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Easwaran S, Montell DJ. A genome-wide association study implicates the olfactory system in Drosophila melanogaster diapause-associated lifespan extension and fecundity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.10.584341. [PMID: 39005458 PMCID: PMC11244867 DOI: 10.1101/2024.03.10.584341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The effects of environmental stress on animal life are gaining importance with climate change. Diapause is a dormancy program that occurs in response to an adverse environment, followed by resumption of development and reproduction upon the return of favorable conditions. Diapause is a complex trait, so we leveraged the Drosophila genetic reference panel (DGRP) lines and conducted a Genome-Wide Association Study (GWAS) to characterize the genetic basis of diapause. We assessed post-diapause and non-diapause fecundity across 193 DGRP lines. GWAS revealed 546 genetic variants, encompassing single nucleotide polymorphisms, insertions and deletions associated with post-diapause fecundity. We identified 291 candidate diapause-associated genes, 40 of which had previously been associated with diapause. 89 of the candidates were associated with more than one SNP. Gene network analysis indicated that the diapause-associated genes were primarily linked to neuronal and reproductive system development. Similarly, comparison with results from other fly GWAS revealed the greatest overlap with olfactory-behavior-associated and fecundity-and-lifespan-associated genes. An RNAi screen of the top candidates identified two neuronal genes, Dip-γ and Scribbler, to be required during recovery for post-diapause fecundity. We complemented the genetic analysis with a test of which neurons are required for successful diapause. We found that although amputation of the antenna had little to no effect on non-diapause lifespan, it reduced diapause lifespan and postdiapause fecundity. We further show that olfactory receptor neurons and temperature-sensing neurons are required for successful recovery from diapause. Our results provide insights into the molecular, cellular, and genetic basis of adult reproductive diapause in Drosophila .
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Yamamoto A, Huang W, Anholt RR, Mackay TF. The genetic basis of variation in Drosophila melanogaster mating behavior. iScience 2024; 27:109837. [PMID: 38766354 PMCID: PMC11099327 DOI: 10.1016/j.isci.2024.109837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/01/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Mating behavior is an essential fitness trait. We used the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP) to gain insights into the evolution of mating success and to evaluate the overlap in genetic architecture of mating behavior between the sexes. We found significant genetic variation for mating success when DGRP males and females from the same line were mated together, and when DGRP males and females were mated to an unrelated strain of the opposite sex. The mating success of DGRP males and females was not correlated when they were paired with the unrelated strain, suggesting independent genetic architecture of mating success in males and females that was confirmed by genome-wide association analyses. However, the mating success between pairs of the same or different DGRP lines was predicted accurately by the respective female and male mating success with the unrelated line.
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Affiliation(s)
- Akihiko Yamamoto
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Robert R.H. Anholt
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F.C. Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
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3
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Odriozola A, González A, Álvarez-Herms J, Corbi F. Sleep regulation and host genetics. ADVANCES IN GENETICS 2024; 111:497-535. [PMID: 38908905 DOI: 10.1016/bs.adgen.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Due to the multifactorial and complex nature of rest, we focus on phenotypes related to sleep. Sleep regulation is a multifactorial process. In this chapter, we focus on those phenotypes inherent to sleep that are highly prevalent in the population, and that can be modulated by lifestyle, such as sleep quality and duration, insomnia, restless leg syndrome and daytime sleepiness. We, therefore, leave in the background those phenotypes that constitute infrequent pathologies or for which the current level of scientific evidence does not favour the implementation of practical approaches of this type. Similarly, the regulation of sleep quality is intimately linked to the regulation of the circadian rhythm. Although this relationship is discussed in the sections that require it, the in-depth study of circadian rhythm regulation at the molecular level deserves a separate chapter, and this is how it is dealt with in this volume.
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Affiliation(s)
- Adrián Odriozola
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Adriana González
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jesús Álvarez-Herms
- Phymo® Lab, Physiology, and Molecular Laboratory, Collado Hermoso, Segovia, Spain
| | - Francesc Corbi
- Institut Nacional d'Educació Física de Catalunya (INEFC), Centre de Lleida, Universitat de Lleida (UdL), Lleida, Spain
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4
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Wynne NE, Applebach E, Chandrasegaran K, Ajayi OM, Chakraborty S, Bonizzoni M, Lahondère C, Benoit JB, Vinauger C. Aedes albopictus colonies from different geographic origins differ in their sleep and activity levels but not in the time of peak activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585187. [PMID: 38559099 PMCID: PMC10980008 DOI: 10.1101/2024.03.15.585187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Mosquitoes occupy a wide range of habitats where they experience various environmental conditions. The ability of some species, such as the tiger mosquito, Aedes albopictus, to adapt to local conditions certainly contributes to their invasive success. Among traits that remain to be examined, mosquitoes' ability to time their activity with that of the local host population has been suggested to be of significant epidemiological importance. However, whether different populations display heritable differences in their chronotype has not been examined. Here, we compared laboratory strains originating from 8 populations from 3 continents, monitored their spontaneous locomotor activity patterns, and analyzed their sleep-like states. Overall, all strains showed conserved diurnal activity concentrated in the hours preceding the crepuscule. Similarly, they all showed increased sleep levels during the morning and night hours. However, we observed strain-specific differences in the activity levels at each phase of the day. We also observed differences in the fraction of time that each strain spends in a sleep-like state, explained by variations in the sleep architecture across strains. Human population density and the latitude of the site of geographic origin of the tested strain showed significant effects on sleep and activity patterns. Altogether, these results suggest that Ae. albopictus mosquitoes adapt to local environmental conditions via heritable adaptations of their chronotype.
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Affiliation(s)
- Nicole E Wynne
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Emilie Applebach
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Karthikeyan Chandrasegaran
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Oluwaseun M Ajayi
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Souvik Chakraborty
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Mariangela Bonizzoni
- Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy
| | - Chloé Lahondère
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Clément Vinauger
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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5
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Draper IR, Roberts MA, Gailloud M, Jackson FR. Drosophila noktochor regulates night sleep via a local mushroom body circuit. iScience 2024; 27:109106. [PMID: 38380256 PMCID: PMC10877950 DOI: 10.1016/j.isci.2024.109106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 11/22/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
We show that a sleep-regulating, Ig-domain protein (NKT) is secreted from Drosophila mushroom body (MB) α'/β' neurons to act locally on other MB cell types. Pan-neuronal or broad MB expression of membrane-tethered NKT (tNkt) protein reduced sleep, like that of an NKT null mutant, suggesting blockade of a receptor mediating endogenous NKT action. In contrast, expression in neurons requiring NKT (the MB α'/β' cells), or non-MB sleep-regulating centers, did not reduce night sleep, indicating the presence of a local MB sleep-regulating circuit consisting of communicating neural subtypes. We suggest that the leucocyte-antigen-related like (Lar) transmembrane receptor may mediate NKT action. Knockdown or overexpression of Lar in the MB increased or decreased sleep, respectively, indicating the receptor promotes wakefulness. Surprisingly, selective expression of tNkt or knockdown of Lar in MB wake-promoting cells increased rather than decreased sleep, suggesting that NKT acts on wake- as well as sleep-promoting cell types to regulate sleep.
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Affiliation(s)
- Isabelle R. Draper
- Department of Neuroscience, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
- Department of Medicine, Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington Street, Boston, MA 02111, USA
| | - Mary A. Roberts
- Department of Neuroscience, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Matthew Gailloud
- Department of Neuroscience, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
| | - F. Rob Jackson
- Department of Neuroscience, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
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6
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Dopp J, Ortega A, Davie K, Poovathingal S, Baz ES, Liu S. Single-cell transcriptomics reveals that glial cells integrate homeostatic and circadian processes to drive sleep-wake cycles. Nat Neurosci 2024; 27:359-372. [PMID: 38263460 PMCID: PMC10849968 DOI: 10.1038/s41593-023-01549-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 12/07/2023] [Indexed: 01/25/2024]
Abstract
The sleep-wake cycle is determined by circadian and sleep homeostatic processes. However, the molecular impact of these processes and their interaction in different brain cell populations are unknown. To fill this gap, we profiled the single-cell transcriptome of adult Drosophila brains across the sleep-wake cycle and four circadian times. We show cell type-specific transcriptomic changes, with glia displaying the largest variation. Glia are also among the few cell types whose gene expression correlates with both sleep homeostat and circadian clock. The sleep-wake cycle and sleep drive level affect the expression of clock gene regulators in glia, and disrupting clock genes specifically in glia impairs homeostatic sleep rebound after sleep deprivation. These findings provide a comprehensive view of the effects of sleep homeostatic and circadian processes on distinct cell types in an entire animal brain and reveal glia as an interaction site of these two processes to determine sleep-wake dynamics.
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Affiliation(s)
- Joana Dopp
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Antonio Ortega
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Kristofer Davie
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Suresh Poovathingal
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - El-Sayed Baz
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Sha Liu
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.
- Department of Neurosciences, KU Leuven, Leuven, Belgium.
- Leuven Brain Institute, KU Leuven, Leuven, Belgium.
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7
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Eiman MN, Kumar S, Serrano Negron YL, Tansey TR, Harbison ST. Genome-wide association in Drosophila identifies a role for Piezo and Proc-R in sleep latency. Sci Rep 2024; 14:260. [PMID: 38168575 PMCID: PMC10761942 DOI: 10.1038/s41598-023-50552-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Sleep latency, the amount of time that it takes an individual to fall asleep, is a key indicator of sleep need. Sleep latency varies considerably both among and within species and is heritable, but lacks a comprehensive description of its underlying genetic network. Here we conduct a genome-wide association study of sleep latency. Using previously collected sleep and activity data on a wild-derived population of flies, we calculate sleep latency, confirming significant, heritable genetic variation for this complex trait. We identify 520 polymorphisms in 248 genes contributing to variability in sleep latency. Tests of mutations in 23 candidate genes and additional putative pan-neuronal knockdown of 9 of them implicated CG44153, Piezo, Proc-R and Rbp6 in sleep latency. Two large-effect mutations in the genes Proc-R and Piezo were further confirmed via genetic rescue. This work greatly enhances our understanding of the genetic factors that influence variation in sleep latency.
