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Sharma S, Kajjo S, Harra Z, Hasaj B, Delisle V, Ray D, Gutierrez RL, Carrier I, Kleinman C, Morris Q, Hughes TR, McInnes R, Fabian MR. Uncovering a mammalian neural-specific poly(A) binding protein with unique properties. Genes Dev 2023; 37:760-777. [PMID: 37704377 PMCID: PMC10546976 DOI: 10.1101/gad.350597.123] [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: 03/03/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023]
Abstract
The mRNA 3' poly(A) tail plays a critical role in regulating both mRNA translation and turnover. It is bound by the cytoplasmic poly(A) binding protein (PABPC), an evolutionarily conserved protein that can interact with translation factors and mRNA decay machineries to regulate gene expression. Mammalian PABPC1, the prototypical PABPC, is expressed in most tissues and interacts with eukaryotic translation initiation factor 4G (eIF4G) to stimulate translation in specific contexts. In this study, we uncovered a new mammalian PABPC, which we named neural PABP (neuPABP), as it is predominantly expressed in the brain. neuPABP maintains a unique architecture as compared with other PABPCs, containing only two RNA recognition motifs (RRMs) and maintaining a unique N-terminal domain of unknown function. neuPABP expression is activated in neurons as they mature during synaptogenesis, where neuPABP localizes to the soma and postsynaptic densities. neuPABP interacts with the noncoding RNA BC1, as well as mRNAs coding for ribosomal and mitochondrial proteins. However, in contrast to PABPC1, neuPABP does not associate with actively translating mRNAs in the brain. In keeping with this, we show that neuPABP has evolved such that it does not bind eIF4G and as a result fails to support protein synthesis in vitro. Taken together, these results indicate that mammals have expanded their PABPC repertoire in the brain and propose that neuPABP may support the translational repression of select mRNAs.
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Affiliation(s)
- Sahil Sharma
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Sam Kajjo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Zineb Harra
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Benedeta Hasaj
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Victoria Delisle
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Rodrigo L Gutierrez
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Isabelle Carrier
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Claudia Kleinman
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Quaid Morris
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Roderick McInnes
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Marc R Fabian
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada;
- Department of Biochemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Oncology, McGill University, Montreal, Quebec H3A 0G4, Canada
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2
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Matthey-Doret C, Colp MJ, Escoll P, Thierry A, Moreau P, Curtis B, Sahr T, Sarrasin M, Gray MW, Lang BF, Archibald JM, Buchrieser C, Koszul R. Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin reorganization. Genome Res 2022; 32:gr.276375.121. [PMID: 36109147 PMCID: PMC9528979 DOI: 10.1101/gr.276375.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/25/2022] [Indexed: 11/24/2022]
Abstract
The unicellular amoeba Acanthamoeba castellanii is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high-quality genome sequences for two extensively studied A. castellanii strains, Neff and C3. Combining long- and short-read data with Hi-C, we generated near chromosome-level assemblies for both strains with 90% of the genome contained in 29 scaffolds for the Neff strain and 31 for the C3 strain. Comparative genomics revealed strain-specific functional enrichment, most notably genes related to signal transduction in the C3 strain and to viral replication in Neff. Furthermore, we characterized the spatial organization of the A. castellanii genome and showed that it is reorganized during infection by Legionella pneumophila Infection-dependent chromatin loops were found to be enriched in genes for signal transduction and phosphorylation processes. In genomic regions where chromatin organization changed during Legionella infection, we found functional enrichment for genes associated with metabolism, organelle assembly, and cytoskeleton organization. Given Legionella infection is known to alter its host's cell cycle, to exploit the host's organelles, and to modulate the host's metabolism in its favor, these changes in chromatin organization may partly be related to mechanisms of host control during Legionella infection.
