1
|
Lee DG, Kim EJ, Kim YH, Cho WC, Cho Y, Han JY, Kim SJ, Park JH, Lee J, Kim E, Jung JY. Mutational analysis of 23 autosomal short tandem repeats based on trio paternity testing in the Korean population. Leg Med (Tokyo) 2024; 69:102447. [PMID: 38640874 DOI: 10.1016/j.legalmed.2024.102447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 04/15/2024] [Indexed: 04/21/2024]
Abstract
This study aimed to estimate A-STR mutation rates in 2,317 Korean parent-child trios by examining 20 Combined DNA Index System (CODIS) core loci (D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, CSF1PO, FGA, TH01, TPOX, vWA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045) and three non-CODIS loci (Penta E, Penta D, and SE33). Locus-specific mutation rate estimates varied from 0.00 to 8.63 × 10-3 per generation, with an average mutation rate of 1.62 × 10-3 (95 % CI, 1.39-1.88 × 10-3). We also combined data from previous studies to obtain comprehensive genetic values for the Korean population, and the average mutation rate was 1.59 × 10-3 (95 % CI, 1.38-1.82 × 10-3). Single-step mutations (95.69 %) and double-step mutations (3.35 %) were observed in the mutation pattern analysis, and cases expected to have multi-step mutations (0.96 %) were also observed. Large-sized alleles exhibited more loss mutations than gain mutations, and paternal mutations (62.68 %) were more frequently observed than maternal mutations (19.62 %). The calculated values and features of the 23 A-STRs explored in this study are expected to play a crucial role in establishing criteria for forensic genetic interpretation.
Collapse
Affiliation(s)
- Dong Gyu Lee
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea; Department of Forensic Sciences, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do 16419, Republic of Korea
| | - Eun Jin Kim
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Yoo Hee Kim
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Woo-Cheol Cho
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Yoonjung Cho
- DNA Analysis Division, National Forensic Service Gwangju Institute, 60-15, Nanosandan 5-ro, Nam-myeon, Jangseong-gun, Gwangju 57248, Republic of Korea
| | - Ji Yeon Han
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Su Jin Kim
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Ji Hwan Park
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea
| | - Jinmyung Lee
- DNA Analysis Division, National Forensic Service Seoul Institute, 139, Jiyang-ro, Yangcheon-gu, Seoul 08036, Republic of Korea
| | - Eungsoo Kim
- Forensic DNA Division, National Forensic Service, 10, Ipchun-ro, Wonju-si, Gangwon-do 26460, Republic of Korea.
| | - Ju Yeon Jung
- Forensic DNA Section, National Forensic Service Jeju Branch, 221, Cheomdan-ro, Jeju-si, Jeju-do 63309, Republic of Korea; Department of Forensic Medicine, Seoul National University College of Medicine, 103, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea.
| |
Collapse
|
2
|
Puch-Solis R, Pope S, Tully G. Considerations on the application of a mutation model for Y-STR interpretation. Sci Justice 2024; 64:180-192. [PMID: 38431375 DOI: 10.1016/j.scijus.2024.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 03/05/2024]
Abstract
If Y-STR profiling is to be more effective in criminal casework, the methods used to evaluate evidential weight require improvement. Many forensic scientists assign an evidential weight by estimating the number of times a Y-STR profile obtained from a questioned sample has been observed in YHRD datasets. More sophisticated models have been suggested but not yet implemented into routine casework, e.g. Andersen & Balding [1]. Mutation is inherent to STR meiosis (or inheritance) and is encountered in practice. We evaluated a mutation model that can be incorporated into a method for assigning evidential weight to Y-STR profiles, an essential part of bringing any method into practice. Since an important part of implementation to casework is communication, the article is written in an accessible format for practitioners as well as statisticians. The mutation component within the MUTEA model by Willems et al. [2] incorporates the potential for multistep mutations and a tendency for alleles to revert towards a central length, reflecting observed mutation data, e.g. [3]. We have estimated the parameters in this model and in a simplified symmetric version of this model, using sequence data from father/son pairs [4] and deep-rooted pedigrees [5]. Both datasets contain multistep mutations, which may have an effect on models based on simulations [1]. We introduce Beta-Binomial and Beta-Geometric conjugate analyses for estimating rate and step parameters for the mutation models presented here, which require only summations and multiplications. We proved mathematically that the parameters can be estimated independently. We show the importance of reporting the variability of the parameters and not only a point estimate. The parameters can be easily incorporated into statistical models, and updated sequentially as more data becomes available. We recommend fuller publication of data to enable the development and evaluation of a wider range of mutation models.
Collapse
Affiliation(s)
- Roberto Puch-Solis
- Leverhulme Research Centre for Forensic Science, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Susan Pope
- Principal Forensic Services, 34 Southborough Road, Bromley, Kent BR1 2EB, United Kingdom
| | - Gillian Tully
- King's Forensics, King's College London, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom
| |
Collapse
|
3
|
Zein-Eddine R, Hak F, Le Meur A, Genestet C, Dumitrescu O, Guyeux C, Senelle G, Sola C, Refrégier G. The paradoxes of Mycobacterium tuberculosis molecular evolution and consequences for the inference of tuberculosis emergence date. Tuberculosis (Edinb) 2023; 143S:102378. [PMID: 38012921 DOI: 10.1016/j.tube.2023.102378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 11/29/2023]
Abstract
The date of Mycobacterium tuberculosis complex emergence has been the subject of long debates. New studies joining archaeological efforts with sequencing methods raise high hopes for solving whether this emergence is closer to 70,000 or to 6000 years before present. Inferring the date of emergence of this pathogen based on sequence data requires a molecular clock. Several clocks inferred from different types of loci and/or different samples, using both sound reasoning and reliable data, are actually very different, which we refer to as the paradoxes of M. tuberculosis molecular evolution. After having presented these paradoxes, we will remind the limits of the molecular clocks used in the different studies such as the assumption of homogeneous substitution rate. We will then review recent results that shed new light on the characteristics of M. tuberculosis molecular evolution: traces of diverse selection pressures, the impact of host dynamics, etc. We provide some ideas on what to do next to get nearer to a reliable dating of Mycobacterium tuberculosis complex emergence. Among them, the collection of additional remains from ancient tuberculosis seems still essential.
Collapse
Affiliation(s)
- R Zein-Eddine
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Institut National de la Santé et de la Recherche Médicale: U1182, Centre National de la Recherche Scientifique: UMR7645, France
| | - F Hak
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
| | - A Le Meur
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
| | - C Genestet
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - O Dumitrescu
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - C Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000, Besançon, France
| | - G Senelle
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000, Besançon, France
| | - C Sola
- Université de Paris, IAME, UMR1137, INSERM, Paris, France; AP-HP, GHU Nord, Service de mycobactériologie spécialisée et de référence, Paris, France; Université Paris-Saclay, Saint-Aubin, France
| | - G Refrégier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France.
| |
Collapse
|
4
|
Zheng Q. Methods for two nonstandard problems arising from the Luria-Delbrück experiment. Genetica 2023; 151:369-373. [PMID: 38010477 DOI: 10.1007/s10709-023-00200-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
The fluctuation experiment, devised by Luria and Delbrück in 1943, remains the method of choice for measuring microbial mutation rates in the laboratory. While most inference problems commonly encountered in a fluctuation experiment can be tackled by existing standard algorithms, investigators from time to time run into nonstandard problems not amenable to any existing algorithms. A major obstacle to solving these nonstandard problems is the construction of confidence intervals for mutation rates. This note describes methods for two important categories of nonstandard problems, namely, pooling data from separate experiments and analyzing grouped mutant count data, focusing on the construction of likelihood ratio confidence intervals. In addition to illustrative examples using real-world data, simulation results are presented to help assess the proposed methods.
Collapse
Affiliation(s)
- Qi Zheng
- Department of Epidemiology and Biostatistics, Texas A &M School of Public Health, College Station, TX, 77843, USA.
| |
Collapse
|
5
|
Chung WH. Signification and Application of Mutator and Antimutator Phenotype-Induced Genetic Variations in Evolutionary Adaptation and Cancer Therapeutics. J Microbiol 2023; 61:1013-1024. [PMID: 38100001 DOI: 10.1007/s12275-023-00091-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 01/11/2024]
Abstract
Mutations present a dichotomy in their implications for cellular processes. They primarily arise from DNA replication errors or damage repair processes induced by environmental challenges. Cumulative mutations underlie genetic variations and drive evolution, yet also contribute to degenerative diseases such as cancer and aging. The mutator phenotype elucidates the heightened mutation rates observed in malignant tumors. Evolutionary adaptation, analogous to bacterial and eukaryotic systems, manifests through mutator phenotypes during changing environmental conditions, highlighting the delicate balance between advantageous mutations and their potentially detrimental consequences. Leveraging the genetic tractability of Saccharomyces cerevisiae offers unique insights into mutator phenotypes and genome instability akin to human cancers. Innovative reporter assays in yeast model organisms enable the detection of diverse genome alterations, aiding a comprehensive analysis of mutator phenotypes. Despite significant advancements, our understanding of the intricate mechanisms governing spontaneous mutation rates and preserving genetic integrity remains incomplete. This review outlines various cellular pathways affecting mutation rates and explores the role of mutator genes and mutation-derived phenotypes, particularly prevalent in malignant tumor cells. An in-depth comprehension of mutator and antimutator activities in yeast and higher eukaryotes holds promise for effective cancer control strategies.
Collapse
Affiliation(s)
- Woo-Hyun Chung
- College of Pharmacy, Duksung Women's University, Seoul, 01369, Republic of Korea.
- Innovative Drug Center, Duksung Women's University, Seoul, 01369, Republic of Korea.
| |
Collapse
|
6
|
Mani S, Tlusty T. Gene birth in a model of non-genic adaptation. BMC Biol 2023; 21:257. [PMID: 37957718 PMCID: PMC10644530 DOI: 10.1186/s12915-023-01745-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Over evolutionary timescales, genomic loci can switch between functional and non-functional states through processes such as pseudogenization and de novo gene birth. Particularly, de novo gene birth is a widespread process, and many examples continue to be discovered across diverse evolutionary lineages. However, the general mechanisms that lead to functionalization are poorly understood, and estimated rates of de novo gene birth remain contentious. Here, we address this problem within a model that takes into account mutations and structural variation, allowing us to estimate the likelihood of emergence of new functions at non-functional loci. RESULTS Assuming biologically reasonable mutation rates and mutational effects, we find that functionalization of non-genic loci requires the realization of strict conditions. This is in line with the observation that most de novo genes are localized to the vicinity of established genes. Our model also provides an explanation for the empirical observation that emerging proto-genes are often lost despite showing signs of adaptation. CONCLUSIONS Our work elucidates the properties of non-genic loci that make them fertile for adaptation, and our results offer mechanistic insights into the process of de novo gene birth.
Collapse
Affiliation(s)
- Somya Mani
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Republic of Korea.
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Departments of Physics and Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| |
Collapse
|
7
|
El-Haddad K, Adhikari TM, Tu ZJ, Cheng YW, Leng X, Zhang X, Rhoads D, Ko JS, Worley S, Li J, Rubin BP, Esper FP. Intra-host mutation rate of acute SARS-CoV-2 infection during the initial pandemic wave. Virus Genes 2023; 59:653-661. [PMID: 37310519 DOI: 10.1007/s11262-023-02011-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2 mutation is minimized through a proofreading function encoded by NSP-14. Most estimates of the SARS-CoV-2 mutation rate are derived from population based sequence data. Our understanding of SARS-CoV-2 evolution might be enhanced through analysis of intra-host viral mutation rates in specific populations. Viral genome analysis was performed between paired samples and mutations quantified at allele frequencies (AF) ≥ 0.25, ≥ 0.5 and ≥ 0.75. Mutation rate was determined employing F81 and JC69 evolution models and compared between isolates with (ΔNSP-14) and without (wtNSP-14) non-synonymous mutations in NSP-14 and by patient comorbidity. Forty paired samples with median interval of 13 days [IQR 8.5-20] were analyzed. The estimated mutation rate by F81 modeling was 93.6 (95%CI 90.8-96.4], 40.7 (95%CI 38.9-42.6) and 34.7 (95%CI 33.0-36.4) substitutions/genome/year at AF ≥ 0.25, ≥ 0.5, ≥ 0.75 respectively. Mutation rate in ΔNSP-14 were significantly elevated at AF ≥ 0.25 vs wtNSP-14. Patients with immune comorbidities had higher mutation rate at all allele frequencies. Intra-host SARS-CoV-2 mutation rates are substantially higher than those reported through population analysis. Virus strains with altered NSP-14 have accelerated mutation rate at low AF. Immunosuppressed patients have elevated mutation rate at all AF. Understanding intra-host virus evolution will aid in current and future pandemic modeling.
