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Biswas S, Hilser JR, Woodward NC, Wang Z, Gukasyan J, Nemet I, Schwartzman WS, Huang P, Han Y, Fouladian Z, Charugundla S, Spencer NJ, Pan C, Tang WW, Lusis AJ, Hazen SL, Hartiala JA, Allayee H. Effect of Genetic and Dietary Perturbation of Glycine Metabolism on Atherosclerosis in Humans and Mice. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.08.23299748. [PMID: 38168321 PMCID: PMC10760269 DOI: 10.1101/2023.12.08.23299748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Objective Epidemiological and genetic studies have reported inverse associations between circulating glycine levels and risk of coronary artery disease (CAD). However, these findings have not been consistently observed in all studies. We sought to evaluate the causal relationship between circulating glycine levels and atherosclerosis using large-scale genetic analyses in humans and dietary supplementation experiments in mice. Methods Serum glycine levels were evaluated for association with prevalent and incident CAD in the UK Biobank. A multi-ancestry genome-wide association study (GWAS) meta-analysis was carried out to identify genetic determinants for circulating glycine levels, which were then used to evaluate the causal relationship between glycine and risk of CAD by Mendelian randomization (MR). A glycine feeding study was carried out with atherosclerosis-prone apolipoprotein E deficient (ApoE-/-) mice to determine the effects of increased circulating glycine levels on amino acid metabolism, metabolic traits, and aortic lesion formation. Results Among 105,718 subjects from the UK Biobank, elevated serum glycine levels were associated with significantly reduced risk of prevalent CAD (Quintile 5 vs. Quintile 1 OR=0.76, 95% CI 0.67-0.87; P<0.0001) and incident CAD (Quintile 5 vs. Quintile 1 HR=0.70, 95% CI 0.65-0.77; P<0.0001) in models adjusted for age, sex, ethnicity, anti-hypertensive and lipid-lowering medications, blood pressure, kidney function, and diabetes. A meta-analysis of 13 GWAS datasets (total n=230,947) identified 61 loci for circulating glycine levels, of which 26 were novel. MR analyses provided modest evidence that genetically elevated glycine levels were causally associated with reduced systolic blood pressure and risk of type 2 diabetes, but did provide evidence for an association with risk of CAD. Furthermore, glycine-supplementation in ApoE-/- mice did not alter cardiometabolic traits, inflammatory biomarkers, or development of atherosclerotic lesions. Conclusions Circulating glycine levels were inversely associated with risk of prevalent and incident CAD in a large population-based cohort. While substantially expanding the genetic architecture of circulating glycine levels, MR analyses and in vivo feeding studies in humans and mice, respectively, did not provide evidence that the clinical association of this amino acid with CAD represents a causal relationship, despite being associated with two correlated risk factors.
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Affiliation(s)
- Subarna Biswas
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - James R. Hilser
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Nicholas C. Woodward
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Zeneng Wang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
- Department of Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Janet Gukasyan
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Ina Nemet
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
- Department of Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195
| | - William S. Schwartzman
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Pin Huang
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Yi Han
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Zachary Fouladian
- Department of Medicine, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
| | - Sarada Charugundla
- Department of Medicine, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
| | - Neal J. Spencer
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Calvin Pan
- Department of Human Genetics, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
| | - W.H. Wilson Tang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
- Department of Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Aldons J. Lusis
- Department of Medicine, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
- Department of Human Genetics, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
- Department of Microbiology, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, Los Angeles, CA 90095
| | - Stanley L. Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
- Department of Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH 44195
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Jaana A. Hartiala
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Hooman Allayee
- Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
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2
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Sun K, Han Y, Li J, Yu S, Huang Y, Zhang Y, Reilly J, Tu J, Gao P, Jia D, Chen X, Hu H, Ren M, Li P, Luo J, Ren X, Zhang X, Shu X, Liu F, Liu M, Tang Z. The splicing factor DHX38 enables retinal development through safeguarding genome integrity. iScience 2023; 26:108103. [PMID: 37867960 PMCID: PMC10589891 DOI: 10.1016/j.isci.2023.108103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/03/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
DEAH-Box Helicase 38 (DHX38) is a pre-mRNA splicing factor and also a disease-causing gene of autosomal recessive retinitis pigmentosa (arRP). The role of DHX38 in the development and maintenance of the retina remains largely unknown. In this study, by using the dhx38 knockout zebrafish model, we demonstrated that Dhx38 deficiency causes severe differentiation defects and apoptosis of retinal progenitor cells (RPCs) through disrupted mitosis and increased DNA damage. Furthermore, we found a significant accumulation of R-loops in the dhx38-deficient RPCs and human cell lines. Finally, we found that DNA replication stress is the prerequisite for R-loop-induced DNA damage in the DHX38 knockdown cells. Taken together, our study demonstrates a necessary role of DHX38 in the development of retina and reveals a DHX38/R-loop/replication stress/DNA damage regulatory axis that is relatively independent of the known functions of DHX38 in mitosis control.
