina Legal, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Norbert Hübner
- Genetics and Genomics of Cardiovascular Diseases Research Group, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Center for Cardiovascular Research) Partner Site Berlin, Berlin, Germany
- Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jonathan Flint
- Department of Psychiatry and Behavioral Sciences, Brain Research Institute, University of California, Los Angeles, CA, USA
| | - Richard Mott
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Lusheng Huang
- National Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
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2
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Abstract
The diet and age of mice can modulate how different genetic variants impact body weight, demonstrating the need to take context into account when performing genetic studies.
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Affiliation(s)
- Hélène Tonnelé
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amelie Baud
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
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3
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Abstract
Indirect genetic effects (IGE) occur when an individual's phenotype is influenced by genetic variation in conspecifics. Opportunities for IGE are ubiquitous, and, when present, IGE have profound implications for behavioral, evolutionary, agricultural, and biomedical genetics. Despite their importance, the empirical study of IGE lags behind the development of theory. In large part, this lag can be attributed to the fact that measuring IGE, and deconvoluting them from the direct genetic effects of an individual's own genotype, is subject to many potential pitfalls. In this Perspective, we describe current challenges that empiricists across all disciplines will encounter in measuring and understanding IGE. Using ideas and examples spanning evolutionary, agricultural, and biomedical genetics, we also describe potential solutions to these challenges, focusing on opportunities provided by recent advances in genomic, monitoring, and phenotyping technologies. We hope that this cross-disciplinary assessment will advance the goal of understanding the pervasive effects of conspecific interactions in biology.
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Affiliation(s)
- Amelie Baud
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,the Universitat Pompeu Fabra (UPF), Barcelona,Spain
| | - Sarah McPeek
- the Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Nancy Chen
- the Department of Biology, University of Rochester, Rochester, NY 14627,USA
| | - Kimberly A Hughes
- the Department of Biological Science, Florida State University, Tallahassee, FL 32303,USA
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4
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Baud A, Casale FP, Barkley-Levenson AM, Farhadi N, Montillot C, Yalcin B, Nicod J, Palmer AA, Stegle O. Dissecting indirect genetic effects from peers in laboratory mice. Genome Biol 2021; 22:216. [PMID: 34311762 PMCID: PMC8311926 DOI: 10.1186/s13059-021-02415-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/27/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The phenotype of an individual can be affected not only by the individual's own genotypes, known as direct genetic effects (DGE), but also by genotypes of interacting partners, indirect genetic effects (IGE). IGE have been detected using polygenic models in multiple species, including laboratory mice and humans. However, the underlying mechanisms remain largely unknown. Genome-wide association studies of IGE (igeGWAS) can point to IGE genes, but have not yet been applied to non-familial IGE arising from "peers" and affecting biomedical phenotypes. In addition, the extent to which igeGWAS will identify loci not identified by dgeGWAS remains an open question. Finally, findings from igeGWAS have not been confirmed by experimental manipulation. RESULTS We leverage a dataset of 170 behavioral, physiological, and morphological phenotypes measured in 1812 genetically heterogeneous laboratory mice to study IGE arising between same-sex, adult, unrelated mice housed in the same cage. We develop and apply methods for igeGWAS in this context and identify 24 significant IGE loci for 17 phenotypes (FDR < 10%). We observe no overlap between IGE loci and DGE loci for the same phenotype, which is consistent with the moderate genetic correlations between DGE and IGE for the same phenotype estimated using polygenic models. Finally, we fine-map seven significant IGE loci to individual genes and find supportive evidence in an experiment with a knockout model that Epha4 gives rise to IGE on stress-coping strategy and wound healing. CONCLUSIONS Our results demonstrate the potential for igeGWAS to identify IGE genes and shed light into the mechanisms of peer influence.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
- Current Address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- Microsoft Research New England, Cambridge, MA USA
| | | | - Nilgoun Farhadi
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
| | - Charlotte Montillot
- INSERM U1231 GAD Laboratory, University Bourgogne Franche-Comté, 21070 Dijon, France
| | - Binnaz Yalcin
- INSERM U1231 GAD Laboratory, University Bourgogne Franche-Comté, 21070 Dijon, France
| | - Jerome Nicod
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Current Address: The Francis Crick Institute, London, UK
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, 69120 Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
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5