Collapse
Affiliation(s)
- Kim El-Haddad
- Center for Pediatric Infectious Disease, Cleveland Clinic Children's, R3, 9500 Euclid Avenue, Cleveland, 44195 , OH, USA.
| | - Thamali M Adhikari
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Zheng Jin Tu
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yu-Wei Cheng
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaoyi Leng
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Xiangyi Zhang
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Daniel Rhoads
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jennifer S Ko
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sarah Worley
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Jing Li
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Frank P Esper
- Center for Pediatric Infectious Disease, Cleveland Clinic Children's, R3, 9500 Euclid Avenue, Cleveland, 44195 , OH, USA.
| |
Collapse
|
8
|
Poulsgaard GA, Sørensen SG, Juul RI, Nielsen MM, Pedersen JS. Sequence dependencies and mutation rates of localized mutational processes in cancer. Genome Med 2023; 15:63. [PMID: 37592287 PMCID: PMC10436389 DOI: 10.1186/s13073-023-01217-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Cancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show nucleotide sequence and functional region preferences. As a result, some sequence contexts mutate at much higher rates than others, with additional variation found between functional regions. Mutational hotspots, with recurrent mutations across cancer samples, represent genomic positions with elevated mutation rates, often caused by highly localized mutational processes. METHODS We count the 11-mer genomic sequences across the genome, and using the PCAWG set of 2583 pan-cancer whole genomes, we associate 11-mers with mutational signatures, hotspots of single nucleotide variants, and specific genomic regions. We evaluate the mutation rates of individual and combined sets of 11-mers and derive mutational sequence motifs. RESULTS We show that hotspots generally identify highly mutable sequence contexts. Using these, we show that some mutational signatures are enriched in hotspot sequence contexts, corresponding to well-defined sequence preferences for the underlying localized mutational processes. This includes signature 17b (of unknown etiology) and signatures 62 (POLE deficiency), 7a (UV), and 72 (linked to lymphomas). In some cases, the mutation rate and sequence preference increase further when focusing on certain genomic regions, such as signature 62 in transcribed regions, where the mutation rate is increased up to 9-folds over cancer type and mutational signature average. CONCLUSIONS We summarize our findings in a catalog of localized mutational processes, their sequence preferences, and their estimated mutation rates.
Collapse
Affiliation(s)
- Gustav Alexander Poulsgaard
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Simon Grund Sørensen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Randi Istrup Juul
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Morten Muhlig Nielsen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Jakob Skou Pedersen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark.
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
- Bioinformatics Research Centre (BiRC), Aarhus University, University City 81, Building 1872, 3Rd Floor, 8000, Aarhus C, Denmark.
| |
Collapse
|
9
|
Gazali FM, Wijayanti N, Hakim MS, Supriyati E, Arguni E, Daniwijaya MEW, Nuryastuti T, Nuhamunada M, Nabilla R, Haryana SM, Wibawa T. The high mutation rate at the D614G hotspot-furin cleavage site region increases the priming efficiency of the Spike protein by furin protease: analysis of Indonesian SARS-CoV-2 G614 variants obtained during the early COVID-19 pandemic. Virusdisease 2023:1-10. [PMID: 37363361 PMCID: PMC10231289 DOI: 10.1007/s13337-023-00827-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
D614G mutation plays a significant role in the transmissibility of SARS-CoV-2. Identification of other mutations related to D614G mutation within the Spike protein is pivotal as they might contribute to the pathogenicity of SARS-CoV-2. This study aims to analyze the mutation rate of furin cleavage site (FCS) region of Indonesian origin SARS-CoV-2 and to predict the effect of mutation against Spike priming efficiency by furin. A total of 375 sequences of Indonesian isolates obtained during the early pandemic were used for mutation analysis. Mutation analysis includes mutation pattern, variability, frequency of mutation, amino acid conservation, and mutation rate. The effect of mutation against Spike priming efficiency by furin protease from eight sequences with mutation in the FCS region was analyzed by protein-protein docking. We showed that mutations related to the G614 variant were increasing through time, in contrast to the D614 variant. The FCS region at the position 675-692 contained the most variable (66.67%) as well as the highest mutation frequency (85.92%) and has been observed to be the hotspot mutations linked to the D614G mutation. The D614G hotspot-FCS region (residue 600-700) had the highest amino acid change per site (20.8%) as well as the highest mutation rate as 1.34 × 10-2 substitution per site per year (95% CI 1.79 × 10-3-2.74 × 10-2), compared with other Spike protein regions. Mutations in the FCS region were the most common mutation found after the D614G mutation. These mutations were predicted to increase the Spike priming efficiency by furin. Thus, this study elucidates the importance of D614G mutation to other mutations located in the FCS region and their significance to Spike priming efficiency by furin. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00827-w.
Collapse
Affiliation(s)
- Faris Muhammad Gazali
- Master Program in Biotechnology, Postgraduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nastiti Wijayanti
- Animal Physiology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Matin Nuhamunada
- Biotechnology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rahma Nabilla
- Graduate Program in Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology and Cell Biology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| |
Collapse
|
10
|
Lee DG, Kim SJ, Cho WC, Cho Y, Park JH, Lee J, Jung JY. Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father-son pairs. Forensic Sci Int Genet 2023; 65:102875. [PMID: 37084624 DOI: 10.1016/j.fsigen.2023.102875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/10/2023] [Accepted: 04/16/2023] [Indexed: 04/23/2023]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic genetics, and accurate knowledge of mutation rates at Y-STR loci is essential in kinship analysis. The main aim of this study was to estimate Y-STR mutation rates in Korean males. To obtain locus-specific mutations and haplotypes at 23 Y-STRs, we analyzed samples from 620 Korean father-son pairs. In addition, we also analyzed 476 unrelated individuals using the PowerPlex® Y23 System, with the aim of augmenting the available data for the Korean population. The PowerPlex® Y23 system facilitates analysis of the 23 Y-STR loci (DYS576, DYS570, DYS458, DYS635, DYS389 II, DYS549, DYS385, DYS481, DYS439, DYS456, DYS389 I, DYS19, DYS393, DYS391, DYS533, DYS437, DYS390, Y GATA H4, DYS448, DYS438, DYS392, and DYS643). Locus-specific mutation rate estimates varied from 0.00 to 8.06 × 10-3 per generation, with an average mutation rate of 2.17 × 10-3 (95% CI, 1.5-3.1 × 10-3). To obtain comprehensive genetic values for the Korean population, we combined data obtained in this study with previously reported values, thereby enabling us to estimate the locus-specific mutation rates regarding 22,711 allele transmissions. By combining these data, we obtained an overall average mutation rate of 2.91 × 10-3 (95% CI, 2.3-3.7 × 10-3). In addition, among the 476 unrelated Korean males, we detected 467 different haplotypes, with an overall haplotype diversity value of 0.9999. By extracting haplotypes of Y-STRs described in previous literature on 23 Y-STR reported in Korea, we obtained gene diversities for 1133 Korean individuals. We believe that the values and characteristics of the 23 Y-STRs analyzed in this study will contribute to establishing criteria for forensic genetic interpretation, including kinship analysis.
Collapse
Affiliation(s)
- Dong Gyu Lee
- Forensic DNA Division, National Forensic Service, Wonju, South Korea; Department of forensics Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Su Jin Kim
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Woo-Cheol Cho
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Yoonjung Cho
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Ji Hwan Park
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Jinmyung Lee
- DNA Analysis Division, National Forensic Service Busan Institute, Busan, South Korea
| | - Ju Yeon Jung
- Forensic DNA Section, National Forensic Service Jeju Branch, Jeju, South Korea; Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea.
| |
Collapse
|
11
|
Crespo-Bellido A, Duffy S. The how of counter-defense: viral evolution to combat host immunity. Curr Opin Microbiol 2023; 74:102320. [PMID: 37075547 DOI: 10.1016/j.mib.2023.102320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Viruses are locked in an evolutionary arms race with their hosts. What ultimately determines viral evolvability, or capacity for adaptive evolution, is their ability to efficiently explore and expand sequence space while under the selective regime imposed by their ecology, which includes innate and adaptive host defenses. Viral genomes have significantly higher evolutionary rates than their host counterparts and should have advantages relative to their slower-evolving hosts. However, functional constraints on virus evolutionary landscapes along with the modularity and mutational tolerance of host defense proteins may help offset the advantage conferred to viruses by high evolutionary rates. Additionally, cellular life forms from all domains of life possess many highly complex defense mechanisms that act as hurdles to viral replication. Consequently, viruses constantly probe sequence space through mutation and genetic exchange and are under pressure to optimize diverse counter-defense strategies.
Collapse
Affiliation(s)
- Alvin Crespo-Bellido
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA.
| |
Collapse
|
12
|
Łazowski K. Efficient, robust, and versatile fluctuation data analysis using MLE MUtation Rate calculator (mlemur). Mutat Res 2023; 826:111816. [PMID: 37104996 DOI: 10.1016/j.mrfmmm.2023.111816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023]
Abstract
The fluctuation assay remains an important tool for analyzing the levels of mutagenesis in microbial populations. The mutant counts originating from some average number of mutations are usually assumed to obey the Luria-Delbrück distribution. While several tools for estimating mutation rates are available, they sometimes lack accuracy or versatility under non-standard conditions. In this work, extensions to the Luria-Delbrück protocol to account for phenotypic lag and cellular death with either perfect or partial plating were developed. Hence, the novel MLE MUtation Rate calculator, or mlemur, is the first tool that provides a user-friendly graphical interface allowing the researchers to model their data with consideration for partial plating, differential growth of mutants and non-mutants, phenotypic lag, cellular death, variability of the final number of cells, post-exponential-phase mutations, and the size of the inoculum. Additionally, mlemur allows the users to incorporate most of these special conditions at the same time to obtain highly accurate estimates of mutation rates and P values, confidence intervals for an arbitrary function of data (such as fold), and perform power analysis and sample size determination for the likelihood ratio test. The accuracy of point and interval estimates produced by mlemur against historical and simulated fluctuation experiments are assessed. Both mlemur and the analyses in this work might be of great help when evaluating fluctuation experiments and increase the awareness of the limitations of the widely-used Lea-Coulson formulation of the Luria-Delbrück distribution in the more realistic biological contexts.
