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Xue A, Jiang L, Zhu Z, Wray NR, Visscher PM, Zeng J, Yang J. Genome-wide analyses of behavioural traits are subject to bias by misreports and longitudinal changes. Nat Commun 2021; 12:20211. [PMID: 33436567 PMCID: PMC7804181 DOI: 10.1038/s41467-020-20237-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/20/2020] [Indexed: 01/28/2023] Open
Abstract
Genome-wide association studies (GWAS) have discovered numerous genetic variants associated with human behavioural traits. However, behavioural traits are subject to misreports and longitudinal changes (MLC) which can cause biases in GWAS and follow-up analyses. Here, we demonstrate that individuals with higher disease burden in the UK Biobank (n = 455,607) are more likely to misreport or reduce their alcohol consumption levels, and propose a correction procedure to mitigate the MLC-induced biases. The alcohol consumption GWAS signals removed by the MLC corrections are enriched in metabolic/cardiovascular traits. Almost all the previously reported negative estimates of genetic correlations between alcohol consumption and common diseases become positive/non-significant after the MLC corrections. We also observe MLC biases for smoking and physical activities in the UK Biobank. Our findings provide a plausible explanation of the controversy about the effects of alcohol consumption on health outcomes and a caution for future analyses of self-reported behavioural traits in biobank data.
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Affiliation(s)
- Angli Xue
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Longda Jiang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhihong Zhu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310024, China.
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Serra C, Petruzzelli S, Seu GF, Lampis G, Pompei R. Antimicrobial activity of 5-substituted-3-amino-1,2,4-triazoles. Pharmacol Res 1994; 29:59-64. [PMID: 8202443 DOI: 10.1016/1043-6618(94)80098-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Some dyes derived from 3-amino-5-(ortho, meta, and para-pyridyl)-1,2,4-triazoles were tested for antimicrobial activity. 13 compounds showed anti-staphylococcal activity and one had anti-candida activity. Some substances had antimicrobial activity only after light irradiation.
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Affiliation(s)
- C Serra
- Istituto di Medicina Interna, Facoltà di Medicina e Chirurgia, Università degli Studi di Cagliari, Italy
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Abstract
In Escherichia coli, UV and many chemicals appear to cause mutagenesis by a process of translesion synthesis that requires some form of DNA polymerase III and the SOS-regulated proteins UmuD, UmuC and RecA. An analysis of SOS mutagenesis offers insights into the molecular basis of induced mutagenesis and into mechanisms of DNA damage tolerance.
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Affiliation(s)
- S Murli
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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4
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Livneh Z, Cohen-Fix O, Skaliter R, Elizur T. Replication of damaged DNA and the molecular mechanism of ultraviolet light mutagenesis. Crit Rev Biochem Mol Biol 1993; 28:465-513. [PMID: 8299359 DOI: 10.3109/10409239309085136] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
On UV irradiation of Escherichia coli cells, DNA replication is transiently arrested to allow removal of DNA damage by DNA repair mechanisms. This is followed by a resumption of DNA replication, a major recovery function whose mechanism is poorly understood. During the post-UV irradiation period the SOS stress response is induced, giving rise to a multiplicity of phenomena, including UV mutagenesis. The prevailing model is that UV mutagenesis occurs by the filling in of single-stranded DNA gaps present opposite UV lesions in the irradiated chromosome. These gaps can be formed by the activity of DNA replication or repair on the damaged DNA. The gap filling involves polymerization through UV lesions (also termed bypass synthesis or error-prone repair) by DNA polymerase III. The primary source of mutations is the incorporation of incorrect nucleotides opposite lesions. UV mutagenesis is a genetically regulated process, and it requires the SOS-inducible proteins RecA, UmuD, and UmuC. It may represent a minor repair pathway or a genetic program to accelerate evolution of cells under environmental stress conditions.
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Affiliation(s)
- Z Livneh
- Department of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
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Bordin F, Dall'Acqua F, Guiotto A. Angelicins, angular analogs of psoralens: chemistry, photochemical, photobiological and phototherapeutic properties. Pharmacol Ther 1991; 52:331-63. [PMID: 1820581 DOI: 10.1016/0163-7258(91)90031-g] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Angelicin and some of its derivatives are naturally occuring compounds which show interesting photobiological properties. In this review various aspects of angelicin and its derivatives have been reported. The natural occurrence and the chemical synthesis both of naturally occurring and synthetic angelicins have been reviewed. Photochemical and photophysical properties of angelicins have been considered with particular reference to the capacity to generate active forms of oxygen, photoreactions with nucleic acids, proteins and unsaturated fatty acids. Photobiological effects have been considered: skin phototoxicity, antiproliferative effects, genotoxicity, ability to induce hemolysis in erythrocytes, inactivation of prokaryotic and eukaryotic microorganism and of viruses. The ability of some angelicins to induce photocarcinogenesis has been reviewed as well as in the activity as photochemotherapeutic agents.
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Affiliation(s)
- F Bordin
- Department of Pharmaceutical Science of Padua University, Centro di Studio sulla Chimica del Farmaco e dei Prodotti Biologicamente Attivi del C.N.R., Italy
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Moustacchi E. Photomutagenicity Induced by Psoralens: Mechanism of Repair and Photomutagenicity. Arch Toxicol 1988. [DOI: 10.1007/978-3-642-73113-6_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Orrego C, Eisenstadt E. An inducible pathway is required for mutagenesis in Salmonella typhimurium LT2. J Bacteriol 1987; 169:2885-8. [PMID: 3294811 PMCID: PMC212206 DOI: 10.1128/jb.169.6.2885-2888.1987] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
UV mutability of Salmonella typhimurium LT2 was eliminated in the presence of a multicopy plasmid carrying the Escherichia coli lexA+ gene. This result suggests that inducible, SOS-like functions are required for UV mutagenesis in S. typhimurium. S. typhimurium strains carrying either point or deletion mutations in topA had previously been shown to lose their mutability by UV or methyl methanesulfonate (K. Overbye and P. Margolin, J. Bacteriol. 146:170-178, 1981; K. Overbye, S. M. Basu, and P. Margolin, Cold Spring Harbor Symp. Quant. Biol. 47:785-791, 1983). Mitomycin C induction of the phi(mucB'-lacZ') fusion (a DNA damage-inducible locus carried on plasmid pSE205) in S. typhimurium topA was normal, suggesting that RecA is activated in topA mutants. These observations lead us to deduce that S. typhimurium has at least one DNA damage-inducible locus in addition to recA that is required for UV mutability.
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Drake JW. Photodynamic inactivation and mutagenesis by angelicin (isopsoralen) or thiopyronin (methylene red) in wild-type and repair-deficient strains of bacteriophage T4. J Bacteriol 1985; 162:1311-3. [PMID: 3997779 PMCID: PMC215922 DOI: 10.1128/jb.162.3.1311-1313.1985] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Photodynamic inactivation of bacteriophage T4 particles, mediated by either angelicin or thiopyronin, is enhanced by defects in the T4 uvsW-uvsX-uvsY postreplication repair system but not by a defect in the denV pyrimidine-dimer-excision system. There was no evidence for functional interactions between the two repair systems. As observed previously with 8-methoxypsoralen, photodynamic mutagenesis with angelicin is abolished by defects in the uvsW-uvsX-uvsY system.
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