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Peterson VL, Richards JB, Meyer PJ, Cabrera-Rubio R, Tripi JA, King CP, Polesskaya O, Baud A, Chitre AS, Bastiaanssen TFS, Woods LS, Crispie F, Dinan TG, Cotter PD, Palmer AA, Cryan JF. Sex-dependent associations between addiction-related behaviors and the microbiome in outbred rats. EBioMedicine 2020; 55:102769. [PMID: 32403084 PMCID: PMC7218262 DOI: 10.1016/j.ebiom.2020.102769] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Multiple factors contribute to the etiology of addiction, including genetics, sex, and a number of addiction-related behavioral traits. One behavioral trait where individuals assign incentive salience to food stimuli ("sign-trackers", ST) are more impulsive compared to those that do not ("goal-trackers", GT), as well as more sensitive to drugs and drug stimuli. Furthermore, this GT/ST phenotype predicts differences in other behavioral measures. Recent studies have implicated the gut microbiota as a key regulator of brain and behavior, and have shown that many microbiota-associated changes occur in a sex-dependent manner. However, few studies have examined how the microbiome might influence addiction-related behaviors. To this end, we sought to determine if gut microbiome composition was correlated with addiction-related behaviors determined by the GT/ST phenotype. METHODS Outbred male (N=101) and female (N=101) heterogeneous stock rats underwent a series of behavioral tests measuring impulsivity, attention, reward-learning, incentive salience, and locomotor response. Cecal microbiome composition was estimated using 16S rRNA gene amplicon sequencing. Behavior and microbiome were characterized and correlated with behavioral phenotypes. Robust sex differences were observed in both behavior and microbiome; further analyses were conducted within sex using the pre-established goal/sign-tracking (GT/ST) phenotype and partial least squares differential analysis (PLS-DA) clustered behavioral phenotype. RESULTS Overall microbiome composition was not associated to the GT/ST phenotype. However, microbial alpha diversity was significantly decreased in female STs. On the other hand, a measure of impulsivity had many significant correlations to microbiome in both males and females. Several measures of impulsivity were correlated with the genus Barnesiella in females. Female STs had notable correlations between microbiome and attentional deficient. In both males and females, many measures were correlated with the bacterial families Ruminocococcaceae and Lachnospiraceae. CONCLUSIONS These data demonstrate correlations between several addiction-related behaviors and the microbiome specific to sex.
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Affiliation(s)
- Veronica L Peterson
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Room 2.33, 2nd Floor, Western Gateway Building, Cork, Ireland
| | - Jerry B Richards
- Department of Pharmacology and Toxicology, University at Buffalo, Buffalo, NY, USA
| | - Paul J Meyer
- Department of Psychology, University at Buffalo, Buffalo, NY, USA
| | - Raul Cabrera-Rubio
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Jordan A Tripi
- Department of Psychology, University at Buffalo, Buffalo, NY, USA
| | | | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, CA, USA
| | - Amelie Baud
- Department of Psychiatry, University of California San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, CA, USA
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Room 2.33, 2nd Floor, Western Gateway Building, Cork, Ireland
| | | | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, CA, USA; Center for Microbiome Innovation, University of California San Diego, CA, USA
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Room 2.33, 2nd Floor, Western Gateway Building, Cork, Ireland.
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6
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Baud A, Aymé L, Gonnet F, Salard I, Gohon Y, Jolivet P, Brodolin K, Da Silva P, Giuliani A, Sclavi B, Chardot T, Mercère P, Roblin P, Daniel R. SOLEIL shining on the solution-state structure of biomacromolecules by synchrotron X-ray footprinting at the Metrology beamline. J Synchrotron Radiat 2017; 24:576-585. [PMID: 28452748 DOI: 10.1107/s1600577517002478] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/13/2017] [Indexed: 06/07/2023]
Abstract
Synchrotron X-ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small-angle X-ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X-ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France. This work presents X-ray footprinting of biomolecules performed for the first time at the X-ray Metrology beamline at the SOLEIL synchrotron radiation source. The installation at this beamline of a stopped-flow apparatus for sample delivery, an irradiation capillary and an automatic sample collector enabled the X-ray footprinting study of the structure of the soluble protein factor H (FH) from the human complement system as well as of the lipid-associated hydrophobic protein S3 oleosin from plant seed. Mass spectrometry analysis showed that the structural integrity of both proteins was not affected by the short exposition to the oxygen radicals produced during the irradiation. Irradiated molecules were subsequently analysed using high-resolution mass spectrometry to identify and locate oxidized amino acids. Moreover, the analyses of FH in its free state and in complex with complement C3b protein have allowed us to create a map of reactive solvent-exposed residues on the surface of FH and to observe the changes in oxidation of FH residues upon C3b binding. Studies of the solvent accessibility of the S3 oleosin show that X-ray footprinting offers also a unique approach to studying the structure of proteins embedded within membranes or lipid bodies. All the biomolecular applications reported herein demonstrate that the Metrology beamline at SOLEIL can be successfully used for synchrotron X-ray footprinting of biomolecules.