Collapse
Affiliation(s)
- Krystian Łazowski
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Pawińskiego 5a, Warsaw 02-106, Poland.
| |
Collapse
|
13
|
张 世, 蹇 慧, 王 倩, 王 威, 丁 艳, 张 宵, 徐 冬, 杜 冰, 金 波. [Polymorphism and Mutation Rate of 20 Rapidly Mutating Y-Chromosomal Short Tandem Repeats in Chinese Han Population of Sichuan Province]. Sichuan Da Xue Xue Bao Yi Xue Ban 2023; 54:367-373. [PMID: 36949700 PMCID: PMC10409182 DOI: 10.12182/20230260308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 03/24/2023]
Abstract
Objective To explore the applicability of 20 rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) in Chinese Han population of Sichuan province. Methods Two RM Y-STR multiple amplification systems (RM1, including DYF404S1, DYF399S1, DYS547, DYS526a/b, DYS626, DYF403S1a/b, and DYS612, and RM2, including DYS1003, DYS1007, DYR88, DYS712, DYS711, DYS724, and DYF1002, with 14 RM Y-STR loci in total) and Y41SE-V1.2 (including 6 RM Y-STR loci of DYS627, DYS576, DYF387S1, DYS518, DYS570, and DYS449, 30 ordinary Y-chromosomal short tandem repeats [Y-STR] loci, and 1 Indel locus) were used for the amplification and typing of 200 unrelated males and 260 father-son pairs. The polymorphisms and mutation rates of 20 RM Y-STRs and 30 ordinary Y-STRs in Chinese Han population of Sichuan province were investigated and compared. Results In the 200 unrelated males, the gene diversity (GD) of 20 RM Y-STR loci ranged from 0.7910 to 0.9975, and there were 200 haplotypes. Haplotype diversity (HD) was 1 and the discriminative capacity (DC) was 1. A total of 198 haplotypes were found in Y41se-v1.2 (the 30 Y-STRs), with 4 cases sharing two haplotypes, the haplotype diversity being 0.9999, and the discriminative capacity being 0.99. A total of 68 mutations were found at the 20 RM Y-STRs loci in the 260 father-son pairs, and there was slightly more increase than decrease of allele repeats (1.19∶1), with the mutation rate ranging from <3.85×10 -3 (95% C I: 0.00-1.41×10 -2) to 2.69×10 -2 (95% CI: 1.09×10 -2-5.47×10 -2), and the average mutation rate being 1.19×10 -2 (95% CI: 9.20×10 -3-1.51×10 -2). The 20 RM Y-STRs and the Y41SE-V1.2 (the 30 Y-STRs) could be used to distinguish 22.3% and 13.8% father-son pairs, respectively. Conclusion The 20 RM Y-STRs have high gene and haplotype diversity and paternal lineage differentiation rate in Chinese Han population of Sichuan province, showing great potential for application in Chinese Han population of Sichuan province.
Collapse
Affiliation(s)
- 世林 张
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 慧 蹇
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 倩 王
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 威 王
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 艳杰 丁
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 宵 张
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 冬冬 徐
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 冰 杜
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 波 金
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| |
Collapse
|
14
|
Tomita K, Indo HP, Sato T, Tangpong J, Majima HJ. Development of a sensitive double TaqMan Probe-based qPCR Angle-Degree method to detect mutation frequencies. Mitochondrion 2023; 70:1-7. [PMID: 36841519 DOI: 10.1016/j.mito.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/10/2023] [Accepted: 02/18/2023] [Indexed: 02/26/2023]
Abstract
We designed a method to examine the mutation frequencies of the A3243G mutation of mitochondrial DNA (mtDNA) in patients with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome. We performed a qPCR assay using the FAM and VIC TaqMan probes, which detect the 3243G (mutated) and 3243A (wild-type) sequences of mtDNA, respectively. The results obtained by "degree" in a series of differential mutation frequencies were used to plot a standard curve of the mutation frequency. The standard curve was then applied for qPCR assays of the desired samples. The standard deviation (%) of the samples calculated using the standard curve for the TaqMan probe was 2.4 ± 1.5%. This method could be used to examine mutation frequencies in the context of diabetes, aging, cancer, and neurodegenerative diseases.
Collapse
Affiliation(s)
- Kazuo Tomita
- Department of Maxillofacial Radiology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Department of Applied Pharmacology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Hiroko P Indo
- Department of Maxillofacial Radiology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Amanogawa Galactic Astronomy Research Center (AGARC), Kagoshima University Graduate School of Sciences and Engineering, 1-21-35 Korimoto, Kagoshima 890-0065, Japan.
| | - Tomoaki Sato
- Department of Applied Pharmacology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Jitbanjong Tangpong
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand; Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Hideyuki J Majima
- Department of Maxillofacial Radiology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Amanogawa Galactic Astronomy Research Center (AGARC), Kagoshima University Graduate School of Sciences and Engineering, 1-21-35 Korimoto, Kagoshima 890-0065, Japan; School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand; Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand; Center of Excellence Research for Melioidosis and Microorganisms, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand.
| |
Collapse
|
15
|
Gill SE, Chain FJJ. Very Low Rates of Spontaneous Gene Deletions and Gene Duplications in Dictyostelium discoideum. J Mol Evol 2023; 91:24-32. [PMID: 36484794 PMCID: PMC9849192 DOI: 10.1007/s00239-022-10081-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
The study of spontaneous mutation rates has revealed a wide range of heritable point mutation rates across species, but there are comparatively few estimates for large-scale deletion and duplication rates. The handful of studies that have directly calculated spontaneous rates of deletion and duplication using mutation accumulation lines have estimated that genes are duplicated and deleted at orders of magnitude greater rates than the spontaneous point mutation rate. In our study, we tested whether spontaneous gene deletion and gene duplication rates are also high in Dictyostelium discoideum, a eukaryote with among the lowest point mutation rates (2.5 × 10-11 per site per generation) and an AT-rich genome (GC content of 22%). We calculated mutation rates of gene deletions and duplications using whole-genome sequencing data originating from a mutation accumulation experiment and determined the association between the copy number mutations and GC content. Overall, we estimated an average of 3.93 × 10-8 gene deletions and 1.18 × 10-8 gene duplications per gene per generation. While orders of magnitude greater than their point mutation rate, these rates are much lower compared to gene deletion and duplication rates estimated from mutation accumulation lines in other organisms (that are on the order of ~ 10-6 per gene/generation). The deletions and duplications were enriched in regions that were AT-rich even compared to the genomic background, in contrast to our expectations if low GC content was contributing to low mutation rates. The low deletion and duplication mutation rates in D. discoideum compared to other eukaryotes mirror their low point mutation rates, supporting previous work suggesting that this organism has high replication fidelity and effective molecular machinery to avoid the accumulation of mutations in their genome.
Collapse
Affiliation(s)
- Shelbi E Gill
- Department of Biology, University of Massachusetts Lowell, Lowell, MA, 01854-2874, USA.
| | - Frédéric J J Chain
- Department of Biology, University of Massachusetts Lowell, Lowell, MA, 01854-2874, USA.
| |
Collapse
|
16
|
Zheng Q. Estimation of Rates of Non-neutral Mutations When Bacteria are Exposed to Subinhibitory Levels of Antibiotics. Bull Math Biol 2022; 84:131. [PMID: 36178523 DOI: 10.1007/s11538-022-01085-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 09/12/2022] [Indexed: 11/24/2022]
Abstract
The increasingly widespread use of antibiotics has raised an urgent public health question: how does nonlethal exposure of antibiotics increase rates of bacterial mutations that confer antibiotic resistance? Quantitative studies of this sort are rare, and interested investigators tend to neglect scenarios where the mutation inducer and the selective agent are the same. One possible reason for this puzzling neglect is that such an investigation may lead to results that are prone to a Lamarckian interpretation, but a more tangible reason is that successful estimation of mutation rates in such scenarios requires new computational methods. This study presents computational methods tailored for a mutation model in which some wide-type cells may be killed by nonlethal exposure to an antibiotic, but in which mutants proliferate unimpeded. Methods for computing maximum likelihood estimates of mutation rates and their corresponding confidence intervals are devised and evaluated by simulations.
Collapse
Affiliation(s)
- Qi Zheng
- Department of Epidemiology and Biostatistics, Texas A &M University School of Public Health, College Station, Texas, 77843, USA.
| |
Collapse
|
17
|
Schmidt SBI, Rodríguez-Rojas A, Rolff J, Schreiber F. Biocides used as material preservatives modify rates of de novo mutation and horizontal gene transfer in bacteria. J Hazard Mater 2022; 437:129280. [PMID: 35714537 DOI: 10.1016/j.jhazmat.2022.129280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/13/2021] [Revised: 05/20/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Antimicrobial resistance (AMR) is a global health problem with the environment being an important compartment for the evolution and transmission of AMR. Previous studies showed that de-novo mutagenesis and horizontal gene transfer (HGT) by conjugation or transformation - important processes underlying resistance evolution and spread - are affected by antibiotics, metals and pesticides. However, natural microbial communities are also frequently exposed to biocides used as material preservatives, but it is unknown if these substances induce mutagenesis and HGT. Here, we show that active substances used in material preservatives can increase rates of mutation and conjugation in a species- and substance-dependent manner, while rates of transformation are not increased. The bisbiguanide chlorhexidine digluconate, the quaternary ammonium compound didecyldimethylammonium chloride, the metal copper, the pyrethroid-insecticide permethrin, and the azole-fungicide propiconazole increase mutation rates in Escherichia coli, whereas no increases were identified for Bacillus subtilis and Acinetobacter baylyi. Benzalkonium chloride, chlorhexidine and permethrin increased conjugation in E. coli. Moreover, our results show a connection between the RpoS-mediated general stress and the RecA-linked SOS response with increased rates of mutation and conjugation, but not for all biocides. Taken together, our data show the importance of assessing the contribution of material preservatives on AMR evolution and spread.
Collapse
Affiliation(s)
- Selina B I Schmidt
- Division of Biodeterioration and Reference Organisms (4.1), Department of Materials and the Environment, Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 87, 12205 Berlin, Germany.
| | - Alexandro Rodríguez-Rojas
- Evolutionary Biology, Institute of Biology, Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195 Berlin, Germany; Internal Medicine - Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
| | - Jens Rolff
- Evolutionary Biology, Institute of Biology, Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195 Berlin, Germany.
| | - Frank Schreiber
- Division of Biodeterioration and Reference Organisms (4.1), Department of Materials and the Environment, Federal Institute for Materials Research and Testing (BAM), Unter den Eichen 87, 12205 Berlin, Germany.
| |
Collapse
|
18
|
Otagiri T, Sato N, Asamura H, Parvanova E, Kayser M, Ralf A. RMplex reveals population differences in RM Y-STR mutation rates and provides improved father-son differentiation in Japanese. Forensic Sci Int Genet 2022; 61:102766. [PMID: 36007266 DOI: 10.1016/j.fsigen.2022.102766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022]
Abstract
Rapidly mutating Y chromosomal short tandem repeat markers (RM Y-STRs) -characterized by at least one mutation per 100 generations- are suitable for differentiating both related and unrelated males. The recently introduced multiplex method RMplex allows for the efficient analysis of 30 Y-STRs with increased mutation rates, including all 26 currently known RM Y-STRs. While currently available RM Y-STR mutation rates were established mostly from European individuals, here we applied RMplex to DNA samples of 178 genetically confirmed father-son pairs from East Asia. For several Y-STRs, we found significantly higher mutation rates in Japanese compared to previous estimates. The consequent father-son differentiation rate based on RMplex was significantly higher (52%) in Japanese than previously reported for Europeans (42%), and much higher than with Yfiler Plus in both sample sets (14% and 13%, respectively). Further analysis suggests that the higher mutation and relative differentiation rates in Japanese can in part be explained by on average longer Y-STR alleles relative to Europeans. Moreover, we show that the most striking difference, which was found in DYS712, could be linked to a Y-SNP haplogroup (O1b2-P49) that is common in Japanese and rare in other populations. We encourage the forensic Y-STR community to generate more RMplex data from more population samples of sufficiently large sample size in combination with Y-SNP data to further investigate population effects on mutation and relative differentiation rates. Until more RMplex data from more populations become available, caution shall be placed when applying RM Y-STR mutation rate estimates established in one population, such as Europeans, to forensic casework involving male suspects of paternal origin from other populations, such as non-Europeans.
