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Tao M, Chen J, Cui C, Xu Y, Xu J, Shi Z, Yun J, Zhang J, Ou GZ, Liu C, Chen Y, Zhu ZR, Pan R, Xu S, Chen XX, Rokas A, Zhao Y, Wang S, Huang J, Shen XX. Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes. NATURE AGING 2024:10.1038/s43587-024-00641-z. [PMID: 38834883 DOI: 10.1038/s43587-024-00641-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 05/02/2024] [Indexed: 06/06/2024]
Abstract
Oxidative phosphorylation, essential for energy metabolism and linked to the regulation of longevity, involves mitochondrial and nuclear genes. The functions of these genes and their evolutionary rate covariation (ERC) have been extensively studied, but little is known about whether other nuclear genes not targeted to mitochondria evolutionarily and functionally interact with mitochondrial genes. Here we systematically examined the ERC of mitochondrial and nuclear benchmarking universal single-copy ortholog (BUSCO) genes from 472 insects, identifying 75 non-mitochondria-targeted nuclear genes. We found that the uncharacterized gene CG11837-a putative ortholog of human DIMT1-regulates insect lifespan, as its knockdown reduces median lifespan in five diverse insect species and Caenorhabditis elegans, whereas its overexpression extends median lifespans in fruit flies and C. elegans and enhances oxidative phosphorylation gene activity. Additionally, DIMT1 overexpression protects human cells from cellular senescence. Together, these data provide insights into the ERC of mito-nuclear genes and suggest that CG11837 may regulate longevity across animals.
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Affiliation(s)
- Mei Tao
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China
| | - Jiani Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chunlai Cui
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yandong Xu
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Jingxiu Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Zheyi Shi
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiaqi Yun
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Junwei Zhang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guo-Zheng Ou
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chao Liu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zeng-Rong Zhu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ronghui Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Suhong Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Xue-Xin Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Yang Zhao
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Sibao Wang
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Jianhua Huang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China.
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China.
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Kokot M, Dehghannasiri R, Baharav T, Salzman J, Deorowicz S. SPLASH2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.17.533189. [PMID: 36993432 PMCID: PMC10055302 DOI: 10.1101/2023.03.17.533189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
SPLASH is an unsupervised, reference-free, and unifying algorithm that discovers regulated sequence variation through statistical analysis of k-mer composition, subsuming many application-specific methods. Here, we introduce SPLASH2, a fast, scalable implementation of SPLASH based on an efficient k-mer counting approach. SPLASH2 enables rapid analysis of massive datasets from a wide range of sequencing technologies and biological contexts, delivering unparalleled scale and speed. The SPLASH2 algorithm unveils new biology (without tuning) in single-cell RNA-sequencing data from human muscle cells, as well as bulk RNA-seq from the entire Cancer Cell Line Encyclopedia (CCLE), including substantial unannotated alternative splicing in cancer transcriptome. The same untuned SPLASH2 algorithm recovers the BCR-ABL gene fusion, and detects circRNA sensitively and specifically, underscoring SPLASH2's unmatched precision and scalability across diverse RNA-seq detection tasks.
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Affiliation(s)
- Marek Kokot
- Department of Algorithmics and Software, Silesian University of Technology, Gliwice, Poland
| | - Roozbeh Dehghannasiri
- Department of Biomedical Data Science, Stanford University, Stanford, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, 94305, USA
| | - Tavor Baharav
- Department of Electrical Engineering, Stanford University, Stanford, 94305, USA
| | - Julia Salzman
- Department of Biomedical Data Science, Stanford University, Stanford, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, 94305, USA
- Department of Statistics (by courtesy), Stanford University, Stanford, 94305, USA
| | - Sebastian Deorowicz
- Department of Algorithmics and Software, Silesian University of Technology, Gliwice, Poland
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Guo X, Xie NB, Chen W, Ji TT, Xiong J, Feng T, Wang M, Zhang S, Gu SY, Feng YQ, Yuan BF. AlkB-Facilitated Demethylation Enables Quantitative and Site-Specific Detection of Dual Methylation of Adenosine in RNA. Anal Chem 2024; 96:847-855. [PMID: 38159051 DOI: 10.1021/acs.analchem.3c04457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
RNA molecules undergo various chemical modifications that play critical roles in a wide range of biological processes. N6,N6-Dimethyladenosine (m6,6A) is a conserved RNA modification and is essential for the processing of rRNA. To gain a deeper understanding of the functions of m6,6A, site-specific and accurate quantification of this modification in RNA is indispensable. In this study, we developed an AlkB-facilitated demethylation (AD-m6,6A) method for the site-specific detection and quantification of m6,6A in RNA. The N6,N6-dimethyl groups in m6,6A can cause reverse transcription to stall at the m6,6A site, resulting in truncated cDNA. However, we found that Escherichia coli AlkB demethylase can effectively demethylate m6,6A in RNA, generating full-length cDNA from AlkB-treated RNA. By quantifying the amount of full-length cDNA produced using quantitative real-time PCR, we were able to achieve site-specific detection and quantification of m6,6A in RNA. Using the AD-m6,6A method, we successfully detected and quantified m6,6A at position 1851 of 18S rRNA and position 937 of mitochondrial 12S rRNA in human cells. Additionally, we found that the level of m6,6A at position 1007 of mitochondrial 12S rRNA was significantly reduced in lung tissues from sleep-deprived mice compared with control mice. Overall, the AD-m6,6A method provides a valuable tool for easy, accurate, quantitative, and site-specific detection of m6,6A in RNA, which can aid in uncovering the functions of m6,6A in human diseases.