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Affiliation(s)
- A Baud
- CNRS, UMR8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, 91025 Evry, France
| | - L Aymé
- INRA, AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, 78000 Versailles, France
| | - F Gonnet
- CNRS, UMR8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, 91025 Evry, France
| | - I Salard
- CNRS, UMR8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, 91025 Evry, France
| | - Y Gohon
- INRA, AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, 78000 Versailles, France
| | - P Jolivet
- INRA, AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, 78000 Versailles, France
| | - K Brodolin
- CPBS, CNRS UMR 5236-UM1/UM2, BP 14491, 34093 Montpellier Cedex 5, France
| | - P Da Silva
- Metrology Beamline, Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - A Giuliani
- Disco Beamline, Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - B Sclavi
- LBPA, CNRS UMR 8113, ENS Cachan, 94235 Cachan, France
| | - T Chardot
- INRA, AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, 78000 Versailles, France
| | - P Mercère
- Metrology Beamline, Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - P Roblin
- INRA, UAR1008 Caractérisation et Élaboration des Produits Issus de l'Agriculture, F-44316 Nantes, France
| | - R Daniel
- CNRS, UMR8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, 91025 Evry, France
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7
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Abstract
Identifying genes and pathways that contribute to differences in neurobehavioural traits is a key goal in psychiatric research. Despite considerable success in identifying quantitative trait loci (QTLs) associated with behaviour in laboratory rodents, pinpointing the causal variants and genes is more challenging. For a long time, the main obstacle was the size of QTLs, which could encompass tens if not hundreds of genes. However, recent studies have exploited mouse and rat resources that allow mapping of phenotypes to narrow intervals, encompassing only a few genes. Here, we review these studies, showcase the rodent resources they have used and highlight the insights into neurobehavioural traits provided to date. We discuss what we see as the biggest challenge in the field - translating QTLs into biological knowledge by experimentally validating and functionally characterizing candidate genes - and propose that the CRISPR/Cas genome-editing system holds the key to overcoming this obstacle. Finally, we challenge traditional views on inbred versus outbred resources in the light of recent resource and technology developments.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan Flint
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095-1761, USA
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8
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Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O. Genetic Variation in the Social Environment Contributes to Health and Disease. PLoS Genet 2017; 13:e1006498. [PMID: 28121987 PMCID: PMC5266220 DOI: 10.1371/journal.pgen.1006498] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 11/21/2016] [Indexed: 11/29/2022] Open
Abstract
Assessing the impact of the social environment on health and disease is challenging. As social effects are in part determined by the genetic makeup of social partners, they can be studied from associations between genotypes of one individual and phenotype of another (social genetic effects, SGE, also called indirect genetic effects). For the first time we quantified the contribution of SGE to more than 100 organismal phenotypes and genome-wide gene expression measured in laboratory mice. We find that genetic variation in cage mates (i.e. SGE) contributes to variation in organismal and molecular measures related to anxiety, wound healing, immune function, and body weight. Social genetic effects explained up to 29% of phenotypic variance, and for several traits their contribution exceeded that of direct genetic effects (effects of an individual's genotypes on its own phenotype). Importantly, we show that ignoring SGE can severely bias estimates of direct genetic effects (heritability). Thus SGE may be an important source of "missing heritability" in studies of complex traits in human populations. In summary, our study uncovers an important contribution of the social environment to phenotypic variation, sets the basis for using SGE to dissect social effects, and identifies an opportunity to improve studies of direct genetic effects.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Megan K. Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jesse F. Ingels
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Casey J. Bohl
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Jacques Callebert
- AP-HP, Hôpital Lariboisière, Department of Biochemistry, INSERM U942, Paris, France
| | - Jean-Marie Launay
- AP-HP, Hôpital Lariboisière, Department of Biochemistry, INSERM U942, Paris, France
| | - Jon Krohn
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | | | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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9
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Dahl A, Iotchkova V, Baud A, Johansson Å, Gyllensten U, Soranzo N, Mott R, Kranis A, Marchini J. A multiple-phenotype imputation method for genetic studies. Nat Genet 2016; 48:466-72. [PMID: 26901065 PMCID: PMC4817234 DOI: 10.1038/ng.3513] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [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: 09/14/2015] [Accepted: 01/25/2016] [Indexed: 12/15/2022]
Abstract
Genetic association studies have yielded a wealth of biological discoveries. However, these studies have mostly analyzed one trait and one SNP at a time, thus failing to capture the underlying complexity of the data sets. Joint genotype-phenotype analyses of complex, high-dimensional data sets represent an important way to move beyond simple genome-wide association studies (GWAS) with great potential. The move to high-dimensional phenotypes will raise many new statistical problems. Here we address the central issue of missing phenotypes in studies with any level of relatedness between samples. We propose a multiple-phenotype mixed model and use a computationally efficient variational Bayesian algorithm to fit the model. On a variety of simulated and real data sets from a range of organisms and trait types, we show that our method outperforms existing state-of-the-art methods from the statistics and machine learning literature and can boost signals of association.