Collapse
Affiliation(s)
- Tomomi Otagiri
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Noriko Sato
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Hideki Asamura
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Evelina Parvanova
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Arwin Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| |
Collapse
|
19
|
Yang H, Park H, Ryu HJ, Heo J, Kim JS, Oh YL, Choe JH, Kim JH, Kim JS, Jang HW, Kim TH, Kim SW, Chung JH. Frequency of TERT Promoter Mutations in Real-World Analysis of 2,092 Thyroid Carcinoma Patients. Endocrinol Metab (Seoul) 2022; 37:652-663. [PMID: 35864728 PMCID: PMC9449103 DOI: 10.3803/enm.2022.1477] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/13/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGRUOUND Telomerase reverse transcriptase (TERT) promoter mutations are associated with increased recurrence and mortality in patients with thyroid carcinoma. Previous studies on TERT promoter mutations were retrospectively conducted on a limited number of patients. METHODS We prospectively collected data on all consecutive patients who underwent thyroid carcinoma surgery between January 2019 and December 2020 at the Samsung Medical Center, Seoul, Korea. We included 2,092 patients with thyroid carcinoma. RESULTS Of 2,092 patients, 72 patients (3.4%) had TERT promoter mutations. However, the frequency of TERT promoter mutations was 0.5% in papillary thyroid microcarcinoma (PTMC) ≤1 cm and it was 5.8% in papillary thyroid carcinoma (PTC) >1 cm. The frequency of TERT promoter mutations was significantly associated with older age at diagnosis (odds ratio [OR], 1.12; P<0.001), larger primary tumor size (OR, 2.02; P<0.001), and aggressive histological type (OR, 7.78 in follicular thyroid carcinoma; OR, 10.33 in poorly differentiated thyroid carcinoma; OR, 45.92 in anaplastic thyroid carcinoma; P<0.001). Advanced T stage, advanced N stage, and distant metastasis at diagnosis were highly prevalent in mutated thyroid cancers. However, initial distant metastasis was not present in patients with TERT promoter mutations in PTMC. Although the C228T mutation was more highly detected than the C250T mutation (64 cases vs. 7 cases), there were no significant clinicopathological differences. CONCLUSION This study is the first attempt to investigate the frequency of TERT promoter mutations in a real-world setting. The frequency of TERT promoter mutations in PTC was lower than expected, and in PTMC, young patients, and female patients, the frequency was very low.
Collapse
Affiliation(s)
- Heera Yang
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyunju Park
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyun Jin Ryu
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jung Heo
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jung-Sun Kim
- Department of Pathology and Translational Genomics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Lyun Oh
- Department of Pathology and Translational Genomics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jun-Ho Choe
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jung Han Kim
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jee Soo Kim
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hye Won Jang
- Department of Medical Education, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Hyuk Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun Wook Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Hoon Chung
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Corresponding author: Jae Hoon Chung. Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Korea Tel: +82-2-3410-3434, Fax: +82-2-3410-3849, E-mail:
| |
Collapse
|
20
|
Chen Y, Liu Q, Zhou L, Zhou Y, Yan H, Lan K. Emerging SARS-CoV-2 variants: Why, how, and what's next? Cell Insight 2022; 1:100029. [PMID: 37193049 PMCID: PMC9057926 DOI: 10.1016/j.cellin.2022.100029] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 01/18/2023]
Abstract
The emergence of the SARS-CoV-2 Omicron variant poses a striking threat to human society. More than 30 mutations in the Spike protein of the Omicron variant severely compromised the protective immunity elicited by either vaccination or prior infection. The persistent viral evolutionary trajectory generates Omicron-associated lineages, such as BA.1 and BA.2. Moreover, the virus recombination upon Delta and Omicron co-infections has been reported lately, although the impact remains to be assessed. This minireview summarizes the characteristics, evolution and mutation control, and immune evasion mechanisms of SARS-CoV-2 variants, which will be helpful for the in-depth understanding of the SARS-CoV-2 variants and policy-making related to COVID-19 pandemic control.
Collapse
Affiliation(s)
- Yu Chen
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qianyun Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Li Zhou
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - You Zhou
- Systems Immunity University Research Institute and Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Huan Yan
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ke Lan
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| |
Collapse
|
21
|
Hamanaka K, Miyake N, Mizuguchi T, Miyatake S, Uchiyama Y, Tsuchida N, Sekiguchi F, Mitsuhashi S, Tsurusaki Y, Nakashima M, Saitsu H, Yamada K, Sakamoto M, Fukuda H, Ohori S, Saida K, Itai T, Azuma Y, Koshimizu E, Fujita A, Erturk B, Hiraki Y, Ch'ng GS, Kato M, Okamoto N, Takata A, Matsumoto N. Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants. Genome Med 2022; 14:40. [PMID: 35468861 PMCID: PMC9040275 DOI: 10.1186/s13073-022-01042-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/25/2022] [Indexed: 12/12/2022] Open
Abstract
Background Previous large-scale studies of de novo variants identified a number of genes associated with neurodevelopmental disorders (NDDs); however, it was also predicted that many NDD-associated genes await discovery. Such genes can be discovered by integrating copy number variants (CNVs), which have not been fully considered in previous studies, and increasing the sample size. Methods We first constructed a model estimating the rates of de novo CNVs per gene from several factors such as gene length and number of exons. Second, we compiled a comprehensive list of de novo single-nucleotide variants (SNVs) in 41,165 individuals and de novo CNVs in 3675 individuals with NDDs by aggregating our own and publicly available datasets, including denovo-db and the Deciphering Developmental Disorders study data. Third, summing up the de novo CNV rates that we estimated and SNV rates previously established, gene-based enrichment of de novo deleterious SNVs and CNVs were assessed in the 41,165 cases. Significantly enriched genes were further prioritized according to their similarity to known NDD genes using a deep learning model that considers functional characteristics (e.g., gene ontology and expression patterns). Results We identified a total of 380 genes achieving statistical significance (5% false discovery rate), including 31 genes affected by de novo CNVs. Of the 380 genes, 52 have not previously been reported as NDD genes, and the data of de novo CNVs contributed to the significance of three genes (GLTSCR1, MARK2, and UBR3). Among the 52 genes, we reasonably excluded 18 genes [a number almost identical to the theoretically expected false positives (i.e., 380 × 0.05 = 19)] given their constraints against deleterious variants and extracted 34 “plausible” candidate genes. Their validity as NDD genes was consistently supported by their similarity in function and gene expression patterns to known NDD genes. Quantifying the overall similarity using deep learning, we identified 11 high-confidence (> 90% true-positive probabilities) candidate genes: HDAC2, SUPT16H, HECTD4, CHD5, XPO1, GSK3B, NLGN2, ADGRB1, CTR9, BRD3, and MARK2. Conclusions We identified dozens of new candidates for NDD genes. Both the methods and the resources developed here will contribute to the further identification of novel NDD-associated genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01042-w.
Collapse
Affiliation(s)
- Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kohei Yamada
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masamune Sakamoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Sachiko Ohori
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Biray Erturk
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey.,Current affiliation: Department of Medical Genetics, Prof. Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Yoko Hiraki
- Hiroshima Municipal Center for Child Health and Development, Hiroshima, Japan
| | | | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan. .,Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Japan.
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| |
Collapse
|
22
|
Hossain MS, Pathan AQMSU, Islam MN, Tonmoy MIQ, Rakib MI, Munim MA, Saha O, Fariha A, Reza HA, Roy M, Bahadur NM, Rahaman MM. Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Inform Med Unlocked 2021; 27:100798. [PMID: 34812411 PMCID: PMC8598266 DOI: 10.1016/j.imu.2021.100798] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/06/2021] [Accepted: 11/15/2021] [Indexed: 01/31/2023] Open
Abstract
Genomic data analysis is a fundamental system for monitoring pathogen evolution and the outbreak of infectious diseases. Based on bioinformatics and deep learning, this study was designed to identify the genomic variability of SARS-CoV-2 worldwide and predict the impending mutation rate. Analysis of 259044 SARS-CoV-2 isolates identified 3334545 mutations with an average of 14.01 mutations per isolate. Globally, single nucleotide polymorphism (SNP) is the most prevalent mutational event. The prevalence of C > T (52.67%) was noticed as a major alteration across the world followed by the G > T (14.59%) and A > G (11.13%). Strains from India showed the highest number of mutations (48) followed by Scotland, USA, Netherlands, Norway, and France having up to 36 mutations. D416G, F106F, P314L, UTR:C241T, L93L, A222V, A199A, V30L, and A220V mutations were found as the most frequent mutations. D1118H, S194L, R262H, M809L, P314L, A8D, S220G, A890D, G1433C, T1456I, R233C, F263S, L111K, A54T, A74V, L183A, A316T, V212F, L46C, V48G, Q57H, W131R, G172V, Q185H, and Y206S missense mutations were found to largely decrease the structural stability of the corresponding proteins. Conversely, D3L, L5F, and S97I were found to largely increase the structural stability of the corresponding proteins. Multi-nucleotide mutations GGG > AAC, CC > TT, TG > CA, and AT > TA have come up in our analysis which are in the top 20 mutational cohort. Future mutation rate analysis predicts a 17%, 7%, and 3% increment of C > T, A > G, and A > T, respectively in the future. Conversely, 7%, 7%, and 6% decrement is estimated for T > C, G > A, and G > T mutations, respectively. T > G\A, C > G\A, and A > T\C are not anticipated in the future. Since SARS-CoV-2 is mutating continuously, our findings will facilitate the tracking of mutations and help to map the progression of the COVID-19 intensity worldwide.
Collapse
Affiliation(s)
- Md Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - A Q M Sala Uddin Pathan
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Nur Islam
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Mahmudul Islam Rakib
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Adnan Munim
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Maitreyee Roy
- School of Optometry and Vision Science, Faculty of Medicine and Health, University of New South Wales, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | |
Collapse
|
23
|
Hobolth A, Bladt M, Andersen LN. Multivariate phase-type theory for the site frequency spectrum. J Math Biol 2021; 83:63. [PMID: 34783900 DOI: 10.1007/s00285-021-01689-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/09/2021] [Accepted: 10/13/2021] [Indexed: 10/19/2022]
Abstract
Linear functions of the site frequency spectrum (SFS) play a major role for understanding and investigating genetic diversity. Estimators of the mutation rate (e.g. based on the total number of segregating sites or average of the pairwise differences) and tests for neutrality (e.g. Tajima's D) are perhaps the most well-known examples. The distribution of linear functions of the SFS is important for constructing confidence intervals for the estimators, and to determine significance thresholds for neutrality tests. These distributions are often approximated using simulation procedures. In this paper we use multivariate phase-type theory to specify, characterize and calculate the distribution of linear functions of the site frequency spectrum. In particular, we show that many of the classical estimators of the mutation rate are distributed according to a discrete phase-type distribution. Neutrality tests, however, are generally not discrete phase-type distributed. For neutrality tests we derive the probability generating function using continuous multivariate phase-type theory, and numerically invert the function to obtain the distribution. A main result is an analytically tractable formula for the probability generating function of the SFS. Software implementation of the phase-type methodology is available in the R package PhaseTypeR, and R code for the reproduction of our results is available as an accompanying vignette.
Collapse
|
24
|
Papaioannou IA, Dutreux F, Peltier FA, Maekawa H, Delhomme N, Bardhan A, Friedrich A, Schacherer J, Knop M. Sex without crossing over in the yeast Saccharomycodes ludwigii. Genome Biol 2021; 22:303. [PMID: 34732243 PMCID: PMC8567612 DOI: 10.1186/s13059-021-02521-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/28/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Intermixing of genomes through meiotic reassortment and recombination of homologous chromosomes is a unifying theme of sexual reproduction in eukaryotic organisms and is considered crucial for their adaptive evolution. Previous studies of the budding yeast species Saccharomycodes ludwigii suggested that meiotic crossing over might be absent from its sexual life cycle, which is predominated by fertilization within the meiotic tetrad. RESULTS We demonstrate that recombination is extremely suppressed during meiosis in Sd. ludwigii. DNA double-strand break formation by the conserved transesterase Spo11, processing and repair involving interhomolog interactions are required for normal meiosis but do not lead to crossing over. Although the species has retained an intact meiotic gene repertoire, genetic and population analyses suggest the exceptionally rare occurrence of meiotic crossovers in its genome. A strong AT bias of spontaneous mutations and the absence of recombination are likely responsible for its unusually low genomic GC level. CONCLUSIONS Sd. ludwigii has followed a unique evolutionary trajectory that possibly derives fitness benefits from the combination of frequent mating between products of the same meiotic event with the extreme suppression of meiotic recombination. This life style ensures preservation of heterozygosity throughout its genome and may enable the species to adapt to its environment and survive with only minimal levels of rare meiotic recombination. We propose Sd. ludwigii as an excellent natural forum for the study of genome evolution and recombination rates.