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Affiliation(s)
- Matthew N Eiman
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Drexel University College of Medicine, Philadelphia, PA, USA
| | - Shailesh Kumar
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Neuroscience and Behavior, National Institute On Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Yazmin L Serrano Negron
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Terry R Tansey
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Susan T Harbison
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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8
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Gessner NR, Peiravi M, Zhang F, Yimam S, Springer D, Harbison ST. A conserved role for frizzled in sleep architecture. SLEEP ADVANCES : A JOURNAL OF THE SLEEP RESEARCH SOCIETY 2023; 4:zpad045. [PMID: 38033424 PMCID: PMC10684271 DOI: 10.1093/sleepadvances/zpad045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/03/2023] [Indexed: 12/02/2023]
Abstract
Previous studies of natural variants in Drosophila melanogaster implicated the Wnt signaling receptor frizzled in sleep. Given that the Wnt signaling pathway is highly conserved across species, we hypothesized that frizzled class receptor 1 (Fzd1), the murine homolog of frizzled, would also have a role in sleep. Using a CRISPR transgenic approach, we removed most of the Fzd1 coding region from C57BL/6N mice. We used a video assay to measure sleep characteristics in Fzd1-deficient mice. As Wnt signaling is known to affect visuospatial memory, we also examined the impact of the deletion on learning and memory using the novel object recognition (NOR) paradigm. Fzd1-deficient mice had altered sleep compared to littermate controls. The mice did not respond differently to the NOR paradigm compared to controls but did display anxiety-like behavior. Our strategy demonstrates that the study of natural variation in Drosophila sleep translates into candidate genes for sleep in vertebrate species such as the mouse.
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Affiliation(s)
- Nicholas R Gessner
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Morteza Peiravi
- Murine Phenotyping Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fan Zhang
- Transgenic Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shemsiya Yimam
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Danielle Springer
- Murine Phenotyping Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Susan T Harbison
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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9
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Ajayi OM, Wynne NE, Chen SC, Vinauger C, Benoit JB. Sleep: An Essential and Understudied Process in the Biology of Blood-Feeding Arthropods. Integr Comp Biol 2023; 63:530-547. [PMID: 37429615 PMCID: PMC10503478 DOI: 10.1093/icb/icad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023] Open
Abstract
Understanding the biology of blood-feeding arthropods is critical to managing them as vectors of etiological agents. Circadian rhythms act in the regulation of behavioral and physiological aspects such as blood feeding, immunity, and reproduction. However, the impact of sleep on these processes has been largely ignored in blood-feeding arthropods, but recent studies in mosquitoes show that sleep-like states directly impact host landing and blood feeding. Our focus in this review is on discussing the relationship between sleep and circadian rhythms in blood-feeding arthropods along with how unique aspects such as blood gluttony and dormancy can impact sleep-like states. We highlight that sleep-like states are likely to have profound impacts on vector-host interactions but will vary between lineages even though few direct studies have been conducted. A myriad of factors, such as artificial light, could directly impact the time and levels of sleep in blood-feeding arthropods and their roles as vectors. Lastly, we discuss underlying factors that make sleep studies in blood-feeding arthropods difficult and how these can be bypassed. As sleep is a critical factor in the fitness of animal systems, a lack of focus on sleep in blood-feeding arthropods represents a significant oversight in understanding their behavior and its role in pathogen transmission.
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Affiliation(s)
- Oluwaseun M Ajayi
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Nicole E Wynne
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Shyh-Chi Chen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Clément Vinauger
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
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10
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Souto-Maior C, Serrano Negron YL, Harbison ST. Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration. PLoS Comput Biol 2023; 19:e1011389. [PMID: 37561813 PMCID: PMC10443883 DOI: 10.1371/journal.pcbi.1011389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/22/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
All but the simplest phenotypes are believed to result from interactions between two or more genes forming complex networks of gene regulation. Sleep is a complex trait known to depend on the system of feedback loops of the circadian clock, and on many other genes; however, the main components regulating the phenotype and how they interact remain an unsolved puzzle. Genomic and transcriptomic data may well provide part of the answer, but a full account requires a suitable quantitative framework. Here we conducted an artificial selection experiment for sleep duration with RNA-seq data acquired each generation. The phenotypic results are robust across replicates and previous experiments, and the transcription data provides a high-resolution, time-course data set for the evolution of sleep-related gene expression. In addition to a Hierarchical Generalized Linear Model analysis of differential expression that accounts for experimental replicates we develop a flexible Gaussian Process model that estimates interactions between genes. 145 gene pairs are found to have interactions that are different from controls. Our method appears to be not only more specific than standard correlation metrics but also more sensitive, finding correlations not significant by other methods. Statistical predictions were compared to experimental data from public databases on gene interactions. Mutations of candidate genes implicated by our results affected night sleep, and gene expression profiles largely met predicted gene-gene interactions.
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Affiliation(s)
- Caetano Souto-Maior
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Yazmin L. Serrano Negron
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Susan T. Harbison
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, Maryland, United States of America
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11
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Rand MD, Tennessen JM, Mackay TFC, Anholt RRH. Perspectives on the Drosophila melanogaster Model for Advances in Toxicological Science. Curr Protoc 2023; 3:e870. [PMID: 37639638 PMCID: PMC10463236 DOI: 10.1002/cpz1.870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The use of Drosophila melanogaster for studies of toxicology has grown considerably in the last decade. The Drosophila model has long been appreciated as a versatile and powerful model for developmental biology and genetics because of its ease of handling, short life cycle, low cost of maintenance, molecular genetic accessibility, and availability of a wide range of publicly available strains and data resources. These features, together with recent unique developments in genomics and metabolomics, make the fly model especially relevant and timely for the development of new approach methodologies and movements toward precision toxicology. Here, we offer a perspective on how flies can be leveraged to identify risk factors relevant to environmental exposures and human health. First, we review and discuss fundamental toxicologic principles for experimental design with Drosophila. Next, we describe quantitative and systems genetics approaches to resolve the genetic architecture and candidate pathways controlling susceptibility to toxicants. Finally, we summarize the current state and future promise of the emerging field of Drosophila metabolomics for elaborating toxic mechanisms. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Matthew D. Rand
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | | | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, South Carolina 29646, USA
| | - Robert R. H. Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, South Carolina 29646, USA
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12
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Kniazkina M, Dyachuk V. Does EGFR Signaling Mediate Orexin System Activity in Sleep Initiation? Int J Mol Sci 2023; 24:ijms24119505. [PMID: 37298454 DOI: 10.3390/ijms24119505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Sleep-wake cycle disorders are an important symptom of many neurological diseases, including Parkinson's disease, Alzheimer's disease, and multiple sclerosis. Circadian rhythms and sleep-wake cycles play a key role in maintaining the health of organisms. To date, these processes are still poorly understood and, therefore, need more detailed elucidation. The sleep process has been extensively studied in vertebrates, such as mammals and, to a lesser extent, in invertebrates. A complex, multi-step interaction of homeostatic processes and neurotransmitters provides the sleep-wake cycle. Many other regulatory molecules are also involved in the cycle regulation, but their functions remain largely unclear. One of these signaling systems is epidermal growth factor receptor (EGFR), which regulates the activity of neurons in the modulation of the sleep-wake cycle in vertebrates. We have evaluated the possible role of the EGFR signaling pathway in the molecular regulation of sleep. Understanding the molecular mechanisms that underlie sleep-wake regulation will provide critical insight into the fundamental regulatory functions of the brain. New findings of sleep-regulatory pathways may provide new drug targets and approaches for the treatment of sleep-related diseases.
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Affiliation(s)
- Marina Kniazkina
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia
| | - Vyacheslav Dyachuk
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia
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13
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Lane JM, Qian J, Mignot E, Redline S, Scheer FAJL, Saxena R. Genetics of circadian rhythms and sleep in human health and disease. Nat Rev Genet 2023; 24:4-20. [PMID: 36028773 PMCID: PMC10947799 DOI: 10.1038/s41576-022-00519-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2022] [Indexed: 12/13/2022]
Abstract
Circadian rhythms and sleep are fundamental biological processes integral to human health. Their disruption is associated with detrimental physiological consequences, including cognitive, metabolic, cardiovascular and immunological dysfunctions. Yet many of the molecular underpinnings of sleep regulation in health and disease have remained elusive. Given the moderate heritability of circadian and sleep traits, genetics offers an opportunity that complements insights from model organism studies to advance our fundamental molecular understanding of human circadian and sleep physiology and linked chronic disease biology. Here, we review recent discoveries of the genetics of circadian and sleep physiology and disorders with a focus on those that reveal causal contributions to complex diseases.
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Affiliation(s)
- Jacqueline M Lane
- Center for Genomic Medicine and Department of Anaesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital; and Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Jingyi Qian
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital; and Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Emmanuel Mignot
- Center for Narcolepsy, Stanford University, Palo Alto, California, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital; and Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Frank A J L Scheer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital; and Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.
| | - Richa Saxena
- Center for Genomic Medicine and Department of Anaesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital; and Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
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14
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Cabana-Domínguez J, Antón-Galindo E, Fernàndez-Castillo N, Singgih EL, O'Leary A, Norton WH, Strekalova T, Schenck A, Reif A, Lesch KP, Slattery D, Cormand B. The translational genetics of ADHD and related phenotypes in model organisms. Neurosci Biobehav Rev 2023; 144:104949. [PMID: 36368527 DOI: 10.1016/j.neubiorev.2022.104949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 11/10/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a highly prevalent neurodevelopmental disorder resulting from the interaction between genetic and environmental risk factors. It is well known that ADHD co-occurs frequently with other psychiatric disorders due, in part, to shared genetics factors. Although many studies have contributed to delineate the genetic landscape of psychiatric disorders, their specific molecular underpinnings are still not fully understood. The use of animal models can help us to understand the role of specific genes and environmental stimuli-induced epigenetic modifications in the pathogenesis of ADHD and its comorbidities. The aim of this review is to provide an overview on the functional work performed in rodents, zebrafish and fruit fly and highlight the generated insights into the biology of ADHD, with a special focus on genetics and epigenetics. We also describe the behavioral tests that are available to study ADHD-relevant phenotypes and comorbid traits in these models. Furthermore, we have searched for new models to study ADHD and its comorbidities, which can be useful to test potential pharmacological treatments.