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Affiliation(s)
- Andrew Dahl
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Valentina Iotchkova
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK
| | - Amelie Baud
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Richard Mott
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andreas Kranis
- Aviagen, Ltd., Newbridge, UK.,Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Jonathan Marchini
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Department of Statistics, University of Oxford, Oxford, UK
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10
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Alam I, Koller DL, Cañete T, Blázquez G, Mont-Cardona C, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T. Fine mapping of bone structure and strength QTLs in heterogeneous stock rat. Bone 2015; 81:417-426. [PMID: 26297441 PMCID: PMC4641024 DOI: 10.1016/j.bone.2015.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 11/26/2022]
Abstract
We previously demonstrated that skeletal structure and strength phenotypes vary considerably in heterogeneous stock (HS) rats. These phenotypes were found to be strongly heritable, suggesting that the HS rat model represents a unique genetic resource for dissecting the complex genetic etiology underlying bone fragility. The purpose of this study was to identify and localize genes associated with bone structure and strength phenotypes using 1524 adult male and female HS rats between 17 to 20 weeks of age. Structure measures included femur length, neck width, head width; femur and lumbar spine (L3-5) areas obtained by DXA; and cross-sectional areas (CSA) at the midshaft, distal femur and femoral neck, and the 5th lumbar vertebra measured by CT. In addition, measures of strength of the whole femur and femoral neck were obtained. Approximately 70,000 polymorphic SNPs distributed throughout the rat genome were selected for genotyping, with a mean linkage disequilibrium coefficient between neighboring SNPs of 0.95. Haplotypes were estimated across the entire genome for each rat using a multipoint haplotype reconstruction method, which calculates the probability of descent at each locus from each of the 8 HS founder strains. The haplotypes were then tested for association with each structure and strength phenotype via a mixed model with covariate adjustment. We identified quantitative trait loci (QTLs) for structure phenotypes on chromosomes 3, 8, 10, 12, 17 and 20, and QTLs for strength phenotypes on chromosomes 5, 10 and 11 that met a conservative genome-wide empiric significance threshold (FDR=5%; P<3×10(-6)). Importantly, most QTLs were localized to very narrow genomic regions (as small as 0.3 Mb and up to 3 Mb), each harboring a small set of candidate genes, both novel and previously shown to have roles in skeletal development and homeostasis.
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Affiliation(s)
- Imranul Alam
- Medicine, Indiana University School of Medicine, IN, USA.