Collapse
Affiliation(s)
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - France A. Peltier
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Hiromi Maekawa
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Current affiliation: Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Amit Bardhan
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| |
Collapse
|
25
|
Linde AM, Eklund DM, Cronberg N, Bowman JL, Lagercrantz U. Rates and patterns of molecular evolution in bryophyte genomes, with focus on complex thalloid liverworts, Marchantiopsida. Mol Phylogenet Evol 2021; 165:107295. [PMID: 34438050 DOI: 10.1016/j.ympev.2021.107295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/30/2021] [Accepted: 08/19/2021] [Indexed: 10/20/2022]
Abstract
Plants commonly referred to as "bryophytes" belong to three major lineages of non-vascular plants: the liverworts, the hornworts and the mosses. They are unique among land plants in having a dominant haploid generation and a short-lived diploid sporophytic generation. The dynamics of selection acting on a haploid genome differs from those acting on a diploid genome: new mutations are directly exposed to selection. The general aim of this paper is to investigate the diversification rateof bryophytes - measured as silent site substitution rate representing neutral evolution (mutation rate) and the nonsynonymous to synonymous substitution rate ratio (dN/dS) representing selective evolution - and compare it with earlier studies on vascular plants. Results show that the silent site substitution rate is lower for liverworts as compared to angiosperms, but not as low as for gymnosperms. The selection pressure, measured as dN/dS, isnot remarkably lower for bryophytes as compared to other diploid dominant plants as would be expected by the masking hypothesis, indicating that other factors are more important than ploidy.
Collapse
Affiliation(s)
- Anna-Malin Linde
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - D Magnus Eklund
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Nils Cronberg
- Biodiversity, Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden.
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Ulf Lagercrantz
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| |
Collapse
|
26
|
Huang Y, Liu C, Xiao C, Chen X, Han X, Yi S, Huang D. Mutation analysis of 28 autosomal short tandem repeats in the Chinese Han population. Mol Biol Rep 2021; 48:5363-5369. [PMID: 34213710 DOI: 10.1007/s11033-021-06522-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/25/2021] [Indexed: 11/26/2022]
Abstract
Short tandem repeats (STRs) have been extensively used in forensic genetics. However, according to previous studies, the mutation rates of STRs are relatively high and are affected by many factors. Therefore, it is important to analyze STR mutations and determine the influence of underlying factors on STR mutation rates. Mutation rates of 28 autosomal STRs were determined from 8708 paternity testing cases in the Chinese Han population, and the relationships between STR mutation rates and population, sex, age, allele length and heterozygosity were investigated. A total of 279 mutations were observed at 27 loci in a total of 233,530 meiosis cases, including 273 (97.8%) one-step, 5 (1.8%) two-step and 1 (0.4%) three-step mutations. The overall average mutation rate was 1.19 × 10-3 (95% CI 1.06 × 10-3 - 1.34 × 10-3) ranging from 0 (TPOX) to 2.79 × 10-3 (D13S325). Mutation rate comparisons revealed statistically significant differences at several STRs among populations. Paternal mutations occurred more frequently than maternal mutations, at a ratio of 6.04:1, and the mutation rate tended to increase with paternal age. Moreover, our study revealed a bias towards contraction mutations for long alleles and expansion mutations for short alleles. No obvious bias was observed in the overall mutation direction. In addition, STR loci with higher expected heterozygosity (Hexp) tended to have higher mutation rates. This work revealed the relationships between STR mutation rates and several influencing factors, providing useful data and information for further research on STR mutations in forensic genetics.
Collapse
Affiliation(s)
- Yujie Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cong Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoying Chen
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xueli Han
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaohua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Daixin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
27
|
Fan H, Zeng Y, Wu W, Liu H, Xu Q, Du W, Hao H, Liu C, Ren W, Wu W, Chen L, Liu C. The Y-STR landscape of coastal southeastern Han: Forensic characteristics, haplotype analyses, mutation rates, and population genetics. Electrophoresis 2021; 42:1578-1593. [PMID: 34018209 DOI: 10.1002/elps.202100037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/16/2021] [Accepted: 05/15/2021] [Indexed: 11/09/2022]
Abstract
The Y-STR landscape of Coastal Southeastern Han (CSEH) living in Chinese southeast areas (including Guangdong, Fujian, and Zhejiang provinces) is still unclear. We investigated 62 Y-STR markers in a reasonably large number of 1021 unrelated males and 1027 DNA-confirmed father-son pairs to broaden the genetic backgrounds of CSEH. In total, 85 null alleles, 121 off-ladder alleles, and 95 copy number variants were observed, and 1012 distinct haplotypes were determined with the overall HD and DC values of 0.999974 and 0.9912. We observed 369 mutations in 76 099 meiotic transfers, and the average estimated Y-STR mutation rate was 4.85 × 10-3 (95% CI, 4.4 × 10-3 -5.4 × 10-3 ). The Spearman correlation analyses indicated that GD values (R2 = 0.6548) and average allele sizes (R2 = 0.5989) have positive correlations with Y-STR mutation rates. Our RM Y-STR set including 8 candidate RM Y-STRs, of which DYS534, DYS630, and DYS713 are new candidates in CSEH, distinguished 18.52% of father-son pairs. This study also clarified the population structures of CSEH which isolated in population-mixed South China relatively. The strategy, SM Y-STRs for familial searching and RM Y-STRs for individual identification regionally, could be applicable based on enough knowledge of the Y-STR mutability of different populations.
Collapse
Affiliation(s)
- Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Ying Zeng
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Weiwei Wu
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Hong Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Quyi Xu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Weian Du
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Honglei Hao
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Wenyan Ren
- Zhejiang Key Laboratory of Forensic Science and Technology, Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Hangzhou, P. R. China
| | - Weibin Wu
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| |
Collapse
|
28
|
Silliman K, Indorf JL, Knowlton N, Browne WE, Hurt C. Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama. BMC Ecol Evol 2021; 21:104. [PMID: 34049492 PMCID: PMC8164322 DOI: 10.1186/s12862-021-01836-3] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
Background The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. Results To estimate the genome-wide neutral mutation rate (µ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. A range of bioinformatic filtering parameters were evaluated in order to minimize potential bias in mutation rate estimates that may result from SNP filtering. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated µ to be 2.64E−9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. Post-divergence gene flow was detected in one species pair. Failure to account for this post-split migration inflates our substitution rate estimates, emphasizing the importance of demographic methods that can accommodate gene flow. Conclusions Results from our study, both parameter estimates and bioinformatic explorations, have broad-ranging implications for phylogeographic studies in other non-model taxa using reduced representation datasets. Our best estimate of µ that accounts for coalescent and demographic processes is remarkably similar to experimentally derived mutation rates in model arthropod systems. These results contradicted recent suggestions that the closure of the Isthmus was completed much earlier (around 10 Ma), as mutation rates based on an early calibration resulted in uncharacteristically low genomic mutation rates. Also, stricter filtering parameters resulted in biased datasets that generated lower mutation rate estimates and influenced demographic parameters, serving as a cautionary tale for the adherence to conservative bioinformatic strategies when generating reduced-representation datasets at the species level. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01836-3.
Collapse
Affiliation(s)
- Katherine Silliman
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA. .,Committee on Evolutionary Biology, University of Chicago, Chicago, IL, 60637, USA.
| | - Jane L Indorf
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Carla Hurt
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.,Department of Biology, Tennessee Tech University, Cookeville, TN, 38505, USA
| |
Collapse
|
29
|
Lu Z, Cui J, Wang L, Teng N, Zhang S, Lam HM, Zhu Y, Xiao S, Ke W, Lin J, Xu C, Jin B. Genome-wide DNA mutations in Arabidopsis plants after multigenerational exposure to high temperatures. Genome Biol 2021; 22:160. [PMID: 34034794 PMCID: PMC8145854 DOI: 10.1186/s13059-021-02381-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 11/11/2020] [Accepted: 05/13/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Elevated temperatures can cause physiological, biochemical, and molecular responses in plants that can greatly affect their growth and development. Mutations are the most fundamental force driving biological evolution. However, how long-term elevations in temperature influence the accumulation of mutations in plants remains unknown. RESULTS Multigenerational exposure of Arabidopsis MA (mutation accumulation) lines and MA populations to extreme heat and moderate warming results in significantly increased mutation rates in single-nucleotide variants (SNVs) and small indels. We observe distinctive mutational spectra under extreme and moderately elevated temperatures, with significant increases in transition and transversion frequencies. Mutation occurs more frequently in intergenic regions, coding regions, and transposable elements in plants grown under elevated temperatures. At elevated temperatures, more mutations accumulate in genes associated with defense responses, DNA repair, and signaling. Notably, the distribution patterns of mutations among all progeny differ between MA populations and MA lines, suggesting that stronger selection effects occurred in populations. Methylation is observed more frequently at mutation sites, indicating its contribution to the mutation process at elevated temperatures. Mutations occurring within the same genome under elevated temperatures are significantly biased toward low gene density regions, special trinucleotides, tandem repeats, and adjacent simple repeats. Additionally, mutations found in all progeny overlap significantly with genetic variations reported in 1001 Genomes, suggesting non-uniform distribution of de novo mutations through the genome. CONCLUSION Collectively, our results suggest that elevated temperatures can accelerate the accumulation, and alter the molecular profiles, of DNA mutations in plants, thus providing significant insight into how environmental temperatures fuel plant evolution.
Collapse
Affiliation(s)
- Zhaogeng Lu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Jiawen Cui
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Li Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Nianjun Teng
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Shoudong Zhang
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region China
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region China
| | - Yingfang Zhu
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Siwei Xiao
- Wuhan Frasergen Bioinformatics Co, Wuhan, China
| | - Wensi Ke
- Wuhan Frasergen Bioinformatics Co, Wuhan, China
| | - Jinxing Lin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Chenwu Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, China
| | - Biao Jin
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| |
Collapse
|
30
|
Jánošíková L, Pálková L, Šalát D, Klepanec A, Soltys K. Response of Escherichia coli minimal ter operon to UVC and auto-aggregation: pilot study. PeerJ 2021; 9:e11197. [PMID: 34026346 PMCID: PMC8123226 DOI: 10.7717/peerj.11197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/09/2021] [Indexed: 11/20/2022] Open
Abstract
Aim The study of minimal ter operon as a determinant of tellurium resistance (TeR) is important for the purpose of confirming the relationship of these genes to the pathogenicity of microorganisms. The ter operon is widespread among bacterial species and pathogens, implicated also in phage inhibition, oxidative stress and colicin resistance. So far, there is no experimental evidence for the role of the Escherichia coli (E. coli) minimal ter operon in ultraviolet C (UVC) resistance, biofilm formation and auto-aggregation. To identify connection with UVC resistance of the minimal ter operon, matched pairs of Ter-positive and -negative E. coli cells were stressed and differences in survival and whole genome sequence analysis were performed. This study was aimed also to identify differences in phenotype of cells induced by environmental stress. Methods In the current study, a minimal ter operon(terBCDEΔF) originating from the uropathogenic strain E. coli KL53 was used. Clonogenic assay was the method of choice to determine cell reproductive death after treatment with UVC irradiation at certain time intervals. Bacterial suspensions were irradiated with 254 nm UVC-light (germicidal lamp in biological safety cabinet) in vitro. UVC irradiance output was 2.5 mW/cm2 (calculated at the UVC device aperture) and plate-lamp distance of 60 cm. DNA damage analysis was performed using shotgun sequencing on Illumina MiSeq platform. Biofilm formation was measured by a crystal violet retention assay. Auto-aggregation assay was performed according to the Ghane, Babaeekhou & Ketabi (2020). Results A large fraction of Ter-positive E. coli cells survived treatment with 120-s UVC light (300 mJ/cm2) compared to matched Ter-negative cells; ∼5-fold higher resistance of Ter-positive cells to UVC dose (p = 0.0007). Moreover, UVC surviving Ter-positive cells showed smaller mutation rate as Ter-negative cells. The study demonstrated that a 1200-s exposure to UVC (3,000 mJ/cm2) was sufficient for 100% inhibition of growth for all the Ter-positive and -negative E. coli cells. The Ter-positive strain exhibited of 26% higher auto-aggregation activities and was able to inhibit biofilm formation over than Ter- negative strain (**** P < 0.0001). Conclusion Our study shows that Ter-positive cells display lower sensitivity to UVC radiation, corresponding to a presence in minimal ter operon. In addition, our study suggests that also auto-aggregation ability is related to minimal ter operon. The role of the minimal ter operon (terBCDEΔF) in resistance behavior of E. coli under environmental stress is evident.