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Affiliation(s)
- Judit Cabana-Domínguez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
| | - Ester Antón-Galindo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain
| | - Euginia L Singgih
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Aet O'Leary
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University, Frankfurt, Germany; Division of Neuropsychopharmacology, Department of Psychology, University of Tartu, Tartu, Estonia
| | - William Hg Norton
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Tatyana Strekalova
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany, and Department of Neuropsychology and Psychiatry, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University, Frankfurt, Germany
| | - Klaus-Peter Lesch
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany, and Department of Neuropsychology and Psychiatry, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands
| | - David Slattery
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University, Frankfurt, Germany
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
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15
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Saha S, Spinelli L, Castro Mondragon JA, Kervadec A, Lynott M, Kremmer L, Roder L, Krifa S, Torres M, Brun C, Vogler G, Bodmer R, Colas AR, Ocorr K, Perrin L. Genetic architecture of natural variation of cardiac performance from flies to humans. eLife 2022; 11:82459. [DOI: 10.7554/elife.82459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
Deciphering the genetic architecture of human cardiac disorders is of fundamental importance but their underlying complexity is a major hurdle. We investigated the natural variation of cardiac performance in the sequenced inbred lines of the Drosophila Genetic Reference Panel (DGRP). Genome-wide associations studies (GWAS) identified genetic networks associated with natural variation of cardiac traits which were used to gain insights as to the molecular and cellular processes affected. Non-coding variants that we identified were used to map potential regulatory non-coding regions, which in turn were employed to predict transcription factors (TFs) binding sites. Cognate TFs, many of which themselves bear polymorphisms associated with variations of cardiac performance, were also validated by heart-specific knockdown. Additionally, we showed that the natural variations associated with variability in cardiac performance affect a set of genes overlapping those associated with average traits but through different variants in the same genes. Furthermore, we showed that phenotypic variability was also associated with natural variation of gene regulatory networks. More importantly, we documented correlations between genes associated with cardiac phenotypes in both flies and humans, which supports a conserved genetic architecture regulating adult cardiac function from arthropods to mammals. Specifically, roles for PAX9 and EGR2 in the regulation of the cardiac rhythm were established in both models, illustrating that the characteristics of natural variations in cardiac function identified in Drosophila can accelerate discovery in humans.
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Affiliation(s)
- Saswati Saha
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Lionel Spinelli
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | | | - Anaïs Kervadec
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Michaela Lynott
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Laurent Kremmer
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Laurence Roder
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Sallouha Krifa
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Magali Torres
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Christine Brun
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
- CNRS
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Karen Ocorr
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Laurent Perrin
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
- CNRS
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16
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Harbison ST. What have we learned about sleep from selective breeding strategies? Sleep 2022; 45:zsac147. [PMID: 36111812 PMCID: PMC9644121 DOI: 10.1093/sleep/zsac147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/19/2022] [Indexed: 09/18/2023] Open
Abstract
Selective breeding is a classic technique that enables an experimenter to modify a heritable target trait as desired. Direct selective breeding for extreme sleep and circadian phenotypes in flies successfully alters these behaviors, and sleep and circadian perturbations emerge as correlated responses to selection for other traits in mice, rats, and dogs. The application of sequencing technologies to the process of selective breeding identifies the genetic network impacting the selected trait in a holistic way. Breeding techniques preserve the extreme phenotypes generated during selective breeding, generating community resources for further functional testing. Selective breeding is thus a unique strategy that can explore the phenotypic limits of sleep and circadian behavior, discover correlated responses of traits having shared genetic architecture with the target trait, identify naturally-occurring genomic variants and gene expression changes that affect trait variability, and pinpoint genes with conserved roles.
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Affiliation(s)
- Susan T Harbison
- Laboratory of Systems Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD,USA
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17
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Roberts RJV, Pop S, Prieto-Godino LL. Evolution of central neural circuits: state of the art and perspectives. Nat Rev Neurosci 2022; 23:725-743. [DOI: 10.1038/s41583-022-00644-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 11/09/2022]
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18
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Anderson L, Camus MF, Monteith KM, Salminen TS, Vale PF. Variation in mitochondrial DNA affects locomotor activity and sleep in Drosophila melanogaster. Heredity (Edinb) 2022; 129:225-232. [PMID: 35764697 PMCID: PMC9519576 DOI: 10.1038/s41437-022-00554-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 01/20/2023] Open
Abstract
Mitochondria are organelles that produce cellular energy in the form of ATP through oxidative phosphorylation, and this primary function is conserved among many taxa. Locomotion is a trait that is highly reliant on metabolic function and expected to be greatly affected by disruptions to mitochondrial performance. To this end, we aimed to examine how activity and sleep vary between Drosophila melanogaster strains with different geographic origins, how these patterns are affected by mitochondrial DNA (mtDNA) variation, and how breaking up co-evolved mito-nuclear gene combinations affect the studied activity traits. Our results demonstrate that Drosophila strains from different locations differ in sleep and activity, and that females are generally more active than males. By comparing activity and sleep of mtDNA variants introgressed onto a common nuclear background in cytoplasmic hybrid (cybrid) strains, we were able to quantify the among-line variance attributable to mitochondrial DNA, and we establish that mtDNA variation affects both activity and sleep, in a sex-specific manner. Altogether our study highlights the important role that mitochondrial genome variation plays on organismal physiology and behaviour.
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Affiliation(s)
- Lucy Anderson
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - M Florencia Camus
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Katy M Monteith
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tiina S Salminen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pedro F Vale
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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19
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Tran S, Prober DA. Validation of Candidate Sleep Disorder Risk Genes Using Zebrafish. Front Mol Neurosci 2022; 15:873520. [PMID: 35465097 PMCID: PMC9021570 DOI: 10.3389/fnmol.2022.873520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/14/2022] [Indexed: 12/31/2022] Open
Abstract
Sleep disorders and chronic sleep disturbances are common and are associated with cardio-metabolic diseases and neuropsychiatric disorders. Several genetic pathways and neuronal mechanisms that regulate sleep have been described in animal models, but the genes underlying human sleep variation and sleep disorders are largely unknown. Identifying these genes is essential in order to develop effective therapies for sleep disorders and their associated comorbidities. To address this unmet health problem, genome-wide association studies (GWAS) have identified numerous genetic variants associated with human sleep traits and sleep disorders. However, in most cases, it is unclear which gene is responsible for a sleep phenotype that is associated with a genetic variant. As a result, it is necessary to experimentally validate candidate genes identified by GWAS using an animal model. Rodents are ill-suited for this endeavor due to their poor amenability to high-throughput sleep assays and the high costs associated with generating, maintaining, and testing large numbers of mutant lines. Zebrafish (Danio rerio), an alternative vertebrate model for studying sleep, allows for the rapid and cost-effective generation of mutant lines using the CRISPR/Cas9 system. Numerous zebrafish mutant lines can then be tested in parallel using high-throughput behavioral assays to identify genes whose loss affects sleep. This process identifies a gene associated with each GWAS hit that is likely responsible for the human sleep phenotype. This strategy is a powerful complement to GWAS approaches and holds great promise to identify the genetic basis for common human sleep disorders.
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20
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Buchert SN, Murakami P, Kalavadia AH, Reyes MT, Sitaraman D. Sleep correlates with behavioral decision making critical for reproductive output in Drosophila melanogaster. Comp Biochem Physiol A Mol Integr Physiol 2022; 264:111114. [PMID: 34785379 PMCID: PMC9299756 DOI: 10.1016/j.cbpa.2021.111114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 02/03/2023]
Abstract
Balance between sleep, wakefulness and arousal is important for survival of organisms and species as a whole. While, the benefits of sleep both in terms of quantity and quality is widely recognized across species, sleep has a cost for organismal survival and reproduction. Here we focus on how sleep duration, sleep depth and sleep pressure affect the ability of animals to engage in courtship and egg-laying behaviors critical for reproductive success. Using isogenic lines from the Drosophila Genetic Reference Panel with variable sleep phenotypes we investigated the relationship between sleep and reproductive behaviors, courtship and oviposition. We found that three out of five lines with decreased sleep and increased arousal phenotypes, showed increased courtship and decreased latency to court as compared to normal and long sleeping lines. However, the male courtship phenotype is dependent on context and genotype as some but not all long sleeping-low courting lines elevate their courtship in the presence of short sleeping-high courting flies. We also find that unlike courtship, sleep phenotypes were less variable and minimally susceptible to social experience. In addition to male courtship, we also investigated egg-laying phenotype, a readout of female reproductive output and find oviposition to be less sensitive to sleep length and parameters that are indicative of switch between sleep and wake states. Taken together our extensive behavioral analysis here shows complex bidirectional interactions between genotype and environment and add to the growing evidence linking sleep duration and sleep-wake switch parameters to behavioral decision making critical to reproductive output.