| | - Daniel L Koller
- Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
| | - Toni Cañete
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Gloria Blázquez
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Carme Mont-Cardona
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | | | - Esther Martínez-Membrives
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Sira Díaz-Morán
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Adolf Tobeña
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Alberto Fernández-Teruel
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Pernilla Stridh
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Margarita Diez
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Tomas Olsson
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Martina Johannesson
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Amelie Baud
- Wellcome Trust Center for Human Genetics, Oxford OX3 7BN, United Kingdom
| | - Michael J Econs
- Medicine, Indiana University School of Medicine, IN, USA; Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
| | - Tatiana Foroud
- Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
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11
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Alam I, Koller DL, Cañete T, Blázquez G, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T. High-resolution genome screen for bone mineral density in heterogeneous stock rat. J Bone Miner Res 2014; 29:1619-26. [PMID: 24643965 PMCID: PMC4074219 DOI: 10.1002/jbmr.2195] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 01/25/2014] [Accepted: 02/03/2014] [Indexed: 01/09/2023]
Abstract
We previously demonstrated that skeletal mass, structure, and biomechanical properties vary considerably in heterogeneous stock (HS) rat strains. In addition, we observed strong heritability for several of these skeletal phenotypes in the HS rat model, suggesting that it represents a unique genetic resource for dissecting the complex genetics underlying bone fragility. The purpose of this study was to identify and localize genes associated with bone mineral density in HS rats. We measured bone phenotypes from 1524 adult male and female HS rats between 17 and 20 weeks of age. Phenotypes included dual-energy X-ray absorptiometry (DXA) measurements for bone mineral content and areal bone mineral density (aBMD) for femur and lumbar spine (L3-L5), and volumetric BMD measurements by CT for the midshaft and distal femur, femur neck, and fifth lumbar vertebra (L5). A total of 70,000 polymorphic single-nucleotide polymorphisms (SNPs) distributed throughout the genome were selected from genotypes obtained from the Affymetrix rat custom SNPs array for the HS rat population. These SNPs spanned the HS rat genome with a mean linkage disequilibrium coefficient between neighboring SNPs of 0.95. Haplotypes were estimated across the entire genome for each rat using a multipoint haplotype reconstruction method, which calculates the probability of descent for each genotyped locus from each of the eight founder HS strains. The haplotypes were tested for association with each bone density phenotype via a mixed model with covariate adjustment. We identified quantitative trait loci (QTLs) for BMD phenotypes on chromosomes 2, 9, 10, and 13 meeting a conservative genomewide empiric significance threshold (false discovery rate [FDR] = 5%; p < 3 × 10(-6)). Importantly, most QTLs were localized to very small genomic regions (1-3 megabases [Mb]), allowing us to identify a narrow set of potential candidate genes including both novel genes and genes previously shown to have roles in skeletal development and homeostasis.
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Affiliation(s)
- Imranul Alam
- Medicine, Indiana University School of Medicine, IN, USA
| | - Daniel L. Koller
- Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
| | - Toni Cañete
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma deBarcelona, 08193-Bellaterra, Barcelona, Spain
| | - Gloria Blázquez
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma deBarcelona, 08193-Bellaterra, Barcelona, Spain
| | | | - Esther Martínez-Membrives
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma deBarcelona, 08193-Bellaterra, Barcelona, Spain
| | - Sira Díaz-Morán
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma deBarcelona, 08193-Bellaterra, Barcelona, Spain
| | - Adolf Tobeña
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma deBarcelona, 08193-Bellaterra, Barcelona, Spain
| | - Alberto Fernández-Teruel
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma deBarcelona, 08193-Bellaterra, Barcelona, Spain
| | - Pernilla Stridh
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Margarita Diez
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Tomas Olsson
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Martina Johannesson
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Amelie Baud
- Wellcome Trust Center for Human Genetics, Oxford OX3 7BN, United Kingdom
| | - Michael J. Econs
- Medicine, Indiana University School of Medicine, IN, USA
- Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
| | - Tatiana Foroud
- Medicine, Indiana University School of Medicine, IN, USA
- Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
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12
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Falak S, Schafer S, Baud A, Hummel O, Schulz H, Gauguier D, Hubner N, Osborne-Pellegrin M. Protease inhibitor 15, a candidate gene for abdominal aortic internal elastic lamina ruptures in the rat. Physiol Genomics 2014; 46:418-28. [PMID: 24790086 PMCID: PMC4060037 DOI: 10.1152/physiolgenomics.00004.2014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The inbred Brown Norway (BN) rat develops spontaneous ruptures of the internal elastic lamina (RIEL) of the abdominal aorta (AA) and iliac arteries. Prior studies with crosses of the BN/Orl RJ (susceptible) and LOU/M (resistant) showed the presence of a significant QTL on chromosome 5 and the production of congenic rats proved the involvement of this locus. In this study, we further dissected the above-mentioned QTL by creating a new panel of LOU.BN(chr5) congenic and subcongenic lines and reduced the locus to 5.2 Mb. Then we studied 1,002 heterogeneous stock (HS) rats, whose phenotyping revealed a low prevalence and high variability for RIEL. High-resolution mapping in the HS panel detected the major locus on chromosome 5 (log P > 35) and refined it to 1.4 Mb. Subsequently, RNA-seq analysis on AA of BN, congenics, and LOU revealed expression differences for only protease inhibitor 15 (Pi15) gene and a putative long intergenic noncoding RNA (lincRNA) within the linkage region. The high abundance of lincRNA with respect to reduced Pi15 expression, in conjunction with exertion of longitudinal strain, may be related to RIEL, indicating the potential importance of proteases in biological processes related to defective aortic internal elastic lamina structure. Similar mechanisms may be involved in aneurysm initiation in the human AA.