Collapse
Affiliation(s)
- Lenka Jánošíková
- Faculty of Health Sciences, University of St. Cyril and Methodius in Trnava, Trnava, Slovak Republic
| | | | - Dušan Šalát
- Faculty of Health Sciences, University of St. Cyril and Methodius in Trnava, Trnava, Slovak Republic
| | - Andrej Klepanec
- Faculty of Health Sciences, University of St. Cyril and Methodius in Trnava, Trnava, Slovak Republic
| | - Katarina Soltys
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic.,Comenius University Science Park, Comenius University in Bratislava, Bratislava, Slovak Republic
| |
Collapse
|
31
|
Zhang H. A game-theoretical dynamic imitation model on networks. J Math Biol 2021; 82:30. [PMID: 33683438 DOI: 10.1007/s00285-021-01573-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/09/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
A game-theoretical model is constructed to capture the effect of imitation on the evolution of cooperation. This imitation describes the case where successful individuals are more likely to be imitated by newcomers who will employ their strategies and social networks. Two classical repeated strategies 'always defect (ALLD)' and 'tit-for-tat (TFT)' are adopted. Mathematical analyses are mainly conducted by the method of coalescence theory. Under the assumption of a large population size and weak selection, the results show that the evolution of cooperation is promoted in this dynamic network. As we observed that the critical benefit-to-cost ratio is smaller compared to that in well-mixed populations. The critical benefit-to-cost ratio approaches a specific value which depends on three parameters, the repeated rounds of the game, the effective strategy mutation rate, and the effective link mutation rate. Specifically, for a very high value of the effective link mutation rate, the critical benefit-to-cost ratio approaches 1. Remarkably, for a low value of the effective link mutation rate, by letting the effective strategy mutation is nearly equal to zero, the critical benefit-to-cost ratio approaches [Formula: see text] for the resulting highly connected networks, which allows TFT to be evolutionary stable. It illustrates that dominance of TFTs is associated with more connected networks. This research can enrich the theory of the coevolution of game strategy and network structure with dynamic imitation.
Collapse
Affiliation(s)
- Hui Zhang
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China.
| |
Collapse
|
32
|
Otagiri T, Sato N, Shiozaki T, Harayama Y, Hayashi T, Kobayashi K, Asamura H. Mutation analysis for 25 Y-STR markers in Japanese population. Leg Med (Tokyo) 2021; 50:101860. [PMID: 33607450 DOI: 10.1016/j.legalmed.2021.101860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/22/2021] [Accepted: 02/05/2021] [Indexed: 11/27/2022]
Abstract
In this study, we analyzed DNA samples from 213 Japanese father son pairs with 25 Y-chromosome short tandem repeat (Y-STR) (DYS576, DYS389I, DYS635, DYS389II, DYS627, DYS460, DYS458, DYS19, YGATAH4, DYS448, DYS391, DYS456, DYS390, DYS438, DYS392, DYS518, DYS570, DYS437, DYS385, DYS449, DYS393, DYS439, DYS481, DYF387S1, and DYS533) markers using the Yfiler™ Plus PCR amplification kit. We calculated Y-STR mutation rates for each locus to evaluate the efficacy of the 25 Y-STR markers for paternity testing and forensic identification using samples from male relatives. Six rapidly mutating Y-STR markers (DYS576, DYS627, DYS518, DYS570, DYS449 and DYF387S1), previously reported to have high mutation rates (>1.0 × 10-2), are included in the 25 Y-STR markers, but our findings revealed that the mutation rates for all Y-STR markers except for DYS576 and DYS458 were lower than 1.0 × 10-2. Therefore, the use of these 25 Y-STR markers may be useful for forensic identification in the Japanese population.
Collapse
|
33
|
Zheng GY, Zhang XB, Li HZ, Zhang YS, Deng JH, Wu XC. Sum of High-Risk Gene Mutation (SHGM): A Novel Attempt to Assist Differential Diagnosis for Adrenocortical Carcinoma with Benign Adenoma, Based on Detection of Mutations of Nine Target Genes. Biochem Genet 2021; 59:902-918. [PMID: 33564960 PMCID: PMC8249247 DOI: 10.1007/s10528-021-10039-w] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 01/19/2021] [Indexed: 11/30/2022]
Abstract
There has been no research on applying gene detection to differential diagnosis of adrenocortical carcinoma (ACC). We attempted to explore a novel auxiliary method for differential diagnosis between ACC with benign adrenocortical adenoma (ACA), based on mutations of target genes in tissues. Nine genes were chosen as target genes, including TP53, CTNNB1, ARMC5, PRKAR1A, ZNRF3, RB1, APC, MEN1, and RPL22. Exons sequencing of target genes were performed in 98 cases of tissue samples by FastTarget technology, including 41 ACC tissues, 32 ACA tissues, and 25 normal adrenal gland tissues. Significant mutations were detected and identified, and the clinical information was collected, for further comparative analysis and application to assist differential diagnosis of ACC. We identified 132 significant gene mutations and 227 significant mutation sites in 37 ACC tissues, much more than ACA and normal adrenal gland tissues. Mutation rates of 6 genes in ACC tissues were obviously higher than ACA tissues, including ZNRF3, ARMC5, TP53, APC, RB1, and PRKAR1A, regarded as high-risk genes. The sum of mutated high-risk genes detected in each sample was denominated sum of high-risk gene mutation (SHGM), and the rates of SHGM > 0 and SHGM > 1 in ACC tissues were 73.0% and 62.2%, respectively, both obviously higher than those in ACA tissues, with significant statistic differences. Especially for 8 cases of ACC with diameter < 5 cm, SHGM > 0 and SHGM > 1 were found in 6 samples (75%) and 4 samples (50%), respectively. However, no relevance was found between SHGM and clinical characteristics of ACC. We identified 6 high-risk genes in ACC tissues, with significantly higher mutation rates than ACA or normal adrenal gland tissues. The sum of mutated high-risk genes detected in ACC tissues was denominated SHGM, which was potential to assist the differential diagnosis of ACC with ACA, especially for the small-size ACC.
Collapse
Affiliation(s)
- Guo-Yang Zheng
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan Road, Dongcheng District, Beijing, 100730, China
| | - Xue-Bin Zhang
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan Road, Dongcheng District, Beijing, 100730, China
| | - Han-Zhong Li
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan Road, Dongcheng District, Beijing, 100730, China.
| | - Yu-Shi Zhang
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan Road, Dongcheng District, Beijing, 100730, China
| | - Jian-Hua Deng
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan Road, Dongcheng District, Beijing, 100730, China
| | - Xing-Cheng Wu
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan Road, Dongcheng District, Beijing, 100730, China
| |
Collapse
|
34
|
Dimonte S, Babakir-Mina M, Hama-Soor T, Ali S. Genetic Variation and Evolution of the 2019 Novel Coronavirus. Public Health Genomics 2021; 24:54-66. [PMID: 33406522 PMCID: PMC7900485 DOI: 10.1159/000513530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/27/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION SARS-CoV-2 is a new type of coronavirus causing a pandemic severe acute respiratory syndrome (SARS-2). Coronaviruses are very diverting genetically and mutate so often periodically. The natural selection of viral mutations may cause host infection selectivity and infectivity. METHODS This study was aimed to indicate the diversity between human and animal coronaviruses through finding the rate of mutation in each of the spike, nucleocapsid, envelope, and membrane proteins. RESULTS The mutation rate is abundant in all 4 structural proteins. The most number of statistically significant amino acid mutations were found in spike receptor-binding domain (RBD) which may be because it is responsible for a corresponding receptor binding in a broad range of hosts and host selectivity to infect. Among 17 previously known amino acids which are important for binding of spike to angiotensin-converting enzyme 2 (ACE2) receptor, all of them are conservative among human coronaviruses, but only 3 of them significantly are mutated in animal coronaviruses. A single amino acid aspartate-454, that causes dissociation of the RBD of the spike and ACE2, and F486 which gives the strength of binding with ACE2 remain intact in all coronaviruses. DISCUSSION/CONCLUSION Observations of this study provided evidence of the genetic diversity and rapid evolution of SARS-CoV-2 as well as other human and animal coronaviruses.
Collapse
Affiliation(s)
| | | | - Taib Hama-Soor
- Technical College of Health, Sulaimani Polytechnic University, KGR, Sulaimani, Iraq
| | - Salar Ali
- Technical College of Health, Sulaimani Polytechnic University, KGR, Sulaimani, Iraq
| |
Collapse
|
35
|
Neves HI, Machado GT, Ramos TCDS, Yang HM, Yagil E, Spira B. Competition for nutritional resources masks the true frequency of bacterial mutants. BMC Biol 2020; 18:194. [PMID: 33317515 PMCID: PMC7737367 DOI: 10.1186/s12915-020-00913-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/03/2020] [Indexed: 12/02/2022] Open
Abstract
Background It is widely assumed that all mutant microorganisms present in a culture are able to grow and form colonies, provided that they express the features required for selection. Unlike wild-type Escherichia coli, PHO-constitutive mutants overexpress alkaline phosphatase and hence can hydrolyze glycerol-2-phosphate (G2P) to glycerol and form colonies on plates having G2P as the sole carbon source. These mutations mostly occur in the pst operon. However, the frequency of PHO-constitutive colonies on the G2P selective plate is exceptionally low. Results We show that the rate in which spontaneous PHO-constitutive mutations emerge is about 8.0 × 10−6/generation, a relatively high rate, but the growth of most existing mutants is inhibited by their neighboring wild-type cells. This inhibition is elicited only by non-mutant viable bacteria that can take up and metabolize glycerol formed by the mutants. Evidence indicates that the few mutants that do form colonies derive from microclusters of mutants on the selective plate. A mathematical model that describes the fate of the wild-type and mutant populations under these circumstances supports these results. Conclusion This scenario in which neither the wild-type nor the majority of the mutants are able to grow resembles an unavoidable “tragedy of the commons” case which results in the collapse of the majority of the population. Cooperation between rare adjacent mutants enables them to overcome the competition and eventually form mutant colonies. The inhibition of PHO-constitutive mutants provides an example of mutant frequency masked by orders of magnitude due to a competition between mutants and their ancestral wild-type cells. Similar “tragedy of the commons-like” cases may occur in other settings and should be taken into consideration while estimating true mutant frequencies and mutation rates. Supplementary Information The online version contains supplementary material available at (doi:10.1186/s12915-020-00913-1).