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Affiliation(s)
- Steven N. Buchert
- Department of Psychology, College of Science, 25800 Carlos Bee Blvd, California State University, Hayward, CA 94542, United States of America
| | - Pomai Murakami
- Department of Psychological Sciences, College of Arts and Sciences, 5998 Alcala Park, University of San Diego, San Diego, CA 92110, United States of America
| | - Aashaka H. Kalavadia
- Department of Psychology, College of Science, 25800 Carlos Bee Blvd, California State University, Hayward, CA 94542, United States of America
| | - Martin T. Reyes
- Department of Psychology, College of Science, 25800 Carlos Bee Blvd, California State University, Hayward, CA 94542, United States of America
| | - Divya Sitaraman
- Department of Psychology, College of Science, 25800 Carlos Bee Blvd, California State University, Hayward, CA 94542, United States of America,Department of Psychological Sciences, College of Arts and Sciences, 5998 Alcala Park, University of San Diego, San Diego, CA 92110, United States of America,Corresponding author at: Department of Psychology, College of Science, 25800 Carlos Bee Blvd, California State University, Hayward, CA 94542, United States of America. (D. Sitaraman)
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21
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Francis D, Ghazanfar S, Havula E, Krycer JR, Strbenac D, Senior A, Minard AY, Geddes T, Nelson ME, Weiss F, Stöckli J, Yang JYH, James DE. Genome-wide analysis in Drosophila reveals diet-by-gene interactions and uncovers diet-responsive genes. G3-GENES GENOMES GENETICS 2021; 11:6287063. [PMID: 34568906 PMCID: PMC8496270 DOI: 10.1093/g3journal/jkab171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/08/2021] [Indexed: 11/26/2022]
Abstract
Genetic and environmental factors play a major role in metabolic health. However, they do not act in isolation, as a change in an environmental factor such as diet may exert different effects based on an individual’s genotype. Here, we sought to understand how such gene–diet interactions influenced nutrient storage and utilization, a major determinant of metabolic disease. We subjected 178 inbred strains from the Drosophila genetic reference panel (DGRP) to diets varying in sugar, fat, and protein. We assessed starvation resistance, a holistic phenotype of nutrient storage and utilization that can be robustly measured. Diet influenced the starvation resistance of most strains, but the effect varied markedly between strains such that some displayed better survival on a high carbohydrate diet (HCD) compared to a high-fat diet while others had opposing responses, illustrating a considerable gene × diet interaction. This demonstrates that genetics plays a major role in diet responses. Furthermore, heritability analysis revealed that the greatest genetic variability arose from diets either high in sugar or high in protein. To uncover the genetic variants that contribute to the heterogeneity in starvation resistance, we mapped 566 diet-responsive SNPs in 293 genes, 174 of which have human orthologs. Using whole-body knockdown, we identified two genes that were required for glucose tolerance, storage, and utilization. Strikingly, flies in which the expression of one of these genes, CG4607 a putative homolog of a mammalian glucose transporter, was reduced at the whole-body level, displayed lethality on a HCD. This study provides evidence that there is a strong interplay between diet and genetics in governing survival in response to starvation, a surrogate measure of nutrient storage efficiency and obesity. It is likely that a similar principle applies to higher organisms thus supporting the case for nutrigenomics as an important health strategy.
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Affiliation(s)
- Deanne Francis
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Shila Ghazanfar
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Essi Havula
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - James R Krycer
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Dario Strbenac
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alistair Senior
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Annabel Y Minard
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Thomas Geddes
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Marin E Nelson
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Fiona Weiss
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jacqueline Stöckli
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jean Y H Yang
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - David E James
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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22
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Nazario-Yepiz NO, Fernández Sobaberas J, Lyman R, Campbell MR, Shankar V, Anholt RRH, Mackay TFC. Physiological and metabolomic consequences of reduced expression of the Drosophila brummer triglyceride Lipase. PLoS One 2021; 16:e0255198. [PMID: 34547020 PMCID: PMC8454933 DOI: 10.1371/journal.pone.0255198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/07/2021] [Indexed: 11/18/2022] Open
Abstract
Disruption of lipolysis has widespread effects on intermediary metabolism and organismal phenotypes. Defects in lipolysis can be modeled in Drosophila melanogaster through genetic manipulations of brummer (bmm), which encodes a triglyceride lipase orthologous to mammalian Adipose Triglyceride Lipase. RNAi-mediated knock-down of bmm in all tissues or metabolic specific tissues results in reduced locomotor activity, altered sleep patterns and reduced lifespan. Metabolomic analysis on flies in which bmm is downregulated reveals a marked reduction in medium chain fatty acids, long chain saturated fatty acids and long chain monounsaturated and polyunsaturated fatty acids, and an increase in diacylglycerol levels. Elevated carbohydrate metabolites and tricarboxylic acid intermediates indicate that impairment of fatty acid mobilization as an energy source may result in upregulation of compensatory carbohydrate catabolism. bmm downregulation also results in elevated levels of serotonin and dopamine neurotransmitters, possibly accounting for the impairment of locomotor activity and sleep patterns. Physiological phenotypes and metabolomic changes upon reduction of bmm expression show extensive sexual dimorphism. Altered metabolic states in the Drosophila model are relevant for understanding human metabolic disorders, since pathways of intermediary metabolism are conserved across phyla.
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Affiliation(s)
- Nestor O. Nazario-Yepiz
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Jaime Fernández Sobaberas
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Roberta Lyman
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Marion R. Campbell
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Vijay Shankar
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Robert R. H. Anholt
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Trudy F. C. Mackay
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
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23
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Abstract
Sleep is critical for diverse aspects of brain function in animals ranging from invertebrates to humans. Powerful genetic tools in the fruit fly Drosophila melanogaster have identified - at an unprecedented level of detail - genes and neural circuits that regulate sleep. This research has revealed that the functions and neural principles of sleep regulation are largely conserved from flies to mammals. Further, genetic approaches to studying sleep have uncovered mechanisms underlying the integration of sleep and many different biological processes, including circadian timekeeping, metabolism, social interactions, and aging. These findings show that in flies, as in mammals, sleep is not a single state, but instead consists of multiple physiological and behavioral states that change in response to the environment, and is shaped by life history. Here, we review advances in the study of sleep in Drosophila, discuss their implications for understanding the fundamental functions of sleep that are likely to be conserved among animal species, and identify important unanswered questions in the field.
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Affiliation(s)
- Orie T Shafer
- The Advanced Science Research Center, City University of New York, New York, NY 10031, USA.
| | - Alex C Keene
- Department of Biological Science, Florida Atlantic University, Jupiter, FL 33458, USA.
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24
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Shah EJ, Gurdziel K, Ruden DM. Sex-Differences in Traumatic Brain Injury in the Absence of Tau in Drosophila. Genes (Basel) 2021; 12:917. [PMID: 34198629 PMCID: PMC8232113 DOI: 10.3390/genes12060917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
Traumatic brain injuries, a leading cause of death and disability worldwide, are caused by a severe impact to the head that impairs physiological and psychological function. In addition to severity, type and brain area affected, brain injury outcome is also influenced by the biological sex of the patient. Traumatic brain injury triggers accumulation of Tau protein and the subsequent development of Tauopathies, including Alzheimer's disease and Chronic traumatic encephalopathy. Recent studies report differences in Tau network connections between healthy males and females, but the possible role of Tau in sex-dependent outcome to brain injury is unclear. Thus, we aimed to determine if Tau ablation would alleviate sex dependent outcomes in injured flies. We first assessed motor function and survival in tau knock-out flies and observed sex-differences in climbing ability, but no change in locomotor activity in either sex post-injury. Sex differences in survival time were also observed in injured tau deficient flies with a dramatically higher percent of female death within 24 h than males. Additionally, 3'mRNA-Seq studies in isolated fly brains found that tau deficient males show more gene transcript changes than females post-injury. Our results suggest that sex differences in TBI outcome and recovery are not dependent on the presence of Tau in Drosophila.
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Affiliation(s)
- Ekta J. Shah
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA;
| | - Katherine Gurdziel
- Office of the Vice President of Research, Wayne State University, Detroit, MI 48201, USA
| | - Douglas M. Ruden
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA;
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
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25
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Lovejoy PC, Foley KE, Conti MM, Meadows SM, Bishop C, Fiumera AC. Genetic basis of susceptibility to low-dose paraquat and variation between the sexes in Drosophila melanogaster. Mol Ecol 2021; 30:2040-2053. [PMID: 33710693 DOI: 10.1111/mec.15878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 02/23/2021] [Indexed: 12/18/2022]
Abstract
Toxicant resistance is a complex trait, affected both by genetics and the environment. Like most complex traits, it can exhibit sexual dimorphism, yet sex is often overlooked as a factor in studies of toxicant resistance. Paraquat, one such toxicant, is a commonly used herbicide and is known to produce mitochondrial oxidative stress, decrease dopaminergic neurons and dopamine (DA) levels, and decrease motor ability. While the main effects of paraquat are well-characterized, less is known about the naturally occurring variation in paraquat susceptibility. The purpose of this study was to map the genes contributing to low-dose paraquat susceptibility in Drosophila melanogaster, and to determine if susceptibility differs between the sexes. One hundred of the Drosophila Genetic Reference Panel (DGRP) lines were scored for susceptibility via climbing ability and used in a genome-wide association study (GWAS). Variation in seventeen genes in females and thirty-five genes in males associated with paraquat susceptibility. Only two candidate genes overlapped between the sexes despite a significant positive correlation between male and female susceptibilities. Many associated polymorphisms had significant interactions with sex, with most having conditionally neutral effects. Conditional neutrality between the sexes probably stems from sex-biased expression which may result from partial resolution of sexual conflict. Candidate genes were verified with RNAi knockdowns, gene expression analyses, and DA quantification. Several of these genes are novel associations with paraquat susceptibility. This research highlights the importance of assessing both sexes when studying toxicant susceptibility.