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Affiliation(s)
- Samreen Falak
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Amelie Baud
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Oliver Hummel
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Herbert Schulz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Dominique Gauguier
- Institute of Cardiometabolism and Nutrition, University Pierre & Marie Curie, Hospital Pitié Salpetrière, Paris, France; and
| | - Norbert Hubner
- Max Delbrück Center for Molecular Medicine, Berlin, Germany;
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13
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Tuncel J, Haag S, Yau ACY, Norin U, Baud A, Lönnblom E, Maratou K, Ytterberg AJ, Ekman D, Thordardottir S, Johannesson M, Gillett A, Stridh P, Jagodic M, Olsson T, Fernández-Teruel A, Zubarev RA, Mott R, Aitman TJ, Flint J, Holmdahl R. Natural polymorphisms in Tap2 influence negative selection and CD4∶CD8 lineage commitment in the rat. PLoS Genet 2014; 10:e1004151. [PMID: 24586191 PMCID: PMC3930506 DOI: 10.1371/journal.pgen.1004151] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 12/16/2013] [Indexed: 12/17/2022] Open
Abstract
Genetic variation in the major histocompatibility complex (MHC) affects CD4∶CD8 lineage commitment and MHC expression. However, the contribution of specific genes in this gene-dense region has not yet been resolved. Nor has it been established whether the same genes regulate MHC expression and T cell selection. Here, we assessed the impact of natural genetic variation on MHC expression and CD4∶CD8 lineage commitment using two genetic models in the rat. First, we mapped Quantitative Trait Loci (QTLs) associated with variation in MHC class I and II protein expression and the CD4∶CD8 T cell ratio in outbred Heterogeneous Stock rats. We identified 10 QTLs across the genome and found that QTLs for the individual traits colocalized within a region spanning the MHC. To identify the genes underlying these overlapping QTLs, we generated a large panel of MHC-recombinant congenic strains, and refined the QTLs to two adjacent intervals of ∼0.25 Mb in the MHC-I and II regions, respectively. An interaction between these intervals affected MHC class I expression as well as negative selection and lineage commitment of CD8 single-positive (SP) thymocytes. We mapped this effect to the transporter associated with antigen processing 2 (Tap2) in the MHC-II region and the classical MHC class I gene(s) (RT1-A) in the MHC-I region. This interaction was revealed by a recombination between RT1-A and Tap2, which occurred in 0.2% of the rats. Variants of Tap2 have previously been shown to influence the antigenicity of MHC class I molecules by altering the MHC class I ligandome. Our results show that a restricted peptide repertoire on MHC class I molecules leads to reduced negative selection of CD8SP cells. To our knowledge, this is the first study showing how a recombination between natural alleles of genes in the MHC influences lineage commitment of T cells. Peptides from degraded cytoplasmic proteins are transported via TAP into the endoplasmic reticulum for loading onto MHC class I molecules. TAP is encoded by Tap1 and Tap2, which in rodents are located close to the MHC class I genes. In the rat, genetic variation in Tap2 gives rise to two different transporters: a promiscuous A variant (TAP-A) and a more restrictive B variant (TAP-B). It has been proposed that the class I molecule in the DA rat (RT1-Aa) has co-evolved with TAP-A and it has been shown that RT1-Aa antigenicity is changed when co-expressed with TAP-B. To study the contribution of different allelic combinations of RT1-A and Tap2 to the variation in MHC expression and T cell selection, we generated DA rats with either congenic or background alleles in the RT1-A and Tap2 loci. We found increased numbers of mature CD8SP cells in the thymus of rats which co-expressed RT1-Aa and TAP-B. This increase of CD8 cells could be explained by reduced negative selection, but did not correlate with RT1-Aa expression levels on thymic antigen presenting cells. Thus, our results identify a crucial role of the TAP and the quality of the MHC class I repertoire in regulating T cell selection.