Collapse
Affiliation(s)
- Henrique Iglesias Neves
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gabriella Trombini Machado
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Hyun Mo Yang
- Departamento de Matemática Aplicada, Instituto de Matemática, Estatística e Computação Científica, Campinas, SP, Brazil
| | - Ezra Yagil
- Departament of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Beny Spira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil.
| |
Collapse
|
36
|
Sandler G, Bartkowska M, Agrawal AF, Wright SI. Estimation of the SNP Mutation Rate in Two Vegetatively Propagating Species of Duckweed. G3 (Bethesda) 2020; 10:4191-200. [PMID: 32973000 DOI: 10.1534/g3.120.401704] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mutation rate estimates for vegetatively reproducing organisms are rare, despite their frequent occurrence across the tree of life. Here we report mutation rate estimates in two vegetatively reproducing duckweed species, Lemna minor and Spirodela polyrhiza We use a modified approach to estimating mutation rates by taking into account the reduction in mutation detection power that occurs when new individuals are produced from multiple cell lineages. We estimate an extremely low per generation mutation rate in both species of duckweed and note that allelic coverage at de novo mutation sites is very skewed. We also find no substantial difference in mutation rate between mutation accumulation lines propagated under benign conditions and those grown under salt stress. Finally, we discuss the implications of interpreting mutation rate estimates in vegetatively propagating organisms.
Collapse
|
37
|
Eskier D, Suner A, Oktay Y, Karakülah G. Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load. PeerJ 2020; 8:e10181. [PMID: 33083157 PMCID: PMC7560320 DOI: 10.7717/peerj.10181] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 is a betacoronavirus responsible for COVID-19, a pandemic with global impact that first emerged in late 2019. Since then, the viral genome has shown considerable variance as the disease spread across the world, in part due to the zoonotic origins of the virus and the human host adaptation process. As a virus with an RNA genome that codes for its own genomic replication proteins, mutations in these proteins can significantly impact the variance rate of the genome, affecting both the survival and infection rate of the virus, and attempts at combating the disease. In this study, we analyzed the mutation densities of viral isolates carrying frequently observed mutations for four proteins in the RNA synthesis complex over time in comparison to wildtype isolates. Our observations suggest mutations in nsp14, an error-correcting exonuclease protein, have the strongest association with increased mutation load without selective pressure and across the genome, compared to nsp7, nsp8 and nsp12, which form the core polymerase complex. We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates and nsp14 mutations as potential predictors for high mutability strains.
Collapse
Affiliation(s)
- Doğa Eskier
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Aslı Suner
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey.,Faculty of Medicine, Department of Medical Biology, Dokuz Eylül University, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| |
Collapse
|
38
|
Hofmeister BT, Denkena J, Colomé-Tatché M, Shahryary Y, Hazarika R, Grimwood J, Mamidi S, Jenkins J, Grabowski PP, Sreedasyam A, Shu S, Barry K, Lail K, Adam C, Lipzen A, Sorek R, Kudrna D, Talag J, Wing R, Hall DW, Jacobsen D, Tuskan GA, Schmutz J, Johannes F, Schmitz RJ. A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biol 2020; 21:259. [PMID: 33023654 PMCID: PMC7539514 DOI: 10.1186/s13059-020-02162-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [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: 12/03/2019] [Accepted: 09/02/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials. RESULTS Here, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions. CONCLUSION Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.
Collapse
Affiliation(s)
| | - Johanna Denkena
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Maria Colomé-Tatché
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Yadollah Shahryary
- Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany
| | - Rashmi Hazarika
- Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Sujan Mamidi
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | | | | | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kathleen Lail
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Catherine Adam
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Rod Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - David W Hall
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Daniel Jacobsen
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Frank Johannes
- Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany.
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany.
| | - Robert J Schmitz
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany.
- Department of Genetics, University of Georgia, Athens, GA, USA.
| |
Collapse
|
39
|
Pathan RK, Biswas M, Khandaker MU. Time series prediction of COVID-19 by mutation rate analysis using recurrent neural network-based LSTM model. Chaos Solitons Fractals 2020; 138:110018. [PMID: 32565626 PMCID: PMC7293453 DOI: 10.1016/j.chaos.2020.110018] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/12/2020] [Indexed: 05/20/2023]
Abstract
SARS-CoV-2, a novel coronavirus mostly known as COVID-19 has created a global pandemic. The world is now immobilized by this infectious RNA virus. As of June 15, already more than 7.9 million people have been infected and 432k people died. This RNA virus has the ability to do the mutation in the human body. Accurate determination of mutation rates is essential to comprehend the evolution of this virus and to determine the risk of emergent infectious disease. This study explores the mutation rate of the whole genomic sequence gathered from the patient's dataset of different countries. The collected dataset is processed to determine the nucleotide mutation and codon mutation separately. Furthermore, based on the size of the dataset, the determined mutation rate is categorized for four different regions: China, Australia, the United States, and the rest of the World. It has been found that a huge amount of Thymine (T) and Adenine (A) are mutated to other nucleotides for all regions, but codons are not frequently mutating like nucleotides. A recurrent neural network-based Long Short Term Memory (LSTM) model has been applied to predict the future mutation rate of this virus. The LSTM model gives Root Mean Square Error (RMSE) of 0.06 in testing and 0.04 in training, which is an optimized value. Using this train and testing process, the nucleotide mutation rate of 400th patient in future time has been predicted. About 0.1% increment in mutation rate is found for mutating of nucleotides from T to C and G, C to G and G to T. While a decrement of 0.1% is seen for mutating of T to A, and A to C. It is found that this model can be used to predict day basis mutation rates if more patient data is available in updated time.
Collapse
Affiliation(s)
- Refat Khan Pathan
- Department of Computer Science and Engineering, BGC Trust University Bangladesh, Chittagong-4381, Bangladesh
| | - Munmun Biswas
- Department of Computer Science and Engineering, BGC Trust University Bangladesh, Chittagong-4381, Bangladesh
| | - Mayeen Uddin Khandaker
- Centre for Biomedical Physics, School of Healthcare and Medical Sciences, Sunway University, 47500 Bandar Sunway, Selangor, Malaysia
| |
Collapse
|
40
|
Abstract
COVID-19, caused by the novel SARS-CoV-2 virus, started in China in late 2019, and soon became a global pandemic. With the help of thousands of viral genome sequences that have been accumulating, it has become possible to track the evolution of the viral genome over time as it spread across the world. An important question that still needs to be answered is whether any of the common mutations affect the viral properties, and therefore the disease characteristics. Therefore, we sought to understand the effects of mutations in RNA-dependent RNA polymerase (RdRp), particularly the common 14408C>T mutation, on mutation rate and viral spread. By focusing on mutations in the slowly evolving M or E genes, we aimed to minimize the effects of selective pressure. Our results indicate that 14408C>T mutation increases the mutation rate, while the third-most common RdRp mutation, 15324C>T, has the opposite effect. It is possible that 14408C>T mutation may have contributed to the dominance of its co-mutations in Europe and elsewhere.
Collapse
Affiliation(s)
- Doğa Eskier
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Aslı Suner
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
- Faculty of Medicine, Department of Medical Biology, Dokuz Eylül University, Izmir, Turkey
| |
Collapse
|
41
|
Abstract
BACKGROUND The molecular clock is an important genetic tool for estimating evolutionary timescales. However, the detection of a time-dependent effect on substitution rate estimates complicates its application. It has been suggested that demographic processes could be the main cause of this confounding effect. In the present study, I propose a new algorithm for estimating the coalescent age of phylogenetically related sequences, taking into account the observed time-dependent effect on the molecular rate detected by others. RESULTS By applying this method to real human mitochondrial DNA trees with shallow and deep topologies, I obtained significantly older molecular ages for the main events of human evolution than were previously estimated. These ages are in close agreement with the most recent archaeological and paleontological records favoring the emergence of early anatomically modern humans in Africa 315 ± 34 thousand years ago (kya) and the presence of recent modern humans outside of Africa as early as 174 ± 48 thousand years ago. Furthermore, during the implementation process, I demonstrated that in a population with fluctuating sizes, the probability of fixation of a new neutral mutant depends on the effective population size, which is in better accordance with the fact that under the neutral theory of molecular evolution, the fate of a molecular mutation is mainly determined by random drift. CONCLUSIONS I suggest that the demographic history of populations has a more decisive effect than purifying selection and/or mutational saturation on the time-dependent effect observed for the substitution rate, and I propose a new method that corrects for this effect.
Collapse
Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| |
Collapse
|
42
|
Kim SY, Kim T, Kim K, Bae JS, Kim JS, Jung CK. Highly prevalent BRAF V600E and low-frequency TERT promoter mutations underlie papillary thyroid carcinoma in Koreans. J Pathol Transl Med 2020; 54:310-317. [PMID: 32527075 PMCID: PMC7385264 DOI: 10.4132/jptm.2020.05.12] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The presence of telomerase reverse transcriptase (TERT) promoter mutations have been associated with a poor prognosis in patients with papillary thyroid carcinomas (PTC). The frequency of TERT promoter mutations varies widely depending on the population and the nature of the study. METHODS Data were prospectively collected in 724 consecutive patients who underwent thyroidectomy for PTC from 2018 to 2019. Molecular testing for BRAF V600E and TERT promoter mutations was performed in all cases. RESULTS TERT promoter alterations in two hotspots (C228T and C250T) and C216T were found in 16 (2.2%) and 4 (0.6%) of all PTCs, respectively. The hotspot mutations were significantly associated with older age at diagnosis, larger tumor size, extrathyroidal extension, higher pathologic T category, lateral lymph node metastasis, and higher American Thyroid Association recurrence risk. The patients with C216T variant were younger and had a lower American Thyroid Association recurrence risk than those with hotspot mutations. Concurrent BRAF V600E was found in 19 of 20 cases with TERT promoter mutations. Of 518 microcarcinomas measuring ≤1.0 cm in size, hotspot mutations and C216T variants were detected in five (1.0%) and three (0.6%) cases, respectively. CONCLUSIONS Our study indicates a low frequency of TERT promoter mutations in Korean patients with PTC and supports previous findings that TERT promoter mutations are more common in older patients with unfavorable clinicopathologic features and BRAF V600E. TERT promoter mutations in patients with microcarcinoma are uncommon and may have a limited role in risk stratification. The C216T variant seems to have no clinicopathologic effect on PTC.
Collapse
Affiliation(s)
- Sue Youn Kim
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Taeeun Kim
- Molecular Pathology Unit, Pathology Laboratory, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kwangsoon Kim
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ja Seong Bae
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jeong Soo Kim
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Chan Kwon Jung
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
| |
Collapse
|
43
|
Ye H, Teng J, Lin Z, Wang Y, Fu X. Analysis of HBsAg mutations in the 25 years after the implementation of the hepatitis B vaccination plan in China. Virus Genes 2020; 56:546-556. [PMID: 32542478 DOI: 10.1007/s11262-020-01773-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/25/2020] [Indexed: 12/18/2022]
Abstract
Since 1992, China has promoted hepatitis B vaccination. Concurrently, during this period, increasing use of immunoglobulins and nucleoside analogues might have exerted selective pressure on the hepatitis B virus (HBV) S gene, driving mutations in the HBsAg and changed the subtype. Using the National Center for Biotechnology Information database, we obtained gene sequence information for HBV strains from China and analysed changes in HBsAg subtypes and substitution mutations in HBsAg in 5-year intervals over 25 years to identify potential challenges to the prevention and treatment of hepatitis B. Most HBV sequences from China were genotype C (1996/2833, 70.46%) or B (706/2833, 24.92%). During the implementation of hepatitis B vaccination (recombinant hepatitis B vaccine was subgenotype A2 and HBsAg subtype adw2), the proportion of subtypes ayw1 and adw3 in genotype B and ayw2 in genotype C increased over the programme period. The overall mutation rate in HBsAg tended to decrease for genotype B, whereas, for genotype C, the rate increased gradually and then decreased slightly. Moreover, the mutation rate at some HBsAg amino acid sites (such as sG145 of genotype B and sG130 and sK141 of genotype C) is gradually increasing. HBV strains with internal stop codons of HBsAg (e.g., sC69*) and additional N-glycosylation (e.g., sG130N) mutations should be studied extensively to prevent them from becoming dominant circulating strains. The development of HBV vaccines and antiviral immunoglobulins and use of antiviral drugs may require making corresponding changes.