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Affiliation(s)
- Pamela C Lovejoy
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA.,Department of Biology, St. Joseph's College, Brooklyn, NY, USA
| | - Kate E Foley
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| | - Melissa M Conti
- Department of Psychology, Binghamton University, Binghamton, NY, USA
| | | | | | - Anthony C Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
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26
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RNA-binding protein syncrip regulates starvation-induced hyperactivity in adult Drosophila. PLoS Genet 2021; 17:e1009396. [PMID: 33617535 PMCID: PMC7932510 DOI: 10.1371/journal.pgen.1009396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/04/2021] [Accepted: 02/03/2021] [Indexed: 11/28/2022] Open
Abstract
How to respond to starvation determines fitness. One prominent behavioral response is increased locomotor activities upon starvation, also known as Starvation-Induced Hyperactivity (SIH). SIH is paradoxical as it promotes food seeking but also increases energy expenditure. Despite its importance in fitness, the genetic contributions to SIH as a behavioral trait remains unexplored. Here, we examined SIH in the Drosophila melanogaster Genetic Reference Panel (DGRP) and performed genome-wide association studies. We identified 23 significant loci, corresponding to 14 genes, significantly associated with SIH in adult Drosophila. Gene enrichment analyses indicated that genes encoding ion channels and mRNA binding proteins (RBPs) were most enriched in SIH. We are especially interested in RBPs because they provide a potential mechanism to quickly change protein expression in response to environmental challenges. Using RNA interference, we validated the role of syp in regulating SIH. syp encodes Syncrip (Syp), an RBP. While ubiquitous knockdown of syp led to semi-lethality in adult flies, adult flies with neuron-specific syp knockdown were viable and exhibited decreased SIH. Using the Temporal and Regional Gene Expression Targeting (TARGET) system, we further confirmed the role of Syp in adult neurons in regulating SIH. To determine how syp is regulated by starvation, we performed RNA-seq using the heads of flies maintained under either food or starvation conditions. RNA-seq analyses revealed that syp was alternatively spliced under starvation while its expression level was unchanged. We further generated an alternatively-spliced-exon-specific knockout (KO) line and found that KO flies showed reduced SIH. Together, this study demonstrates a significant genetic contribution to SIH as a behavioral trait, identifies syp as a SIH gene, and highlights the significance of RBPs and post-transcriptional processes in the brain in regulating behavioral responses to starvation. Animals living in the wild often face periods of starvation. How to physiologically and behaviorally respond to starvation is essential for survival. One behavioral response is Starvation-Induced Hyperactivity (SIH). We used the Drosophila melanogaster Genetic Reference Panel, derived from a wild population, to study the genetic basis of SIH. Our results show that there is a significant genetic contribution to SIH in this population, and that genes encoding RNA binding proteins (RBPs) are especially important. Using RNA interference and the TARGET system, we confirmed the role of an RBP Syp in adult neurons in SIH. Using RNA-seq and Western blotting, we found that syp was alternatively spliced under starvation while its expression level was unchanged. Further studies from syp exon-specific knockout flies showed that alternative splicing involving two exons in syp was important for SIH. Together, this study identifies syp as a SIH gene and highlights an essential role of post-transcriptional modification in regulating this behavior.
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27
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Belfer SJ, Bashaw AG, Perlis ML, Kayser MS. A Drosophila model of sleep restriction therapy for insomnia. Mol Psychiatry 2021; 26:492-507. [PMID: 30824866 PMCID: PMC6717687 DOI: 10.1038/s41380-019-0376-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/23/2019] [Accepted: 02/11/2019] [Indexed: 01/03/2023]
Abstract
Insomnia is the most common sleep disorder among adults, especially affecting individuals of advanced age or with neurodegenerative disease. Insomnia is also a common comorbidity across psychiatric disorders. Cognitive behavioral therapy for insomnia (CBT-I) is the first-line treatment for insomnia; a key component of this intervention is restriction of sleep opportunity, which optimizes matching of sleep ability and opportunity, leading to enhanced sleep drive. Despite the well-documented efficacy of CBT-I, little is known regarding how CBT-I works at a cellular and molecular level to improve sleep, due in large part to an absence of experimentally-tractable animals models of this intervention. Here, guided by human behavioral sleep therapies, we developed a Drosophila model for sleep restriction therapy (SRT) of insomnia. We demonstrate that restriction of sleep opportunity through manipulation of environmental cues improves sleep efficiency in multiple short-sleeping Drosophila mutants. The response to sleep opportunity restriction requires ongoing environmental inputs, but is independent of the molecular circadian clock. We apply this sleep opportunity restriction paradigm to aging and Alzheimer's disease fly models, and find that sleep impairments in these models are reversible with sleep restriction, with associated improvement in reproductive fitness and extended lifespan. This work establishes a model to investigate the neurobiological basis of CBT-I, and provides a platform that can be exploited toward novel treatment targets for insomnia.
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Affiliation(s)
- Samuel J. Belfer
- Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States,Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
| | - Alexander G. Bashaw
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
| | - Michael L. Perlis
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States,Behavioral Sleep Medicine Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States,Center for Sleep and Circadian Neurobiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
| | - Matthew S. Kayser
- Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States,Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States,Center for Sleep and Circadian Neurobiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States,Chronobiology Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States,Lead Contact and Correspondence: Dr. Matthew S. Kayser, Clinical Research Building, Room 320, 415 Curie Boulevard, Philadelphia, PA 19143, , Telephone: 215 898 8268, Fax: 215 898 0509
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28
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Tallo CA, Duncan LH, Yamamoto AH, Slaydon JD, Arya GH, Turlapati L, Mackay TFC, Carbone MA. Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy. G3 (BETHESDA, MD.) 2021; 11:jkaa014. [PMID: 33561224 PMCID: PMC7849908 DOI: 10.1093/g3journal/jkaa014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022]
Abstract
In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans.
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Affiliation(s)
- Christian A Tallo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Laura H Duncan
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Akihiko H Yamamoto
- The Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Joshua D Slaydon
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Gunjan H Arya
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Lavanya Turlapati
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F C Mackay
- The Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, SC 29646, USA
| | - Mary A Carbone
- The Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- The Center for Integrated Fungal Research and Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695-7244, USA
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29
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Tallo CA, Duncan LH, Yamamoto AH, Slaydon JD, Arya GH, Turlapati L, Mackay TFC, Carbone MA. Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy. G3 (BETHESDA, MD.) 2021. [PMID: 33561224 DOI: 10.1093/g3journal/jkaa014.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans.
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Affiliation(s)
- Christian A Tallo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Laura H Duncan
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Akihiko H Yamamoto
- The Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Joshua D Slaydon
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Gunjan H Arya
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Lavanya Turlapati
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F C Mackay
- The Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, SC 29646, USA
| | - Mary A Carbone
- The Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA.,The Center for Integrated Fungal Research and Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695-7244, USA
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30
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Kumar S, Tunc I, Tansey TR, Pirooznia M, Harbison ST. Identification of Genes Contributing to a Long Circadian Period in Drosophila Melanogaster. J Biol Rhythms 2020; 36:239-253. [PMID: 33274675 DOI: 10.1177/0748730420975946] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The endogenous circadian period of animals and humans is typically very close to 24 h. Individuals with much longer circadian periods have been observed, however, and in the case of humans, these deviations have health implications. Previously, we observed a line of Drosophila with a very long average period of 31.3 h for locomotor activity behavior. Preliminary mapping indicated that the long period did not map to known canonical clock genes but instead mapped to multiple chromosomes. Using RNA-Seq, we surveyed the whole transcriptome of fly heads from this line across time and compared it with a wild-type control. A three-way generalized linear model revealed that approximately two-thirds of the genes were expressed differentially among the two genotypes, while only one quarter of the genes varied across time. Using these results, we applied algorithms to search for genes that oscillated over 24 h, identifying genes not previously known to cycle. We identified 166 differentially expressed genes that overlapped with a previous Genome-wide Association Study (GWAS) of circadian behavior, strongly implicating them in the long-period phenotype. We tested mutations in 45 of these genes for their effect on the circadian period. Mutations in Alk, alph, CG10089, CG42540, CG6034, Kairos (CG6123), CG8768, klg, Lar, sick, and tinc had significant effects on the circadian period, with seven of these mutations increasing the circadian period of locomotor activity behavior. Genetic rescue of mutant Kairos restored the circadian period to wild-type levels, suggesting it has a critical role in determining period length in constant darkness.
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Affiliation(s)
- Shailesh Kumar
- Laboratory of Systems Genetics, Systems Biology Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Ilker Tunc
- Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Terry R Tansey
- Laboratory of Systems Genetics, Systems Biology Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Susan T Harbison
- Laboratory of Systems Genetics, Systems Biology Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland
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31
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Souto-Maior C, Serrano Negron YL, Harbison ST. Natural selection on sleep duration in Drosophila melanogaster. Sci Rep 2020; 10:20652. [PMID: 33244154 PMCID: PMC7691507 DOI: 10.1038/s41598-020-77680-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/10/2020] [Indexed: 11/30/2022] Open
Abstract
Sleep is ubiquitous across animal species, but why it persists is not well understood. Here we observe natural selection act on Drosophila sleep by relaxing bi-directional artificial selection for extreme sleep duration for 62 generations. When artificial selection was suspended, sleep increased in populations previously selected for short sleep. Likewise, sleep decreased in populations previously selected for long sleep when artificial selection was relaxed. We measured the corresponding changes in the allele frequencies of genomic variants responding to artificial selection. The allele frequencies of these variants reversed course in response to relaxed selection, and for short sleepers, the changes exceeded allele frequency changes that would be expected under random genetic drift. These observations suggest that the variants are causal polymorphisms for sleep duration responding to natural selection pressure. These polymorphisms may therefore pinpoint the most important regions of the genome maintaining variation in sleep duration.
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Affiliation(s)
- Caetano Souto-Maior
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, MD, USA
| | - Yazmin L Serrano Negron
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, MD, USA
| | - Susan T Harbison
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, MD, USA.
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32
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Riddle NC. Variation in the response to exercise stimulation in Drosophila: marathon runner versus sprinter genotypes. J Exp Biol 2020; 223:jeb229997. [PMID: 32737212 DOI: 10.1242/jeb.229997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/27/2020] [Indexed: 12/13/2022]
Abstract
Animals' behaviors vary in response to their environment, both biotic and abiotic. These behavioral responses have significant impacts on animal survival and fitness, and thus, many behavioral responses are at least partially under genetic control. In Drosophila, for example, genes impacting aggression, courtship behavior, circadian rhythms and sleep have been identified. Animal activity also is influenced strongly by genetics. My lab previously has used the Drosophila melanogaster Genetics Reference Panel (DGRP) to investigate activity levels and identified over 100 genes linked to activity. Here, I re-examined these data to determine whether Drosophila strains differ in their response to rotational exercise stimulation, not simply in the amount of activity, but in activity patterns and timing of activity. Specifically, I asked whether there are fly strains exhibiting either a 'marathoner' pattern of activity, i.e. remaining active throughout the 2 h exercise period, or a 'sprinter' pattern, i.e. carrying out most of the activity early in the exercise period. The DGRP strains examined differ significantly in how much activity is carried out at the beginning of the exercise period, and this pattern is influenced by both sex and genotype. Interestingly, there was no clear link between the activity response pattern and lifespan of the animals. Using genome-wide association studies (GWAS), I identified 10 high confidence candidate genes that control the degree to which Drosophila exercise behaviors fit a marathoner or sprinter activity pattern. This finding suggests that, similar to other aspects of locomotor behavior, the timing of activity patterns in response to exercise stimulation is under genetic control.