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Affiliation(s)
- Cyril Matthey-Doret
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
- Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Morgan J Colp
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Pedro Escoll
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
| | - Pierrick Moreau
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
| | - Bruce Curtis
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Tobias Sahr
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Matt Sarrasin
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Carmen Buchrieser
- Institut Pasteur, Université de Paris, Biologie des Bactéries Intracellulaires and CNRS UMR 6047, F-75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université de Paris, Unité Régulation Spatiale des Génomes, F-75015 Paris, France
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3
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Mourant A, Lecomte N, Moreau G. Size matters: When resource accessibility by ecosystem engineering elicits wood-boring beetle demographic responses. Ecol Evol 2021; 11:784-795. [PMID: 33520166 PMCID: PMC7820143 DOI: 10.1002/ece3.7079] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/06/2019] [Accepted: 10/11/2019] [Indexed: 11/10/2022] Open
Abstract
Episodic natural disturbances play a key role in ecosystem renewal, and ecological engineering could do so by transforming resource accessibility. While such coupling creates nontrophic and lasting interactions between resource consumers and ecosystem engineers, it is unclear how large the disturbance must be to sustain such coupling. Natural disturbances that occur from the ecological engineering by the Canadian beaver (Castor canadensis) modulate deadwood dynamics in many forest ecosystems. Relying on such episodes of fresh woody debris, primary wood-boring beetles, organisms that dig tunnels into those debris for reproduction, act as important deadwood decomposers in the ecosystem. Here, we investigate how the age and size of beaver disturbances act as predictors for primary wood-boring beetle abundance and species richness around beaver-altered habitat patches. To do so, we sampled beetles around 16 beaver-disturbed and unaltered watercourses within the Kouchibouguac National Park (Canada) and modeled beetle demographic responses to site conditions and their physical characteristics, distance from the watercourse, deadwood biomass, and the geographical location of the sites. Our results indicate that the size of the disturbance is positively associated with beetle abundance, which highlights unique deadwood dynamics inherent to large beaver ponds. The role of beavers in forest ecosystems by reaching multiple taxa at multiple spatiotemporal scales further exemplifies the need to study nontrophic interactions and their complex consequences in ecosystem management.
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Affiliation(s)
- Alexandre Mourant
- Département de biologieUniversité de MonctonMonctonNBCanada
- Canada Research Chair in Polar and Boreal EcologyUniversité de MonctonMonctonNBCanada
| | - Nicolas Lecomte
- Canada Research Chair in Polar and Boreal EcologyUniversité de MonctonMonctonNBCanada
| | - Gaétan Moreau
- Département de biologieUniversité de MonctonMonctonNBCanada
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Wu C, Ouk M, Wong YY, Anita NZ, Edwards JD, Yang P, Shah BR, Herrmann N, Lanctôt KL, Kapral MK, MacIntosh BJ, Rabin JS, Black SE, Swardfager W. Relationships between memory decline and the use of metformin or DPP4 inhibitors in people with type 2 diabetes with normal cognition or Alzheimer's disease, and the role APOE carrier status. Alzheimers Dement 2020; 16:1663-1673. [PMID: 32803865 PMCID: PMC7754496 DOI: 10.1002/alz.12161] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [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: 03/05/2020] [Revised: 06/30/2020] [Accepted: 07/07/2020] [Indexed: 01/14/2023]
Abstract
INTRODUCTION Few studies have examined memory decline among patients with type 2 diabetes using different oral hypoglycemic drugs. METHODS Participants with normal cognition (NC) or Alzheimer's disease (AD) dementia using a hypoglycemic medication (2005 to 2019) were identified from the National Alzheimer's Coordinating Center database. Delayed memory was assessed using the Wechsler Memory Scale Revised-Logical Memory test. Associations between oral drug classes and memory over time were examined using mixed-effects models with inverse probability treatment weights. RESULTS In NC (n = 1192), metformin use was associated with better memory performance over time, whereas in AD (n = 807), dipeptidyl peptidase-4 (DPP4) inhibitor use was associated with a slower rate of memory decline. Interaction effects suggested greater benefit associated with DPP4 inhibitor use among APOE ε4 carriers. DISCUSSION Associations between different oral hypoglycemic drugs and memory change were not consistent between cognitively normal elderly and those with AD dementia. APOE ε4 genotype modified some relationships.