Collapse
Affiliation(s)
- Huiming Ye
- Department of Clinical Laboratory, Women and Children's Hospital, School of Medicine, Xiamen University, No. 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Jing Teng
- Department of Clinical Laboratory, Xiamen Hospital of Traditional Chinese Medicine, No. 1739 Xianyue Road, Xiamen, 361009, Fujian Province, China
| | - Zhiyuan Lin
- Department of Clinical Laboratory, Xiamen Hospital of Traditional Chinese Medicine, No. 1739 Xianyue Road, Xiamen, 361009, Fujian Province, China
| | - Ye Wang
- Department of Clinical Laboratory, Women and Children's Hospital, School of Medicine, Xiamen University, No. 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Xiaochun Fu
- Department of Clinical Laboratory, Xiamen Hospital of Traditional Chinese Medicine, No. 1739 Xianyue Road, Xiamen, 361009, Fujian Province, China. .,Department of Clinical Laboratory, Women and Children's Hospital, School of Medicine, Xiamen University, No. 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China.
| |
Collapse
|
44
|
Liu J, Wang R, Shi J, Cheng X, Hao T, Guo J, Wang J, Liu Z, Li W, Fan H, Yun K, Yan J, Zhang G. The construction and application of a new 17-plex Y-STR system using universal fluorescent PCR. Int J Legal Med 2020; 134:2015-27. [PMID: 32322984 DOI: 10.1007/s00414-020-02291-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/30/2020] [Indexed: 01/16/2023]
Abstract
Y-chromosomal short tandem repeat (Y-STR) polymorphisms are useful in forensic identification, population genetics, and human structures. However, the current Y-STR systems are limited in discriminating distant relatives in a family with a low discrimination power. Increasing the capacity of detecting Y chromosomal polymorphisms will drastically narrow down the matching number of genealogy populations or pedigrees. In this study, we developed a system containing 17 Y-STRs that are complementary to the current commercially available Y-STR kits. This system was constructed by multiplex PCR with expected sizes of 126-400 bp labeled by different fluorescence molecules (DYS715, DYS709, DYS716, DYS713, and DYS607 labeled by FAM; DYS718, DYS723, DYS708, and DYS714 labeled by JOE; DYS712, DYS717, DYS721, and DYS605 labeled by TAMRA; and DYS719, DYS726, DYS598, and DYS722 labeled by ROX). The system was extensively tested for sensitivity, male specificity, species specificity, mixture, population genetics, and mutation rates following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The genetic data were obtained from eight populations with a total of 1260 individuals. Our results showed that all the 17 Y-STRs are human- and male-specific and include only one copy of the Y-chromosome. The 17 Y-STR system detects 143 alleles and has a high discrimination power (0.996031746). Mutation rates were different among the 17 Y-STRs, ranging from 0.30 to 3.03%. In conclusion, our study provides a robust, sensitive, and cost-effective genotyping method for human identification, which will be beneficial for narrowing the search scope when applied to genealogy searching with the Y-STR DNA databank.
Collapse
|
45
|
Morales-Arce AY, Harris RB, Stone AC, Jensen JD. Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution. Evolution 2020; 74:992-1001. [PMID: 32233086 DOI: 10.1111/evo.13954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/08/2020] [Indexed: 12/28/2022]
Abstract
The within-host evolutionary dynamics of tuberculosis (TB) remain unclear, and underlying biological characteristics render standard population genetic approaches based upon the Wright-Fisher model largely inappropriate. In addition, the compact genome combined with an absence of recombination is expected to result in strong purifying selection effects. Thus, it is imperative to establish a biologically relevant evolutionary framework incorporating these factors in order to enable an accurate study of this important human pathogen. Further, such a model is critical for inferring fundamental evolutionary parameters related to patient treatment, including mutation rates and the severity of infection bottlenecks. We here implement such a model and infer the underlying evolutionary parameters governing within-patient evolutionary dynamics. Results demonstrate that the progeny skew associated with the clonal nature of TB severely reduces genetic diversity and that the neglect of this parameter in previous studies has led to significant mis-inference of mutation rates. As such, our results suggest an underlying de novo mutation rate that is considerably faster than previously inferred, and a progeny distribution differing significantly from Wright-Fisher assumptions. This inference represents a more appropriate evolutionary null model, against which the periodic effects of positive selection, associated with drug-resistance for example, may be better assessed.
Collapse
Affiliation(s)
- Ana Y Morales-Arce
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Rebecca B Harris
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.,School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
46
|
Kapoor I, Varshney U. Diverse roles of nucleoside diphosphate kinase in genome stability and growth fitness. Curr Genet 2020; 66:671-682. [PMID: 32249353 DOI: 10.1007/s00294-020-01073-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
Nucleoside diphosphate kinase (NDK), a ubiquitous enzyme, catalyses reversible transfer of the γ phosphate from nucleoside triphosphates to nucleoside diphosphates and functions to maintain the pools of ribonucleotides and deoxyribonucleotides in the cell. As even a minor imbalance in the nucleotide pools can be mutagenic, NDK plays an antimutator role in maintaining genome integrity. However, the mechanism of the antimutator roles of NDK is not completely understood. In addition, NDKs play important roles in the host-pathogen interactions, metastasis, gene regulation, and various cellular metabolic processes. To add to these diverse roles of NDK in cells, a recent study now reveals that NDK may even confer mutator phenotypes to the cell by acting on the damaged deoxyribonucleoside diphosphates that may be formed during the oxidative stress. In this review, we discuss the roles of NDK in homeostasis of the nucleotide pools and genome integrity, and its possible implications in conferring growth/survival fitness to the organisms in the changing environmental niches.
Collapse
Affiliation(s)
- Indu Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India. .,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India.
| |
Collapse
|
47
|
Pinto N, Pereira V, Tomas C, Loiola S, Carvalho EF, Modesti N, Maxzud M, Marcucci V, Cano H, Cicarelli R, Januario B, Bento A, Brito P, Burgos G, Paz-Cruz E, Díez-Juárez L, Vannelli S, Pontes ML, Berardi G, Furfuro S, Fernandez A, Sumita D, Bobillo C, García MG, Gusmão L. Paternal and maternal mutations in X-STRs: A GHEP-ISFG collaborative study. Forensic Sci Int Genet 2020; 46:102258. [PMID: 32066109 DOI: 10.1016/j.fsigen.2020.102258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/06/2019] [Accepted: 01/29/2020] [Indexed: 11/22/2022]
Abstract
The GHEP-ISFG organized a collaborative study to estimate mutation rates for the markers included in the Investigator Argus X-12 QS kit Qiagen. A total of 16 laboratories gathered data from 1,612 father/mother/daughter trios, which were used to estimate both maternal and paternal mutation rates, when pooled together with other already published data. Data on fathers and mothers' age at the time of birth of the daughter were also available for ∼93 % of the cases. Population analyses were computed considering the genetic information of a subset of 1,327 unrelated daughters, corresponding to 2,654 haplotypes from residents in several regions of five countries: Argentina, Brazil, Ecuador, Portugal and Spain. Genetic differentiation analyses between the population samples from the same country did not reveal signs of significant stratification, although results from Hardy-Weinberg and linkage disequilibrium tests indicated the need of larger studies for Ecuador and Brazilian populations. The high genetic diversity of the markers resulted in a large number of haplotype combinations, showing the need of huge databases for reliable estimates of their frequencies. It should also be noted the high number of new alleles found, many of them not included in the allelic ladders provided with the kit, as very diverse populations were analyzed. The overall estimates for locus specific average mutation rates varied between 7.5E-04 (for DXS7423) and 1.1E-02 (for DXS10135), the latter being a troublesome figure for kinship analyses. Most of the found mutations (∼92 %) are compatible with the gain or loss of a single repeat. Paternal mutation rates showed to be 5.2 times higher than maternal ones. We also found that older fathers were more prone to transmit mutated alleles, having this trend not been observed in the case of the mothers.
Collapse
|
48
|
Mittal P, Sinha R, Kumar A, Singh P, Ngasainao MR, Singh A, Singh IK. Focusing on DNA Repair and Damage Tolerance Mechanisms in Mycobacterium tuberculosis: An Emerging Therapeutic Theme. Curr Top Med Chem 2020; 20:390-408. [PMID: 31924156 DOI: 10.2174/1568026620666200110114322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/02/2019] [Accepted: 10/10/2019] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is one such disease that has become a nuisance in the world scenario and one of the most deadly diseases of the current times. The etiological agent of tuberculosis, Mycobacterium tuberculosis (M. tb) kills millions of people each year. Not only 1.7 million people worldwide are estimated to harbor M. tb in the latent form but also 5 to 15 percent of which are expected to acquire an infection during a lifetime. Though curable, a long duration of drug regimen and expense leads to low patient adherence. The emergence of multi-, extensive- and total- drug-resistant strains of M. tb further complicates the situation. Owing to high TB burden, scientists worldwide are trying to design novel therapeutics to combat this disease. Therefore, to identify new drug targets, there is a growing interest in targeting DNA repair pathways to fight this infection. Thus, this review aims to explore DNA repair and damage tolerance as an efficient target for drug development by understanding M. tb DNA repair and tolerance machinery and its regulation, its role in pathogenesis and survival, mutagenesis, and consequently, in the development of drug resistance.
Collapse
Affiliation(s)
- Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Rajesh Sinha
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Amit Kumar
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Pooja Singh
- Public Health Research Institute, NJMS-Rutgers University, New Jersey, United States
| | - Moses Rinchui Ngasainao
- Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| |
Collapse
|
49
|
Battaglia M. Epigenomic landscapes and their relationship to variation, fitness, and evolution. Neurosci Biobehav Rev 2020; 109:90-91. [PMID: 31911158 DOI: 10.1016/j.neubiorev.2020.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/22/2019] [Accepted: 01/02/2020] [Indexed: 11/27/2022]
Abstract
Doctor Tan's paper insightfully describes how epigenomic investigations of twins can help clarifying the mediation between environmental pressures, the genome, and behaviour. Here, I will expand on two emerging implications and their connections to the twin method. The first proposition deals with the transgenerational inheritance of epigenetic marks. The second examines the relationship between DNA methylation (DNAmeth) and mutation rate (MR), and their evolutionary implications.
Collapse
Affiliation(s)
- Marco Battaglia
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada; Division of Child and Youth Psychiatry, Centre for Addiction & Mental Health, Toronto, ON, Canada.
| |
Collapse
|
50
|
Tonoyan L, Friel R, O'Flaherty V. Mutation rate and efflux response of bacteria exposed to a novel antimicrobial iodo-thiocyanate complex. J Glob Antimicrob Resist 2020; 22:13-7. [PMID: 31857249 DOI: 10.1016/j.jgar.2019.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES Antimicrobials, at sub-lethal concentrations, can act as selectors and promoters of resistance by increasing mutation rates. We measured the rate of Escherichia coli mutation from levofloxacin (LVX) sensitivity to resistance when it was grown under the near-lethal challenge of the novel biocidal iodo-thiocyanate complex (ITC). Another relevant factor affecting the emergence of antimicrobial resistance is the role of efflux pumps. Consequently, we evaluated whether ITC could potentially be a substrate for efflux pumps, and thus that efflux-mediated resistance could arise towards ITC. METHODS The mutation rate was measured by fluctuation analysis, when multiple parallel E. coli cultures were grown in the absence and presence of ITC. Then the mutational events, which occurred independently in each culture, were scored by plating the fraction of the culture in LVX-selective solid media and compared with the total cell number. To detect if ITC is a substrate for efflux pumps, minimum inhibitory concentrations (MICs) were determined against Pseudomonas aeruginosa in the absence and presence of the efflux pump inhibitor (EPI). RESULTS We have found that the E. coli exposed to the near-lethal level of ITC had a slight, but not significant, increase in mutation rate compared with unexposed cultures. Furthermore, the presence of EPI decreased the MIC of ITC by a modest 2-fold, showing that ITC was not a target for efflux pumps. CONCLUSIONS ITC usage most likely will not promote resistance development via increased mutation rates, and efflux-mediated resistance emergence to it is less likely than for some other antimicrobials.
Collapse
|