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Affiliation(s)
- Nicole C Riddle
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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33
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Shah EJ, Gurdziel K, Ruden DM. Drosophila Exhibit Divergent Sex-Based Responses in Transcription and Motor Function After Traumatic Brain Injury. Front Neurol 2020; 11:511. [PMID: 32636795 PMCID: PMC7316956 DOI: 10.3389/fneur.2020.00511] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/08/2020] [Indexed: 12/31/2022] Open
Abstract
Every year, millions of people in the US suffer brain damage from mild to severe traumatic brain injuries (TBI) that result from a sudden impact to the head. Despite TBI being a leading cause of death and disability worldwide, sex differences that contribute to varied outcomes post-injury are not extensively studied and therefore, poorly understood. In this study, we aimed to explore biological sex as a variable influencing response to TBI using Drosophila melanogaster as a model, since flies have been shown to exhibit symptoms commonly seen in other mammalian models of TBI. After inflicting TBI using the high-impact trauma device, we isolated w1118 fly brains and assessed gene transcription changes in male and female flies at control and 1, 2, and 4 hr after TBI. Our results suggest that overall, Drosophila females show more gene transcript changes than males. Females also exhibit upregulated expression changes in immune response and mitochondrial genes across all time-points. In addition, we looked at the impact of injury on mitochondrial health and motor function in both sexes before and after injury. Although both sexes report similar changes in mitochondrial oxidation and negative geotaxis, locomotor activity appears to be more impaired in males than females. These data suggest that sex-differences not only influence the response to TBI but also contribute to varied outcomes post-injury.
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Affiliation(s)
- Ekta J Shah
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Katherine Gurdziel
- Office of the Vice President for Research, Wayne State University, Detroit, MI, United States
| | - Douglas M Ruden
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States.,Office of the Vice President for Research, Wayne State University, Detroit, MI, United States.,Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States
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34
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Schou MF, Kristensen TN, Hoffmann AA. Patterns of environmental variance across environments and traits in domestic cattle. Evol Appl 2020; 13:1090-1102. [PMID: 32431754 PMCID: PMC7232762 DOI: 10.1111/eva.12924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 01/07/2023] Open
Abstract
The variance in phenotypic trait values is a product of environmental and genetic variation. The sensitivity of traits to environmental variation has a genetic component and is likely to be under selection. However, there are few studies investigating the evolution of this sensitivity, in part due to the challenges of estimating the environmental variance. The livestock literature provides a wealth of studies that accurately partition components of phenotypic variance, including the environmental variance, in well-defined environments. These studies involve breeds that have been under strong selection on mean phenotype in optimal environments for many generations, and therefore represent an opportunity to study the potential evolution of trait sensitivity to environmental conditions. Here, we use literature on domestic cattle to examine the evolution of micro-environmental variance (CVR-the coefficient of residual variance) by testing for differences in expression of CVR in animals from the same breed reared in different environments. Traits that have been under strong selection did not follow a null expectation of an increase in CVR in heterogenous environments (e.g., grazing), a pattern that may reflect evolution of increased uniformity in heterogeneous environments. When comparing CVR across environments of different levels of optimality, here measured by trait mean, we found a reduction in CVR in the more optimal environments for both life history and growth traits. Selection aimed at increasing trait means in livestock breeds typically occurs in the more optimal environments, and we therefore suspect that the decreased CVR is a consequence of evolution of the expression of micro-environmental variance in this environment. Our results highlight the heterogeneity in micro-environmental variance across environments and point to possible connections to the intensity of selection on trait means.
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Affiliation(s)
- Mads F. Schou
- Department of Chemistry and BioscienceAalborg UniversityAalborg EastDenmark
- Department of BiologyLund UniversityLundSweden
| | | | - Ary A. Hoffmann
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVICAustralia
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35
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Abstract
Sleep is a ubiquitous and complex behavior in both its manifestation and regulation. Despite its essential role in maintaining optimal performance, health, and well-being, the genetic mechanisms underlying sleep remain poorly understood. Here, we review the forward genetic approaches undertaken in the last four years to elucidate the genes and gene pathways affecting sleep and its regulation. Despite an increasing number of studies and mining large databases, a coherent picture on “sleep” genes has yet to emerge. We highlight the results achieved by using unbiased genetic screens mainly in humans, mice, and fruit flies with an emphasis on normal sleep and make reference to lessons learned from the circadian field.
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Affiliation(s)
- Maxime Jan
- Centre for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Bruce F O'Hara
- Department of Biology, University of Kentucky, Lexington, 40515, USA
| | - Paul Franken
- Centre for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
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36
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R. Smith B, J. Macdonald S. Dissecting the Genetic Basis of Variation in Drosophila Sleep Using a Multiparental QTL Mapping Resource. Genes (Basel) 2020; 11:genes11030294. [PMID: 32168738 PMCID: PMC7140804 DOI: 10.3390/genes11030294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/07/2020] [Accepted: 03/09/2020] [Indexed: 12/27/2022] Open
Abstract
There is considerable variation in sleep duration, timing and quality in human populations, and sleep dysregulation has been implicated as a risk factor for a range of health problems. Human sleep traits are known to be regulated by genetic factors, but also by an array of environmental and social factors. These uncontrolled, non-genetic effects complicate powerful identification of the loci contributing to sleep directly in humans. The model system, Drosophila melanogaster, exhibits a behavior that shows the hallmarks of mammalian sleep, and here we use a multitiered approach, encompassing high-resolution QTL mapping, expression QTL data, and functional validation with RNAi to investigate the genetic basis of sleep under highly controlled environmental conditions. We measured a battery of sleep phenotypes in >750 genotypes derived from a multiparental mapping panel and identified several, modest-effect QTL contributing to natural variation for sleep. Merging sleep QTL data with a large head transcriptome eQTL mapping dataset from the same population allowed us to refine the list of plausible candidate causative sleep loci. This set includes genes with previously characterized effects on sleep and circadian rhythms, in addition to novel candidates. Finally, we employed adult, nervous system-specific RNAi on the Dopa decarboxylase, dyschronic, and timeless genes, finding significant effects on sleep phenotypes for all three. The genes we resolve are strong candidates to harbor causative, regulatory variation contributing to sleep.
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Affiliation(s)
- Brittny R. Smith
- Department of Molecular Biosciences, 4043 Haworth Hall, 1200 Sunnyside Avenue, University of Kansas, Lawrence, KS 66045, USA
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, 4043 Haworth Hall, 1200 Sunnyside Avenue, University of Kansas, Lawrence, KS 66045, USA
- Center for Computational Biology, University of Kansas, Lawrence, KS 66047, USA
- Correspondence: ; Tel.: +1-785-864-5362
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37
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Everett LJ, Huang W, Zhou S, Carbone MA, Lyman RF, Arya GH, Geisz MS, Ma J, Morgante F, St Armour G, Turlapati L, Anholt RRH, Mackay TFC. Gene expression networks in the Drosophila Genetic Reference Panel. Genome Res 2020; 30:485-496. [PMID: 32144088 PMCID: PMC7111517 DOI: 10.1101/gr.257592.119] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/28/2020] [Indexed: 01/02/2023]
Abstract
A major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. This question is best addressed in a genetic mapping population in which all molecular polymorphisms are known and for which molecular endophenotypes and complex traits are assessed on the same genotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and for which phenotypes of many quantitative traits have been evaluated. We mapped expression quantitative trait loci for annotated genes, novel transcribed regions, transposable elements, and microbial species. We identified host variants that affect expression of transposable elements, independent of their copy number, as well as microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination, as well as genes regulating transposable element expression. This study provides new insights regarding the role of natural genetic variation in regulating gene expression and generates testable hypotheses for future functional analyses.
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Affiliation(s)
- Logan J Everett
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Wen Huang
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Shanshan Zhou
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Mary Anna Carbone
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Richard F Lyman
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Gunjan H Arya
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Matthew S Geisz
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA.,University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27516, USA
| | - Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, JiangXi Agricultural University, JiangXi, China
| | - Fabio Morgante
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Genevieve St Armour
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Lavanya Turlapati
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Robert R H Anholt
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Trudy F C Mackay
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
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Huang W, Campbell T, Carbone MA, Jones WE, Unselt D, Anholt RRH, Mackay TFC. Context-dependent genetic architecture of Drosophila life span. PLoS Biol 2020; 18:e3000645. [PMID: 32134916 PMCID: PMC7077879 DOI: 10.1371/journal.pbio.3000645] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 03/17/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the genetic basis of variation in life span is a major challenge that is difficult to address in human populations. Evolutionary theory predicts that alleles affecting natural variation in life span will have properties that enable them to persist in populations at intermediate frequencies, such as late-life-specific deleterious effects, antagonistic pleiotropic effects on early and late-age fitness components, and/or sex- and environment-specific or antagonistic effects. Here, we quantified variation in life span in males and females reared in 3 thermal environments for the sequenced, inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and an advanced intercross outbred population derived from a subset of DGRP lines. Quantitative genetic analyses of life span and the micro-environmental variance of life span in the DGRP revealed significant genetic variance for both traits within each sex and environment, as well as significant genotype-by-sex interaction (GSI) and genotype-by-environment interaction (GEI). Genome-wide association (GWA) mapping in both populations implicates over 2,000 candidate genes with sex- and environment-specific or antagonistic pleiotropic allelic effects. Over 1,000 of these genes are associated with variation in life span in other D. melanogaster populations. We functionally assessed the effects of 15 candidate genes using RNA interference (RNAi): all affected life span and/or micro-environmental variance of life span in at least one sex and environment and exhibited sex-and environment-specific effects. Our results implicate novel candidate genes affecting life span and suggest that variation for life span may be maintained by variable allelic effects in heterogeneous environments.