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Affiliation(s)
- Che‐Yuan Wu
- Department of Pharmacology & ToxicologyUniversity of TorontoTorontoOntarioCanada
- Hurvitz Brain Sciences ProgramSunnybrook Research InstituteTorontoOntarioCanada
| | - Michael Ouk
- Department of Pharmacology & ToxicologyUniversity of TorontoTorontoOntarioCanada
- Hurvitz Brain Sciences ProgramSunnybrook Research InstituteTorontoOntarioCanada
| | - Yuen Yan Wong
- Department of Pharmacology & ToxicologyUniversity of TorontoTorontoOntarioCanada
- Hurvitz Brain Sciences ProgramSunnybrook Research InstituteTorontoOntarioCanada
| | - Natasha Z. Anita
- Department of Pharmacology & ToxicologyUniversity of TorontoTorontoOntarioCanada
- Hurvitz Brain Sciences ProgramSunnybrook Research InstituteTorontoOntarioCanada
| | - Jodi D. Edwards
- University of Ottawa Heart InstituteUniversity of OttawaOttawaOntarioCanada
- School of Epidemiology and Public HealthUniversity of OttawaOttawaOntarioCanada
- ICESOttawaOntarioCanada
| | - Pearl Yang
- Primary Care Research UnitDepartment of Family and Community MedicineSunnybrook Health Sciences CentreTorontoOntarioCanada
- Department of Family and Community MedicineFaculty of MedicineUniversity of TorontoTorontoOntarioCanada
| | - Baiju R. Shah
- ICESTorontoOntarioCanada
- Divisions of Endocrinology and Obstetric MedicineDepartment of MedicineSunnybrook Health Sciences CentreTorontoOntarioCanada
| | - Nathan Herrmann
- Hurvitz Brain Sciences ProgramSunnybrook Research InstituteTorontoOntarioCanada
- Department of PsychiatrySunnybrook Health Sciences CentreUniversity of TorontoTorontoOntarioCanada
| | - Krista L. Lanctôt
- Department of Pharmacology & ToxicologyUniversity of TorontoTorontoOntarioCanada
- Hurvitz Brain Sciences ProgramSunnybrook Research InstituteTorontoOntarioCanada
- Department of PsychiatrySunnybrook Health Sciences CentreUniversity of TorontoTorontoOntarioCanada
- KITE UHN Toronto Rehabilitation InstituteTorontoOntarioCanada
| | - Moira K. Kapral
- ICESTorontoOntarioCanada
- Department of Medicine (Division of General Internal Medicine) and Institute for Health Policy, Management, and EvaluationUniversity of TorontoTorontoOntarioCanada
| | - Bradley J. MacIntosh
- Hurvitz Brain Sciences ProgramSunnybrook Research InstituteTorontoOntarioCanada
- Canadian Partnership for Stroke RecoverySunnybrook Research InstituteTorontoOntarioCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoOntarioCanada
| | - Jennifer S. Rabin
- Hurvitz Brain Sciences ProgramSunnybrook Research InstituteTorontoOntarioCanada
- Department of MedicineDivision of NeurologyUniversity of TorontoTorontoOntarioCanada
- Harquail Centre for NeuromodulationHurvitz Brain Sciences ProgramSunnybrook Research InstituteTorontoOntarioCanada
- Rehabilitation Sciences InstituteUniversity of TorontoTorontoOntarioCanada
| | - Sandra E. Black
- Hurvitz Brain Sciences ProgramSunnybrook Research InstituteTorontoOntarioCanada
- Canadian Partnership for Stroke RecoverySunnybrook Research InstituteTorontoOntarioCanada
- Department of MedicineDivision of NeurologyUniversity of TorontoTorontoOntarioCanada
- Toronto Dementia Research AllianceTorontoOntarioCanada
| | - Walter Swardfager
- Department of Pharmacology & ToxicologyUniversity of TorontoTorontoOntarioCanada
- Hurvitz Brain Sciences ProgramSunnybrook Research InstituteTorontoOntarioCanada
- KITE UHN Toronto Rehabilitation InstituteTorontoOntarioCanada
- Canadian Partnership for Stroke RecoverySunnybrook Research InstituteTorontoOntarioCanada
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5
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El Andalousi J, Khairallah H, Zhuang Y, Ryan AK, Gupta IR. Role of Claudins in Renal Branching Morphogenesis. Physiol Rep 2020; 8:e14492. [PMID: 32975899 PMCID: PMC7518295 DOI: 10.14814/phy2.14492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 05/18/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 11/26/2022] Open
Abstract
Claudins are a family of tight junction proteins that are expressed during mouse kidney development. They regulate paracellular transport of solutes along the nephron and contribute to the final composition of the urinary filtrate. To understand their roles during development, we used a protein reagent, a truncated version of the Clostridium perfringens enterotoxin (C-CPE), to specifically remove a subset of claudin family members from mouse embryonic kidney explants at embryonic day 12. We observed that treatment with C-CPE decreased the number and the complexity of ureteric bud tips that formed: there were more single and less bifid ureteric bud tips when compared to control-treated explants. In addition, C-CPE-treated explants exhibited ureteric bud tips with larger lumens when compared to control explants (p < .05). Immunofluorescent analysis revealed decreased expression and localization of Claudin-3, -4, -6, and -8 to tight junctions of ureteric bud tips following treatment with C-CPE. Interestingly, Claudin-7 showed higher expression in the basolateral membrane of the ureteric bud lineage and poor localization to the tight junctions of the ureteric bud lineage both in controls and in C-CPE-treated explants. Taken together, it appears that claudin proteins may play a role in ureteric bud branching morphogenesis through changes in lumen formation that may affect the efficiency by which ureteric buds emerge and branch.