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Affiliation(s)
- Jonatan Tuncel
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (JT); (RH)
| | - Sabrina Haag
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anthony C. Y. Yau
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ulrika Norin
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Amelie Baud
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Erik Lönnblom
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Klio Maratou
- Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - A. Jimmy Ytterberg
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Stockholm, Sweden
- Medical Proteomics, Department of Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden and Science for Life Laboratory, Solna, Sweden
| | - Diana Ekman
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Soley Thordardottir
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Martina Johannesson
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alan Gillett
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | | | - Pernilla Stridh
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas Olsson
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Alberto Fernández-Teruel
- Medical Psychology Unit, Department of Psychiatry & Forensic Medicine, Institute of Neurosciences, School of Medicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Roman A. Zubarev
- Medical Proteomics, Department of Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden and Science for Life Laboratory, Solna, Sweden
| | - Richard Mott
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Timothy J. Aitman
- Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Jonathan Flint
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Rikard Holmdahl
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (JT); (RH)
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14
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Baud A, Guryev V, Hummel O, Johannesson M, Flint J. Erratum: Genomes and phenomes of a population of outbred rats and its progenitors. Sci Data 2014; 1:140016. [PMID: 25982460 PMCID: PMC4387707 DOI: 10.1038/sdata.2014.16] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
[This corrects the article DOI: 10.1038/sdata.2014.11.].
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15
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Baud A, Flint J, Fernandez-Teruel A, Consortium TRGSM. Identification of Genetic Variants Underlying Anxiety and Multiple Sclerosis in Heterogeneous Stock Rats. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/wjns.2014.43025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Baud A, Calderari S, Mott R, Flint J, Gauguier D. Nouvelle avancée dans notre connaissance des facteurs génétiques contribuant aux phénotypes complexes. Med Sci (Paris) 2013; 29:671-4. [DOI: 10.1051/medsci/2013296024] [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: 11/14/2022] Open
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17
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Kershaw S, Crasquin S, Li Y, Collin PY, Forel MB, Mu X, Baud A, Wang Y, Xie S, Maurer F, Guo L. Microbialites and global environmental change across the Permian-Triassic boundary: a synthesis. Geobiology 2012; 10:25-47. [PMID: 22077322 DOI: 10.1111/j.1472-4669.2011.00302.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Permian-Triassic boundary microbialites (PTBMs) are thin (0.05-15 m) carbonates formed after the end-Permian mass extinction. They comprise Renalcis-group calcimicrobes, microbially mediated micrite, presumed inorganic micrite, calcite cement (some may be microbially influenced) and shelly faunas. PTBMs are abundant in low-latitude shallow-marine carbonate shelves in central Tethyan continents but are rare in higher latitudes, likely inhibited by clastic supply on Pangaea margins. PTBMs occupied broadly similar environments to Late Permian reefs in Tethys, but extended into deeper waters. Late Permian reefs are also rich in microbes (and cements), so post-extinction seawater carbonate saturation was likely similar to the Late Permian. However, PTBMs lack widespread abundant inorganic carbonate cement fans, so a previous interpretation that anoxic bicarbonate-rich water upwelled to rapidly increase carbonate saturation of shallow seawater, post-extinction, is problematic. Preliminary pyrite framboid evidence shows anoxia in PTBM facies, but interbedded shelly faunas indicate oxygenated water, perhaps there was short-term pulsing of normally saturated anoxic water from the oxygen-minimum zone to surface waters. In Tethys, PTBMs show geographic variations: (i) in south China, PTBMs are mostly thrombolites in open shelf settings, largely recrystallised, with remnant structure of Renalcis-group calcimicrobes; (ii) in south Turkey, in shallow waters, stromatolites and thrombolites, lacking calcimicrobes, are interbedded, likely depth-controlled; and (iii) in the Middle East, especially Iran, stromatolites and thrombolites (calcimicrobes uncommon) occur in different sites on open shelves, where controls are unclear. Thus, PTBMs were under more complex control than previously portrayed, with local facies control playing a significant role in their structure and composition.