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Affiliation(s)
- Xia Guo
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Neng-Bin Xie
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Wei Chen
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Tong-Tong Ji
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Jun Xiong
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Tian Feng
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Min Wang
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Shan Zhang
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Shu-Yi Gu
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Bi-Feng Yuan
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
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4
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Chen AY, Owens MC, Liu KF. Coordination of RNA modifications in the brain and beyond. Mol Psychiatry 2023; 28:2737-2749. [PMID: 37138184 DOI: 10.1038/s41380-023-02083-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023]
Abstract
Gene expression regulation is a critical process throughout the body, especially in the nervous system. One mechanism by which biological systems regulate gene expression is via enzyme-mediated RNA modifications, also known as epitranscriptomic regulation. RNA modifications, which have been found on nearly all RNA species across all domains of life, are chemically diverse covalent modifications of RNA nucleotides and represent a robust and rapid mechanism for the regulation of gene expression. Although numerous studies have been conducted regarding the impact that single modifications in single RNA molecules have on gene expression, emerging evidence highlights potential crosstalk between and coordination of modifications across RNA species. These potential coordination axes of RNA modifications have emerged as a new direction in the field of epitranscriptomic research. In this review, we will highlight several examples of gene regulation via RNA modification in the nervous system, followed by a summary of the current state of the field of RNA modification coordination axes. In doing so, we aim to inspire the field to gain a deeper understanding of the roles of RNA modifications and coordination of these modifications in the nervous system.
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Affiliation(s)
- Anthony Yulin Chen
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, 19081, USA
| | - Michael C Owens
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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5
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Gonskikh Y, Stoute J, Shen H, Budinich K, Pingul B, Schultz K, Elashal H, Marmorstein R, Shi J, Liu KF. Noncatalytic regulation of 18 S rRNA methyltransferase DIMT1 in acute myeloid leukemia. Genes Dev 2023; 37:321-335. [PMID: 37024283 PMCID: PMC10153457 DOI: 10.1101/gad.350298.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/21/2023] [Indexed: 04/08/2023]
Abstract
Several rRNA-modifying enzymes install rRNA modifications while participating in ribosome assembly. Here, we show that 18S rRNA methyltransferase DIMT1 is essential for acute myeloid leukemia (AML) proliferation through a noncatalytic function. We reveal that targeting a positively charged cleft of DIMT1, remote from the catalytic site, weakens the binding of DIMT1 to rRNA and mislocalizes DIMT1 to the nucleoplasm, in contrast to the primarily nucleolar localization of wild-type DIMT1. Mechanistically, rRNA binding is required for DIMT1 to undergo liquid-liquid phase separation, which explains the distinct nucleoplasm localization of the rRNA binding-deficient DIMT1. Re-expression of wild-type or a catalytically inactive mutant E85A, but not the rRNA binding-deficient DIMT1, supports AML cell proliferation. This study provides a new strategy to target DIMT1-regulated AML proliferation via targeting this essential noncatalytic region.
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Affiliation(s)
- Yulia Gonskikh
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Julian Stoute
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hui Shen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Krista Budinich
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Bianca Pingul
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kollin Schultz
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Heidi Elashal
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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6
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Richter F, Plehn JE, Bessler L, Hertler J, Jörg M, Cirzi C, Tuorto F, Friedland K, Helm M. RNA marker modifications reveal the necessity for rigorous preparation protocols to avoid artifacts in epitranscriptomic analysis. Nucleic Acids Res 2022; 50:4201-4215. [PMID: 34850949 PMCID: PMC9071408 DOI: 10.1093/nar/gkab1150] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
The accurate definition of an epitranscriptome is endangered by artefacts resulting from RNA degradation after cell death, a ubiquitous yet little investigated process. By tracing RNA marker modifications through tissue preparation protocols, we identified a major blind spot from daily lab routine, that has massive impact on modification analysis in small RNAs. In particular, m6,6A and Am as co-varying rRNA marker modifications, appeared in small RNA fractions following rRNA degradation in vitro and in cellulo. Analysing mouse tissue at different time points post mortem, we tracked the progress of intracellular RNA degradation after cell death, and found it reflected in RNA modification patterns. Differences were dramatic between liver, where RNA degradation commenced immediately after death, and brain, yielding essentially undamaged RNA. RNA integrity correlated with low amounts of co-varying rRNA markers. Thus validated RNA preparations featured differentially modified tRNA populations whose information content allowed a distinction even among the related brain tissues cortex, cerebellum and hippocampus. Inversely, advanced cell death correlated with high rRNA marker content, and correspondingly little with the naïve state of living tissue. Therefore, unless RNA and tissue preparations are executed with utmost care, interpretation of modification patterns in tRNA and small RNA are prone to artefacts.
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Affiliation(s)
- Florian Richter
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Johanna E Plehn
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Larissa Bessler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Jasmin Hertler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Marko Jörg
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Cansu Cirzi
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ) 69120 Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg 69120 Heidelberg, Germany
| | - Francesca Tuorto
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance69120 Heidelberg, Germany
| | - Kristina Friedland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
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