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Affiliation(s)
- Jasmine El Andalousi
- Research Institute of McGill University Health CentreMontreal Children's HospitalMontréalQuébecCanada
| | - Halim Khairallah
- Department of Human GeneticsMcGill UniversityMontréalQuébecCanada
| | - Yuan Zhuang
- Department of Human GeneticsMcGill UniversityMontréalQuébecCanada
| | - Aimee K. Ryan
- Department of Human GeneticsMcGill UniversityMontréalQuébecCanada
- Department of PediatricsMontreal Children's HospitalMcGill UniversityMontréalQuébecCanada
| | - Indra R. Gupta
- Department of Human GeneticsMcGill UniversityMontréalQuébecCanada
- Department of PediatricsMontreal Children's HospitalMcGill UniversityMontréalQuébecCanada
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Essl F, Lenzner B, Bacher S, Bailey S, Capinha C, Daehler C, Dullinger S, Genovesi P, Hui C, Hulme PE, Jeschke JM, Katsanevakis S, Kühn I, Leung B, Liebhold A, Liu C, MacIsaac HJ, Meyerson LA, Nuñez MA, Pauchard A, Pyšek P, Rabitsch W, Richardson DM, Roy HE, Ruiz GM, Russell JC, Sanders NJ, Sax DF, Scalera R, Seebens H, Springborn M, Turbelin A, van Kleunen M, von Holle B, Winter M, Zenni RD, Mattsson BJ, Roura‐Pascual N. Drivers of future alien species impacts: An expert-based assessment. Glob Chang Biol 2020; 26:4880-4893. [PMID: 32663906 PMCID: PMC7496498 DOI: 10.1111/gcb.15199] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/18/2020] [Indexed: 05/13/2023]
Abstract
Understanding the likely future impacts of biological invasions is crucial yet highly challenging given the multiple relevant environmental, socio-economic and societal contexts and drivers. In the absence of quantitative models, methods based on expert knowledge are the best option for assessing future invasion trajectories. Here, we present an expert assessment of the drivers of potential alien species impacts under contrasting scenarios and socioecological contexts through the mid-21st century. Based on responses from 36 experts in biological invasions, moderate (20%-30%) increases in invasions, compared to the current conditions, are expected to cause major impacts on biodiversity in most socioecological contexts. Three main drivers of biological invasions-transport, climate change and socio-economic change-were predicted to significantly affect future impacts of alien species on biodiversity even under a best-case scenario. Other drivers (e.g. human demography and migration in tropical and subtropical regions) were also of high importance in specific global contexts (e.g. for individual taxonomic groups or biomes). We show that some best-case scenarios can substantially reduce potential future impacts of biological invasions. However, rapid and comprehensive actions are necessary to use this potential and achieve the goals of the Post-2020 Framework of the Convention on Biological Diversity.
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7
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Choi M, Baek S, Lee S, Biondi M, Zheng C, Todorovic P, Li P, Hoogland S, Lu Z, de Arquer FPG, Sargent EH. Colloidal Quantum Dot Bulk Heterojunction Solids with Near-Unity Charge Extraction Efficiency. Adv Sci (Weinh) 2020; 7:2000894. [PMID: 32775165 PMCID: PMC7404161 DOI: 10.1002/advs.202000894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Colloidal quantum dots (CQDs) are of interest for optoelectronic applications owing to their tunable properties and ease of processing. Large-diameter CQDs offer optical response in the infrared (IR), beyond the bandgap of c-Si and perovskites. The absorption coefficient of IR CQDs (≈104 cm-1) entails the need for micrometer-thick films to maximize the absorption of IR light. This exceeds the thickness compatible with the efficient extraction of photogenerated carriers, a fact that limits device performance. Here, CQD bulk heterojunction solids are demonstrated that, with extended carrier transport length, enable efficient IR light harvesting. An in-solution doping strategy for large-diameter CQDs is devised that addresses the complex interplay between (100) facets and doping agents, enabling to control CQD doping, energetic configuration, and size homogeneity. The hetero-offset between n-type CQDs and p-type CQDs is manipulated to drive the transfer of electrons and holes into distinct carrier extraction pathways. This enables to form active layers exceeding thicknesses of 700 nm without compromising open-circuit voltage and fill factor. As a result, >90% charge extraction efficiency across the ultraviolet to IR range (350-1400 nm) is documented.