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Affiliation(s)
- S Kershaw
- Institute for the Environment, Brunel University, Uxbridge, Middlesex, UK.
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18
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Baud A, Cuoc C, Grey J, Chappaz R, Alekseev V. Seasonal variability in the gut ultrastructure of the parasitic copepod Neoergasilus japonicus (Copepoda, Poecilostomatoida). CAN J ZOOL 2004. [DOI: 10.1139/z04-149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The gut structure and ultrastructure of Neoergasilus japonicus (Harada, 1930), a copepod from the family Ergasilidae (Copepoda, Poecilostomatoida) and a parasite of fish, were compared at different periods of the life cycle: in free-living specimens in October and after attaching to fish in January and June. Differences in the depth of the intestinal epithelium were prominent and other cellular characteristics appeared seasonally variable. We relate these to changes in the physiological activity. Preliminary data from stable-isotope analyses of attached specimens suggest nutritional contribution from parasitism. The possibility of a diapause in the life cycle, as well as the relationship between the morphology of the gut and early evolutionary parasitism of N. japonicus, are discussed.
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19
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Baud A, Barthélémy RM, Nival S, Brunet M. Formation of the gut in the first two naupliar stages of Acartia clausi and Hemidiaptomus roubaui (Copepoda, Calanoida): comparative structural and ultrastructural aspects. CAN J ZOOL 2002. [DOI: 10.1139/z01-219] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, the structure and ultrastructure of the digestive system are compared in the early larval stages (nauplii I and II) of two copepod calanoid species, Acartia clausi Giesbrecht, 1889 and Hemidiaptomus roubaui Richard, 1888. The nauplii I of both species have no functional digestive tract, which is represented initially only by a blind esophageal slit and yolky endodermal cells, which fill the most part of the naupliar body, whereas at the nauplius II stage the differentiated digestive tract becomes functional. The resorption cavity corresponding to the future midgut is progressively formed in the endodermal mass during the premolt phase; it is surrounded by differentiating epithelial cells. In the ecdysial phase the foregut has associated labral glands, the midgut young R-, B-, and R'-cells of epithelium, and there is a short open hindgut.
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20
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Stahl JP, Croize J, Baud A, Bru JP, de Rougemont P, Le Noc P, Micoud M. [Treatment of neurosurgical bacterial meningitis using the combination of ceftriaxone-fosfomycin]. Pathol Biol (Paris) 1986; 34:479-82. [PMID: 3534726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
16 patients with bacterial meningitis following a neurosurgical procedure were given a combination of ceftriaxone and fosfomycin. 8 microorganism were isolated: 2 Staphylococcus epidermidis, 1 Staphylococcus aureus, 1 Neisseria meningitidis, 1 Streptococcus pneumoniae, 1 Haemophilus influenzae, 1 Serratia marcescens and 1 Aeromonas hydrophila. No pathogen was identified in the remaining cases. All of the isolated strains were susceptible to both antibiotics. In vitro, neither synergy nor antagonism were observed between the two antimicrobial agents. The acute infectious episode resolved in all patients. One relapse only was observed, in a patient with meningitis related to a ventricular shunt, and successfully treated by the same therapeutic schedule associated with removal of the tubing. Lastly, CSF concentrations of both antibiotics were assayed and found to be comparable with those reported by most author.
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21
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Gratacap B, Lachet B, Chirossel JP, Baud A, Naud G, Barbe M. [Effect of artificial ventilation on the caliber of cerebral arteries]. Agressologie 1982; 23:149-50. [PMID: 6817647] [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: 01/22/2023]
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22
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Grosset J, Glaser P, Baud A, Bismuth R. [Bacterial flora in pneumopathies and its significance in surgical resuscitation]. Lille Med 1976; 21:97-9. [PMID: 950876] [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: 12/25/2022]
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23
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Baud A, Bang S, Baud JP. [Modification of the crystallin network of apatite in dental enamel treated with a fluorated acid solution]. C R Acad Hebd Seances Acad Sci D 1967; 265:1334-6. [PMID: 4967244] [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: 01/13/2023]
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De Szendeffy, Dieupart L, Bernheim S, Baud A. Peptonised Iodine in Tuberculosis. Hospital (Lond 1886) 1911; 50:330. [PMID: 29822407 PMCID: PMC5222265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
| | | | | | - A. Baud
- Assistant de l'Euvre de la Tuberculose Humaine. Paris
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