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Affiliation(s)
- Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Terry Campbell
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Mary Anna Carbone
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - W. Elizabeth Jones
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Desiree Unselt
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert R. H. Anholt
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Trudy F. C. Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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Anholt RRH, O'Grady P, Wolfner MF, Harbison ST. Evolution of Reproductive Behavior. Genetics 2020; 214:49-73. [PMID: 31907301 PMCID: PMC6944409 DOI: 10.1534/genetics.119.302263] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/04/2019] [Indexed: 12/20/2022] Open
Abstract
Behaviors associated with reproduction are major contributors to the evolutionary success of organisms and are subject to many evolutionary forces, including natural and sexual selection, and sexual conflict. Successful reproduction involves a range of behaviors, from finding an appropriate mate, courting, and copulation, to the successful production and (in oviparous animals) deposition of eggs following mating. As a consequence, behaviors and genes associated with reproduction are often under strong selection and evolve rapidly. Courtship rituals in flies follow a multimodal pattern, mediated through visual, chemical, tactile, and auditory signals. Premating behaviors allow males and females to assess the species identity, reproductive state, and condition of their partners. Conflicts between the "interests" of individual males, and/or between the reproductive strategies of males and females, often drive the evolution of reproductive behaviors. For example, seminal proteins transmitted by males often show evidence of rapid evolution, mediated by positive selection. Postmating behaviors, including the selection of oviposition sites, are highly variable and Drosophila species span the spectrum from generalists to obligate specialists. Chemical recognition features prominently in adaptation to host plants for feeding and oviposition. Selection acting on variation in pre-, peri-, and postmating behaviors can lead to reproductive isolation and incipient speciation. Response to selection at the genetic level can include the expansion of gene families, such as those for detecting pheromonal cues for mating, or changes in the expression of genes leading to visual cues such as wing spots that are assessed during mating. Here, we consider the evolution of reproductive behavior in Drosophila at two distinct, yet complementary, scales. Some studies take a microevolutionary approach, identifying genes and networks involved in reproduction, and then dissecting the genetics underlying complex behaviors in D. melanogaster Other studies take a macroevolutionary approach, comparing reproductive behaviors across the genus Drosophila and how these might correlate with environmental cues. A full synthesis of this field will require unification across these levels.
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Affiliation(s)
- Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, South Carolina 29646
- Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina 29646
| | - Patrick O'Grady
- Department of Entomology, Cornell University, Ithaca, New York 14853
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Susan T Harbison
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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40
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Zhang W, Reeves GR, Tautz D. Identification of a genetic network for an ecologically relevant behavioural phenotype in Drosophila melanogaster. Mol Ecol 2019; 29:502-518. [PMID: 31867742 DOI: 10.1111/mec.15341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 11/28/2022]
Abstract
Pupation site choice of Drosophila third-instar larvae is critical for the survival of individuals, as pupae are exposed to various biotic and abiotic dangers while immobilized during the 3-4 days of metamorphosis. This singular behavioural choice is sensitive to both environmental and genetic factors. Here, we developed a high-throughput phenotyping approach to assay the variation in pupation height in Drosophila melanogaster, while controlling for possibly confounding factors. We find substantial variation of mean pupation height among sampled natural stocks and we show that the Drosophila Genetic Reference Panel (DGRP) reflects this variation. Using the DGRP stocks for genome-wide association (GWA) mapping, 16 loci involved in determining pupation height could be resolved. The candidate genes in these loci are enriched for high expression in the larval central nervous system. A genetic network could be constructed from the candidate loci, which places scribble (scrib) at the centre, plus other genes known to be involved in nervous system development, such as Epidermal growth factor receptor (Egfr) and p53. Using gene disruption lines, we could functionally validate several of the initially identified loci, as well as additional loci predicted from network analysis. Our study shows that the combination of high-throughput phenotyping with a genetic analysis of variation captured from the wild can be used to approach the genetic dissection of an environmentally relevant behavioural phenotype.
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Affiliation(s)
- Wenyu Zhang
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Guy Richard Reeves
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nat Metab 2019; 1:1226-1242. [PMID: 32694676 DOI: 10.1038/s42255-019-0147-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 11/07/2019] [Indexed: 01/04/2023]
Abstract
The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype-phenotype relationship studies.
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Affiliation(s)
- Roel P J Bevers
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Genomics England, London, UK
| | - Maria Litovchenko
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Adamandia Kapopoulou
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Virginie S Braman
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matthew R Robinson
- Complex Trait Genetics Group, Université de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Brian Hollis
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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Zhou S, Morgante F, Geisz MS, Ma J, Anholt RRH, Mackay TFC. Systems genetics of the Drosophila metabolome. Genome Res 2019; 30:392-405. [PMID: 31694867 PMCID: PMC7111526 DOI: 10.1101/gr.243030.118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/11/2019] [Indexed: 02/06/2023]
Abstract
How effects of DNA sequence variants are transmitted through intermediate endophenotypes to modulate organismal traits remains a central question in quantitative genetics. This problem can be addressed through a systems approach in a population in which genetic polymorphisms, gene expression traits, metabolites, and complex phenotypes can be evaluated on the same genotypes. Here, we focused on the metabolome, which represents the most proximal link between genetic variation and organismal phenotype, and quantified metabolite levels in 40 lines of the Drosophila melanogaster Genetic Reference Panel. We identified sex-specific modules of genetically correlated metabolites and constructed networks that integrate DNA sequence variation and variation in gene expression with variation in metabolites and organismal traits, including starvation stress resistance and male aggression. Finally, we asked to what extent SNPs and metabolites can predict trait phenotypes and generated trait- and sex-specific prediction models that provide novel insights about the metabolomic underpinnings of complex phenotypes.
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Affiliation(s)
- Shanshan Zhou
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Fabio Morgante
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Matthew S Geisz
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, JiangXi Agricultural University, JiangXi, China
| | - Robert R H Anholt
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Trudy F C Mackay
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
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43
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Unpredictable Effects of the Genetic Background of Transgenic Lines in Physiological Quantitative Traits. G3-GENES GENOMES GENETICS 2019; 9:3877-3890. [PMID: 31540975 PMCID: PMC6829147 DOI: 10.1534/g3.119.400715] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Physiology, fitness and disease phenotypes are complex traits exhibiting continuous variation in natural populations. To understand complex trait gene functions transgenic lines of undefined genetic background are often combined to assess quantitative phenotypes ignoring the impact of genetic polymorphisms. Here, we used inbred wild-type strains of the Drosophila Genetics Reference Panel to assess the phenotypic variation of six physiological and fitness traits, namely, female fecundity, survival and intestinal mitosis upon oral infection, defecation rate and fecal pH upon oral infection, and terminal tracheal cell branching in hypoxia. We found continuous variation in the approximately 150 strains tested for each trait, with extreme values differing by more than four standard deviations for all traits. In addition, we assessed the effects of commonly used Drosophila UAS-RNAi transgenic strains and their backcrossed isogenized counterparts, in the same traits plus baseline intestinal mitosis and tracheal branching in normoxia, in heterozygous conditions, when only half of the genetic background was different among strains. We tested 20 non-isogenic strains (10 KK and 10 GD) from the Vienna Drosophila Resource Center and their isogenized counterparts without Gal4 induction. Survival upon infection and female fecundity exhibited differences in 50% and 40% of the tested isogenic vs. non-isogenic pairs, respectively, whereas all other traits were affected in only 10–25% of the cases. When 11 isogenic and their corresponding non-isogenic UAS-RNAi lines were expressed ubiquitously with Gal4, 4 isogenic vs. non-isogenic pairs exhibited differences in survival to infection. Furthermore, when a single UAS-RNAi line was crossed with the same Gal4 transgene inserted in different genetic backgrounds, the quantitative variations observed were unpredictable on the basis of pure line performance. Thus, irrespective of the trait of interest, the genetic background of commonly used transgenic strains needs to be considered carefully during experimentation.
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Lee DA, Liu J, Hong Y, Lane JM, Hill AJ, Hou SL, Wang H, Oikonomou G, Pham U, Engle J, Saxena R, Prober DA. Evolutionarily conserved regulation of sleep by epidermal growth factor receptor signaling. SCIENCE ADVANCES 2019; 5:eaax4249. [PMID: 31763451 PMCID: PMC6853770 DOI: 10.1126/sciadv.aax4249] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/17/2019] [Indexed: 05/03/2023]
Abstract
The genetic bases for most human sleep disorders and for variation in human sleep quantity and quality are largely unknown. Using the zebrafish, a diurnal vertebrate, to investigate the genetic regulation of sleep, we found that epidermal growth factor receptor (EGFR) signaling is necessary and sufficient for normal sleep levels and is required for the normal homeostatic response to sleep deprivation. We observed that EGFR signaling promotes sleep via mitogen-activated protein kinase/extracellular signal-regulated kinase and RFamide neuropeptide signaling and that it regulates RFamide neuropeptide expression and neuronal activity. Consistent with these findings, analysis of a large cohort of human genetic data from participants of European ancestry revealed that common variants in genes within the EGFR signaling pathway are associated with variation in human sleep quantity and quality. These results indicate that EGFR signaling and its downstream pathways play a central and ancient role in regulating sleep and provide new therapeutic targets for sleep disorders.