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Affiliation(s)
- Min‐Jae Choi
- Department of Electrical and Computer EngineeringUniversity of Toronto10 King's College RoadTorontoONM5S 3G4Canada
| | - Se‐Woong Baek
- Department of Electrical and Computer EngineeringUniversity of Toronto10 King's College RoadTorontoONM5S 3G4Canada
- Present address:
Department of Chemical and Biological EngineeringKorea University145 Anam‐RoSeongbuk‐GuSeoul02841South Korea
| | - Seungjin Lee
- Department of Electrical and Computer EngineeringUniversity of Toronto10 King's College RoadTorontoONM5S 3G4Canada
| | - Margherita Biondi
- Department of Electrical and Computer EngineeringUniversity of Toronto10 King's College RoadTorontoONM5S 3G4Canada
| | - Chao Zheng
- Department of Electrical and Computer EngineeringUniversity of Toronto10 King's College RoadTorontoONM5S 3G4Canada
| | - Petar Todorovic
- Department of Electrical and Computer EngineeringUniversity of Toronto10 King's College RoadTorontoONM5S 3G4Canada
| | - Peicheng Li
- Department of Material Science and EngineeringUniversity of Toronto184 College StTorontoONM5S 3E4Canada
| | - Sjoerd Hoogland
- Department of Electrical and Computer EngineeringUniversity of Toronto10 King's College RoadTorontoONM5S 3G4Canada
| | - Zheng‐Hong Lu
- Department of Material Science and EngineeringUniversity of Toronto184 College StTorontoONM5S 3E4Canada
| | - F. Pelayo García de Arquer
- Department of Electrical and Computer EngineeringUniversity of Toronto10 King's College RoadTorontoONM5S 3G4Canada
| | - Edward H. Sargent
- Department of Electrical and Computer EngineeringUniversity of Toronto10 King's College RoadTorontoONM5S 3G4Canada
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Burma JS, Copeland P, Macaulay A, Khatra O, Smirl JD. Comparison of diurnal variation, anatomical location, and biological sex within spontaneous and driven dynamic cerebral autoregulation measures. Physiol Rep 2020; 8:e14458. [PMID: 32537905 PMCID: PMC7293969 DOI: 10.14814/phy2.14458] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 01/03/2020] [Revised: 04/04/2020] [Accepted: 04/10/2020] [Indexed: 01/31/2023] Open
Abstract
Presently, the literature describing the influence of diurnal variation on dynamic cerebral autoregulation (dCA) metrics is sparse. Additionally, there is little data with respect to dCA comparisons between anterior/posterior circulation beds and biological sexes using squat-stand maneuvers. Eight male and eight female participants (n = 16) performed 5 min of spontaneous upright rest and squat-stand maneuvers at 0.05 and 0.10 Hz across seven time points throughout the day. All testing sessions commenced at 8:00 a.m. each day and dCA parameters were quantified across the cardiac cycle (diastole, mean, and systole) using transcranial Doppler ultrasound to insonate cerebral blood velocity within the middle and posterior cerebral arteries (MCA, PCA). No cardiac cycle alternations were seen spontaneous (all p > .207) while a trend was noted in some driven (all p > .051) dCA metrics. Driven dCA produced much lower coefficient of variances (all <21%) compared with spontaneous (all <58%). Moreover, no sex differences were found within driven metrics (all p > .096). Between vessels, PCA absolute gain was reduced within all spontaneous and driven measures (all p < .014) whereas coherence, phase, and normalized gain were unchanged (all p > .099). There appears to be little influence of diurnal variation on dCA measures across the day (8:00 a.m. to 6:00 p.m.). Absolute gain was blunted in the PCA relative to the MCA and consistent with previous literature, driven methods demonstrated vastly improved reproducibility metrics compared to spontaneous methods. Finally, no dCA differences were found between biological sexes, demonstrating that males and females regulate in a harmonious manner, when females are tested within the early follicular phase of the menstrual cycle.