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Affiliation(s)
- Kui Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Jingzhen Li
- Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Shanshan Yu
- Institute of Visual Neuroscience and Stem Cell Engineering, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Yangjun Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Jamas Reilly
- Department of Life Sciences, Glasgow Caledonian University, Glasgow, Scotland G4 0BA, UK
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Xiang Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Hualei Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Mengmeng Ren
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Pei Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Jiong Luo
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Xianqin Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Xinhua Shu
- Department of Life Sciences, Glasgow Caledonian University, Glasgow, Scotland G4 0BA, UK
| | - Fei Liu
- Institute of Hydrobiology, Chinese Academy of Science, Wuhan 430072, P.R. China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
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Gambelli A, Ferrando A, Boncristiani C, Schoeftner S. Regulation and function of R-loops at repetitive elements. Biochimie 2023; 214:141-155. [PMID: 37619810 DOI: 10.1016/j.biochi.2023.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the human genome, including repetitive regions, hold transcriptional activity. This anticipates that R-loops management plays a central role for the regulation and integrity of genomes. This function is expected to have a particular relevance for repetitive sequences that make up to 75% of the human genome. Here, we review the impact of R-loops on the function and stability of repetitive regions such as centromeres, telomeres, rDNA arrays, transposable elements and triplet repeat expansions and discuss their relevance for associated pathological conditions.
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Affiliation(s)
- Alice Gambelli
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Alessandro Ferrando
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Chiara Boncristiani
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Stefan Schoeftner
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy.
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Tu J, Yu S, Li J, Ren M, Zhang Y, Luo J, Sun K, Lv Y, Han Y, Huang Y, Ren X, Jiang T, Tang Z, Williams MTS, Lu Q, Liu M. Dhx38 is required for the maintenance and differentiation of erythro-myeloid progenitors and hematopoietic stem cells by alternative splicing. Development 2022; 149:276218. [DOI: 10.1242/dev.200450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 07/21/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Mutations that occur in RNA-splicing machinery may contribute to hematopoiesis-related diseases. How splicing factor mutations perturb hematopoiesis, especially in the differentiation of erythro-myeloid progenitors (EMPs), remains elusive. Dhx38 is a pre-mRNA splicing-related DEAH box RNA helicase, for which the physiological functions and splicing mechanisms during hematopoiesis currently remain unclear. Here, we report that Dhx38 exerts a broad effect on definitive EMPs as well as the differentiation and maintenance of hematopoietic stem and progenitor cells (HSPCs). In dhx38 knockout zebrafish, EMPs and HSPCs were found to be arrested in mitotic prometaphase, accompanied by a ‘grape’ karyotype, owing to the defects in chromosome alignment. Abnormal alternatively spliced genes related to chromosome segregation, the microtubule cytoskeleton, cell cycle kinases and DNA damage were present in the dhx38 mutants. Subsequently, EMPs and HSPCs in dhx38 mutants underwent P53-dependent apoptosis. This study provides novel insights into alternative splicing regulated by Dhx38, a process that plays a crucial role in the proliferation and differentiation of fetal EMPs and HSPCs.
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Affiliation(s)
- Jiayi Tu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Shanshan Yu
- Institute of Visual Neuroscience and Stem Cell Engineering, College of Life Sciences and Health, Wuhan University of Science and Technology 2 , Wuhan, Hubei 430065 , P.R. China
| | - Jingzhen Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Mengmeng Ren
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yangjun Zhang
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology 3 , Wuhan 430030 , P.R. China
| | - Jiong Luo
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yuexia Lv
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Tao Jiang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Mark Thomas Shaw Williams
- Charles Oakley Laboratories 4 , Department of Biological and Biomedical Sciences , , Glasgow G4 0BA , UK
- Glasgow Caledonian University 4 , Department of Biological and Biomedical Sciences , , Glasgow G4 0BA , UK
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology 1 , Wuhan 430074 , P.R. China
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Arunkumar G, Melters DP. Centromeric Transcription: A Conserved Swiss-Army Knife. Genes (Basel) 2020; 11:E911. [PMID: 32784923 PMCID: PMC7463856 DOI: 10.3390/genes11080911] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/11/2022] Open
Abstract
In most species, the centromere is comprised of repetitive DNA sequences, which rapidly evolve. Paradoxically, centromeres fulfill an essential function during mitosis, as they are the chromosomal sites wherein, through the kinetochore, the mitotic spindles bind. It is now generally accepted that centromeres are transcribed, and that such transcription is associated with a broad range of functions. More than a decade of work on this topic has shown that centromeric transcripts are found across the eukaryotic tree and associate with heterochromatin formation, chromatin structure, kinetochore structure, centromeric protein loading, and inner centromere signaling. In this review, we discuss the conservation of small and long non-coding centromeric RNAs, their associations with various centromeric functions, and their potential roles in disease.
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Affiliation(s)
| | - Daniël P. Melters
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA;
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6
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Centromeric Non-Coding RNAs: Conservation and Diversity in Function. Noncoding RNA 2020; 6:ncrna6010004. [PMID: 31963472 PMCID: PMC7151564 DOI: 10.3390/ncrna6010004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/16/2019] [Accepted: 01/15/2020] [Indexed: 12/13/2022] Open
Abstract
Chromosome segregation is strictly regulated for the proper distribution of genetic material to daughter cells. During this process, mitotic chromosomes are pulled to both poles by bundles of microtubules attached to kinetochores that are assembled on the chromosomes. Centromeres are specific regions where kinetochores assemble. Although these regions were previously considered to be silent, some experimental studies have demonstrated that transcription occurs in these regions to generate non-coding RNAs (ncRNAs). These centromeric ncRNAs (cenRNAs) are involved in centromere functions. Here, we describe the currently available information on the functions of cenRNAs in several species.
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