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Affiliation(s)
- Daniel A. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Justin Liu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Young Hong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jacqueline M. Lane
- Center for Genomic Medicine and Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Andrew J. Hill
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sarah L. Hou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Heming Wang
- Center for Genomic Medicine and Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Grigorios Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Uyen Pham
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jae Engle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Richa Saxena
- Center for Genomic Medicine and Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital and Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - David A. Prober
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Kumar S, Smith KR, Serrano Negron YL, Harbison ST. Short-Term Memory Deficits in the SLEEP Inbred Panel. Clocks Sleep 2019; 1:471-488. [PMID: 32596662 PMCID: PMC7318870 DOI: 10.3390/clockssleep1040036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Although sleep is heritable and conserved across species, sleep duration varies from individual to individual. A shared genetic architecture between sleep duration and other evolutionarily important traits could explain this variability. Learning and memory are critical traits sharing a genetic architecture with sleep. We wanted to know whether learning and memory would be altered in extreme long or short sleepers. We therefore assessed the short-term learning and memory ability of flies from the Sleep Inbred Panel (SIP), a collection of 39 extreme long- and short-sleeping inbred lines of Drosophila. Neither long nor short sleepers had appreciable learning, in contrast to a moderate-sleeping control. We also examined the response of long and short sleepers to enriched social conditions, a paradigm previously shown to induce morphological changes in the brain. While moderate-sleeping control flies had increased daytime sleep and quantifiable increases in brain structures under enriched social conditions, flies of the Sleep Inbred Panel did not display these changes. The SIP thus emerges as an important model for the relationship between sleep and learning and memory.
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46
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Rohde PD, Jensen IR, Sarup PM, Ørsted M, Demontis D, Sørensen P, Kristensen TN. Genetic Signatures of Drug Response Variability in Drosophila melanogaster. Genetics 2019; 213:633-650. [PMID: 31455722 PMCID: PMC6781897 DOI: 10.1534/genetics.119.302381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/26/2019] [Indexed: 12/27/2022] Open
Abstract
Knowledge of the genetic basis underlying variation in response to environmental exposures or treatments is important in many research areas. For example, knowing the set of causal genetic variants for drug responses could revolutionize personalized medicine. We used Drosophila melanogaster to investigate the genetic signature underlying behavioral variability in response to methylphenidate (MPH), a drug used in the treatment of attention-deficit/hyperactivity disorder. We exposed a wild-type D. melanogaster population to MPH and a control treatment, and observed an increase in locomotor activity in MPH-exposed individuals. Whole-genome transcriptomic analyses revealed that the behavioral response to MPH was associated with abundant gene expression alterations. To confirm these patterns in a different genetic background and to further advance knowledge on the genetic signature of drug response variability, we used a system of inbred lines, the Drosophila Genetic Reference Panel (DGRP). Based on the DGRP, we showed that the behavioral response to MPH was strongly genotype-dependent. Using an integrative genomic approach, we incorporated known gene interactions into the genomic analyses of the DGRP, and identified putative candidate genes for variability in drug response. We successfully validated 71% of the investigated candidate genes by gene expression knockdown. Furthermore, we showed that MPH has cross-generational behavioral and transcriptomic effects. Our findings establish a foundation for understanding the genetic mechanisms driving genotype-specific responses to medical treatment, and highlight the opportunities that integrative genomic approaches have in optimizing medical treatment of complex diseases.
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Affiliation(s)
- Palle Duun Rohde
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus C, Denmark
- Center for Integrative Sequencing, Aarhus University, 8000, Denmark
| | - Iben Ravnborg Jensen
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
| | - Pernille Merete Sarup
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Michael Ørsted
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus C, Denmark
- Center for Integrative Sequencing, Aarhus University, 8000, Denmark
- Department of Biomedicine, Aarhus University, 8000, Denmark
| | - Peter Sørensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Torsten Nygaard Kristensen
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
- Section for Genetics, Ecology and Evolution, Department of Bioscience, Aarhus University, 8000, Denmark
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47
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Miura M, Takahashi A. Starvation tolerance associated with prolonged sleep bouts upon starvation in a single natural population of Drosophila melanogaster. J Evol Biol 2019; 32:1117-1123. [PMID: 31381200 PMCID: PMC6851687 DOI: 10.1111/jeb.13514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/11/2019] [Accepted: 07/30/2019] [Indexed: 12/16/2022]
Abstract
Large genetic variations in starvation tolerance in animals indicate that there are multiple strategies to cope with low-nutrient conditions. Fruit flies (Drosophila melanogaster) typically respond to starvation by suppressing sleep and enhancing locomotor activity presumably to search for food. However, we hypothesized that in a natural population, there are costs and benefits to sleep suppression under low-nutrient conditions and that conserving energy through sleep could be a better strategy depending on food availability. In this study, we quantified the variation in sleep-related traits in 21 wild-derived inbred lines from Katsunuma, Japan, under fed and starved conditions and analysed the relationship between those traits and starvation tolerance. Although most of the lines responded to starvation by suppressing the total time in sleep, there were indeed two lines that responded by significantly increasing the sleep-bout durations and thus not reducing the total time in sleep. These genotypes survived longer in acute starvation conditions compared to genotypes that responded by the immediate suppression of sleep, which could be due to the reduced metabolic rate during the long uninterrupted sleep bouts. The coexistence of the enhanced foraging and resting strategies upon starvation within a single population is consistent with the presence of a behavioural trade-off between food search and energy conservation due to unpredictable food availability in nature. These results provide insights into the evolutionary mechanisms that contribute to the maintenance of genetic variations underlying environmental stress resistance.
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Affiliation(s)
- Mai Miura
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Aya Takahashi
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan.,Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Japan
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48
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Stage-specific genotype-by-environment interactions for cold and heat hardiness in Drosophila melanogaster. Heredity (Edinb) 2019; 123:479-491. [PMID: 31164731 DOI: 10.1038/s41437-019-0236-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 04/29/2019] [Accepted: 05/05/2019] [Indexed: 12/18/2022] Open
Abstract
Environments often vary across a life cycle, imposing fluctuating natural selection across development. Such fluctuating selection can favor different phenotypes in different life stages, but stage-specific evolutionary responses will depend on genetic variance, covariance, and their interaction across development and across environments. Thus, quantifying how genetic architecture varies with plastic responses to the environment and across development is vital to predict whether stage-specific adaptation will occur in nature. Additionally, the interaction of genetic variation and environmental plasticity (GxE) may be stage-specific, leading to a three-way interaction between genotype, environment, and development or GxDxE. To test for these patterns, we exposed larvae and adults of Drosophila melanogaster isogenic lines derived from a natural population to extreme heat and cold stress after developmental acclimation to cool (18 °C) and warm (25 °C) conditions and measured genetic variance for thermal hardiness. We detected significant GxE that was specific to larvae and adults for cold and heat hardiness (GxDxE), but no significant genetic correlation across development for either trait at either acclimation temperature. However, cross-development phenotypic correlations for acclimation responses suggest that plasticity itself may be developmentally constrained, though rigorously testing this hypothesis requires more experimentation. These results illustrate the potential for stage-specific adaptation within a complex life cycle and demonstrate the importance of measuring traits at appropriate developmental stages and environmental conditions when predicting evolutionary responses to changing climates.
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49
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Engel GL, Taber K, Vinton E, Crocker AJ. Studying alcohol use disorder using Drosophila melanogaster in the era of 'Big Data'. BEHAVIORAL AND BRAIN FUNCTIONS : BBF 2019; 15:7. [PMID: 30992041 PMCID: PMC6469124 DOI: 10.1186/s12993-019-0159-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/04/2019] [Indexed: 02/08/2023]
Abstract
Our understanding of the networks of genes and protein functions involved in Alcohol Use Disorder (AUD) remains incomplete, as do the mechanisms by which these networks lead to AUD phenotypes. The fruit fly (Drosophila melanogaster) is an efficient model for functional and mechanistic characterization of the genes involved in alcohol behavior. The fly offers many advantages as a model organism for investigating the molecular and cellular mechanisms of alcohol-related behaviors, and for understanding the underlying neural circuitry driving behaviors, such as locomotor stimulation, sedation, tolerance, and appetitive (reward) learning and memory. Fly researchers are able to use an extensive variety of tools for functional characterization of gene products. To understand how the fly can guide our understanding of AUD in the era of Big Data we will explore these tools, and review some of the gene networks identified in the fly through their use, including chromatin-remodeling, glial, cellular stress, and innate immunity genes. These networks hold great potential as translational drug targets, making it prudent to conduct further research into how these gene mechanisms are involved in alcohol behavior.
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Affiliation(s)
- Gregory L. Engel
- Department of Psychological Sciences, Castleton University, Castleton, VT 05735 USA
| | - Kreager Taber
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753 USA
| | - Elizabeth Vinton
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753 USA
| | - Amanda J. Crocker
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753 USA
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Petino Zappala MA, Satorre I, Fanara JJ. Stage- and thermal-specific genetic architecture for preadult viability in natural populations of Drosophila melanogaster. J Evol Biol 2019; 32:683-693. [PMID: 30924196 DOI: 10.1111/jeb.13448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 11/29/2022]
Abstract
Studying the processes affecting variation for preadult viability is essential to understand the evolutionary trajectories followed by natural populations. This task requires focusing on the complex nature of the phenotype-genotype relationship by taking into account usually neglected aspects of the phenotype and recognizing the modularity between different ontogenetic stages. Here, we describe phenotypic variability for viability during the larval and pupal stages in lines derived from three natural populations of Drosophila melanogaster, as well as the variability for phenotypic plasticity and canalization at two different rearing temperatures. The results indicate that the three populations present significant phenotypic differences for preadult viability. Furthermore, distinct aspects of the phenotype (means, plasticity, canalization, plasticity of canalization) are affected by different genetic bases underlying changes in viability in a stage- and environment-specific manner. These findings explain the generalized maintenance of genetic variability for this fitness trait.
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Affiliation(s)
- María Alejandra Petino Zappala
- Departamento de Ecologia, Genetica y Evolucion - IEGEBA (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CABA, Argentina
| | - Ignacio Satorre
- Departamento de Ecologia, Genetica y Evolucion - IEGEBA (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CABA, Argentina
| | - Juan José Fanara
- Departamento de Ecologia, Genetica y Evolucion - IEGEBA (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CABA, Argentina
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