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Affiliation(s)
- Joel S. Burma
- Concussion Research LaboratoryFaculty of Health and Exercise ScienceUniversity of British ColumbiaKelownaBCCanada
- Sport Injury Prevention Research CentreFaculty of KinesiologyUniversity of CalgaryCalgaryABCanada
- Human Performance LaboratoryFaculty of KinesiologyUniversity of CalgaryCalgaryABCanada
- Hotchkiss Brain InstituteUniversity of CalgaryCalgaryABCanada
- Integrated Concussion Research ProgramUniversity of CalgaryCalgaryABCanada
| | - Paige Copeland
- Concussion Research LaboratoryFaculty of Health and Exercise ScienceUniversity of British ColumbiaKelownaBCCanada
| | - Alannah Macaulay
- Concussion Research LaboratoryFaculty of Health and Exercise ScienceUniversity of British ColumbiaKelownaBCCanada
| | - Omeet Khatra
- Faculty of MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Jonathan D. Smirl
- Concussion Research LaboratoryFaculty of Health and Exercise ScienceUniversity of British ColumbiaKelownaBCCanada
- Sport Injury Prevention Research CentreFaculty of KinesiologyUniversity of CalgaryCalgaryABCanada
- Human Performance LaboratoryFaculty of KinesiologyUniversity of CalgaryCalgaryABCanada
- Hotchkiss Brain InstituteUniversity of CalgaryCalgaryABCanada
- Integrated Concussion Research ProgramUniversity of CalgaryCalgaryABCanada
- Alberta Children's Hospital Research InstituteUniversity of CalgaryCalgaryABCanada
- Libin Cardiovascular Institute of AlbertaUniversity of CalgaryCalgaryABCanada
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9
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Poroca DR, Amer N, Li A, Hanrahan JW, Chappe VM. Changes in the R-region interactions depend on phosphorylation and contribute to PKA and PKC regulation of the cystic fibrosis transmembrane conductance regulator chloride channel. FASEB Bioadv 2020; 2:33-48. [PMID: 32123855 PMCID: PMC6996395 DOI: 10.1096/fba.2019-00053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/19/2019] [Indexed: 01/30/2023] Open
Abstract
The CFTR chloride channel is regulated by phosphorylation at PKA and PKC consensus sites within its regulatory region (R-region) through a mechanism, which is still not completely understood. We used a split-CFTR construct expressing the N-term-TMD1-NBD1 (Front Half; FH), TMD2-NBD2-C-Term (Back Half; BH), and the R-region as separate polypeptides (Split-R) in BHK cells, to investigate in situ how different phosphorylation conditions affect the R-region interactions with other parts of the protein. In proximity ligation assays, we studied the formation of complexes between the R-region and each half of the Split-CFTR. We found that at basal conditions, the density of complexes formed between the R-region and both halves of the split channel were equal. PKC stimulation alone had no effect, whereas PKA stimulation induced the formation of more complexes between the R-region and both halves compared to basal conditions. Moreover, PKC + PKA stimulation further enhanced the formation of FH-R complexes by 40% from PKA level. In cells expressing the Split-R with the two inhibitory PKC sites on the R-region inactivated (SR-S641A/T682A), density of FH-R complexes was much higher than in Split-R WT expressing cells after PKC or PKC + PKA stimulation. No differences were observed for BH-R complexes measured at all phosphorylation conditions. Since full-length CFTR channels display large functional responses to PKC + PKA in WT and S641A/T682A mutant, we conclude that FH-R interactions are important for CFTR function. Inactivation of consensus PKC site serine 686 (S686A) significantly reduced the basal BH-R interaction and prevented the PKC enhancing effect on CFTR function and FH-R interaction. The phospho-mimetic mutation (S686D) restored basal BH-R interaction and the PKC enhancing effect on CFTR function with enhanced FH-R interaction. As the channel function is mainly stimulated by PKA phosphorylation of the R-region, and this response is known to be enhanced by PKC phosphorylation, our data support a model in which the regulation of CFTR activation results from increased interactions of the R-region with the N-term-TMD1-NBD1. Also, serine S686 was found to be critical for the PKC enhancing effect which requires a permissive BH-R interaction at basal level and increased FH-R interaction after PKC + PKA phosphorylation.
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Affiliation(s)
- Diogo R. Poroca
- Department of Physiology & BiophysicsDalhousie UniversityHalifaxNSCanada
| | - Noha Amer
- Department of Physiology & BiophysicsDalhousie UniversityHalifaxNSCanada
| | - Audrey Li
- Department of Physiology & BiophysicsDalhousie UniversityHalifaxNSCanada
| | | | - Valerie M. Chappe
- Department of Physiology & BiophysicsDalhousie UniversityHalifaxNSCanada
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10
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Lumley LM, Pouliot E, Laroche J, Boyle B, Brunet BMT, Levesque RC, Sperling FAH, Cusson M. Continent-wide population genomic structure and phylogeography of North America's most destructive conifer defoliator, the spruce budworm ( Choristoneura fumiferana). Ecol Evol 2020; 10:914-927. [PMID: 32015854 PMCID: PMC6988549 DOI: 10.1002/ece3.5950] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/28/2019] [Accepted: 12/02/2019] [Indexed: 02/01/2023] Open
Abstract
The spruce budworm, Choristoneura fumiferana, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3,650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations: Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba-Ontario border), and Eastern (Manitoba-Ontario border to the Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce (Picea glauca), providing evidence that spruce budworm and spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated spruce budworm populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete. Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co-adapted blocks of genes, and gene flow between subpopulations.
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Affiliation(s)
- Lisa M. Lumley
- Royal Alberta MuseumEdmontonABCanada
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
| | - Esther Pouliot
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
| | | | | | | | | | | | - Michel Cusson
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
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11
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Haase K, Gillrie MR, Hajal C, Kamm RD. Pericytes Contribute to Dysfunction in a Human 3D Model of Placental Microvasculature through VEGF-Ang-Tie2 Signaling. Adv Sci (Weinh) 2019; 6:1900878. [PMID: 31832308 PMCID: PMC6891921 DOI: 10.1002/advs.201900878] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/18/2019] [Indexed: 05/05/2023]
Abstract
Placental vasculopathies are associated with a number of pregnancy-related diseases, including pre-eclampsia (PE)-a leading cause of maternal-fetal morbidity and mortality worldwide. Placental presentations of PE are associated with endothelial dysfunction, reduced vessel perfusion, white blood cell infiltration, and altered production of angiogenic factors within the placenta (a candidate mechanism). Despite maintaining vascular quiescence in other tissues, how pericytes contribute to vascular growth and signaling in the placenta remains unknown. Here, pericytes are hypothesized to play a detrimental role in the pathogenesis of placental vascular growth. A perfusable triculture model is developed, consisting of human endothelial cells, fibroblasts, and pericytes, capable of recapitulating growth and remodeling in a system that mimics inflamed placental microvessels. Placental pericytes are shown to contribute to growth restriction of microvessels over time, an effect that is strongly regulated by vascular endothelial growth factor and Angiopoietin/Tie2 signaling. Furthermore, this model is capable of recapitulating essential processes including tumor necrosis factor alpha (TNFα)-mediated vascular leakage and leukocyte infiltration, both important aspects associated with placental PE. This placental vascular model highlights that an imbalance in endothelial-pericyte crosstalk can play a critical role in the development of vascular pathology and associated diseases.
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Affiliation(s)
- Kristina Haase
- Massachusetts Institute of TechnologyCambridgeMA02139USA
- Present address:
EMBL BarcelonaCarrer del Dr. Aiguader, 88BarcelonaSpain08003
| | - Mark R. Gillrie
- Massachusetts Institute of TechnologyCambridgeMA02139USA
- Department of MedicineUniversity of CalgaryCalgaryABT2N 1N4Canada
| | - Cynthia Hajal
- Massachusetts Institute of TechnologyCambridgeMA02139USA
| | - Roger D. Kamm
- Massachusetts Institute of TechnologyCambridgeMA02139USA
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12
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Abdolahzadeh A, Dolgosheina EV, Unrau PJ. RNA detection with high specificity and sensitivity using nested fluorogenic Mango NASBA. RNA 2019; 25:1806-1813. [PMID: 31551299 PMCID: PMC6859864 DOI: 10.1261/rna.072629.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/16/2019] [Indexed: 05/30/2023]
Abstract
There is a pressing need for nucleic acid-based assays that are capable of rapidly and reliably detecting pathogenic organisms. Many of the techniques available for the detection of pathogenic RNA possess one or more limiting factors that make the detection of low-copy RNA challenging. Although RT-PCR is the most commonly used method for detecting pathogen-related RNA, it requires expensive thermocycling equipment and is comparatively slow. Isothermal methods promise procedural simplicity but have traditionally suffered from amplification artifacts that tend to preclude easy identification of target nucleic acids. Recently, the isothermal SHERLOCK system overcame this problem by using CRISPR to distinguish amplified target sequences from artifactual background signal. However, this system comes at the cost of introducing considerable enzymatic complexity and a corresponding increase in total assay time. Therefore, simpler and less expensive strategies are highly desirable. Here, we demonstrate that by nesting NASBA primers and modifying the NASBA inner primers to encode an RNA Mango aptamer sequence we can dramatically increase the sensitivity of NASBA to 1.5 RNA molecules per microliter. As this isothermal nucleic acid detection scheme directly produces a fluorescent reporter, real-time detection is intrinsic to the assay. Nested Mango NASBA is highly specific and, in contrast to existing RNA detection systems, offers a cheap, simple, and specific way to rapidly detect single-molecule amounts of pathogenic RNA.
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Affiliation(s)
- Amir Abdolahzadeh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Elena V Dolgosheina
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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13
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Abstract
The RNA world hypothesis relies on the ability of ribonucleic acids to spontaneously acquire complex structures capable of supporting essential biological functions. Multiple sophisticated evolutionary models have been proposed for their emergence, but they often assume specific conditions. In this work, we explore a simple and parsimonious scenario describing the emergence of complex molecular structures at the early stages of life. We show that at specific GC content regimes, an undirected replication model is sufficient to explain the apparition of multibranched RNA secondary structures-a structural signature of many essential ribozymes. We ran a large-scale computational study to map energetically stable structures on complete mutational networks of 50-nt-long RNA sequences. Our results reveal that the sequence landscape with stable structures is enriched with multibranched structures at a length scale coinciding with the appearance of complex structures in RNA databases. A random replication mechanism preserving a 50% GC content may suffice to explain a natural enrichment of stable complex structures in populations of functional RNAs. In contrast, an evolutionary mechanism eliciting the most stable folds at each generation appears to help reaching multibranched structures at highest GC content.
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Affiliation(s)
- Carlos G Oliver
- School of Computer Science, McGill University, Montreal, QC H3A 2B3, Canada
| | - Vladimir Reinharz
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 34126, South Korea
| | - Jérôme Waldispühl
- School of Computer Science, McGill University, Montreal, QC H3A 2B3, Canada
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14
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Pickup M, Brandvain Y, Fraïsse C, Yakimowski S, Barton NH, Dixit T, Lexer C, Cereghetti E, Field DL. Mating system variation in hybrid zones: facilitation, barriers and asymmetries to gene flow. New Phytol 2019; 224:1035-1047. [PMID: 31505037 PMCID: PMC6856794 DOI: 10.1111/nph.16180] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/19/2019] [Indexed: 05/11/2023]
Abstract
Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (1) the two-way interaction between introgression and the evolution of reproductive systems, and (2) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation.
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Affiliation(s)
- Melinda Pickup
- Institute of Science and Technology AustriaAm Campus 1Klosterneuburg3400Austria
| | - Yaniv Brandvain
- Department of Plant and Microbial BiologyUniversity of Minnesota1500 Gortner AveSt Paul, MinneapolisMN55108USA
| | - Christelle Fraïsse
- Institute of Science and Technology AustriaAm Campus 1Klosterneuburg3400Austria
| | - Sarah Yakimowski
- Department of BiologyQueen's University116 Barrie StKingstonONK7L 3N6Canada
| | - Nicholas H. Barton
- Institute of Science and Technology AustriaAm Campus 1Klosterneuburg3400Austria
| | - Tanmay Dixit
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeCB2 3EJUK
| | - Christian Lexer
- Department of Botany and Biodiversity ResearchFaculty of Life SciencesUniversity of ViennaA‐1030ViennaAustria
| | - Eva Cereghetti
- Institute of Science and Technology AustriaAm Campus 1Klosterneuburg3400Austria
| | - David L. Field
- Department of Botany and Biodiversity ResearchFaculty of Life SciencesUniversity of ViennaA‐1030ViennaAustria
- School of ScienceEdith Cowan University270 Joondalup DriveJoondalupWestern Australia6027Australia
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15
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Chain FJJ, Flynn JM, Bull JK, Cristescu ME. Accelerated rates of large-scale mutations in the presence of copper and nickel. Genome Res 2019; 29:64-73. [PMID: 30487211 PMCID: PMC6314161 DOI: 10.1101/gr.234724.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022]
Abstract
Mutation rate variation has been under intense investigation for decades. Despite these efforts, little is known about the extent to which environmental stressors accelerate mutation rates and influence the genetic load of populations. Moreover, most studies on stressors have focused on unicellular organisms and point mutations rather than large-scale deletions and duplications (copy number variations [CNVs]). We estimated mutation rates in Daphnia pulex exposed to low levels of environmental stressors as well as the effect of selection on de novo mutations. We conducted a mutation accumulation (MA) experiment in which selection was minimized, coupled with an experiment in which a population was propagated under competitive conditions in a benign environment. After an average of 103 generations of MA propagation, we sequenced 60 genomes and found significantly accelerated rates of deletions and duplications in MA lines exposed to ecologically relevant concentrations of metals. Whereas control lines had gene deletion and duplication rates comparable to other multicellular eukaryotes (1.8 × 10-6 per gene per generation), the presence of nickel and copper increased these rates fourfold. The realized mutation rate under selection was reduced to 0.4× that of control MA lines, providing evidence that CNVs contribute to mutational load. Our CNV breakpoint analysis revealed that nonhomologous recombination associated with regions of DNA fragility is the primary source of CNVs, plausibly linking metal-induced DNA strand breaks with higher CNV rates. Our findings suggest that environmental stress, in particular multiple stressors, can have profound effects on large-scale mutation rates and mutational load of multicellular organisms.
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Affiliation(s)
- Frédéric J J Chain
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Jullien M Flynn
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - James K Bull
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
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