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Williams-Simon PA, Oster C, Moaton JA, Ghidey R, Ng’oma E, Middleton KM, King EG. Naturally segregating genetic variants contribute to thermal tolerance in a Drosophila melanogaster model system. Genetics 2024; 227:iyae040. [PMID: 38506092 PMCID: PMC11075556 DOI: 10.1093/genetics/iyae040] [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: 07/11/2023] [Revised: 07/11/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Thermal tolerance is a fundamental physiological complex trait for survival in many species. For example, everyday tasks such as foraging, finding a mate, and avoiding predation are highly dependent on how well an organism can tolerate extreme temperatures. Understanding the general architecture of the natural variants within the genes that control this trait is of high importance if we want to better comprehend thermal physiology. Here, we take a multipronged approach to further dissect the genetic architecture that controls thermal tolerance in natural populations using the Drosophila Synthetic Population Resource as a model system. First, we used quantitative genetics and Quantitative Trait Loci mapping to identify major effect regions within the genome that influences thermal tolerance, then integrated RNA-sequencing to identify differences in gene expression, and lastly, we used the RNAi system to (1) alter tissue-specific gene expression and (2) functionally validate our findings. This powerful integration of approaches not only allows for the identification of the genetic basis of thermal tolerance but also the physiology of thermal tolerance in a natural population, which ultimately elucidates thermal tolerance through a fitness-associated lens.
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Affiliation(s)
- Patricka A Williams-Simon
- Department of Biology, University of Pennsylvania, 433 S University Ave., 226 Leidy Laboratories, Philadelphia, PA 19104, USA
| | - Camille Oster
- Ash Creek Forest Management, 2796 SE 73rd Ave., Hillsboro, OR 97123, USA
| | | | - Ronel Ghidey
- ECHO Data Analysis Center, Johns Hopkins Bloomberg School of Public Health, 504 Cathedral St., Baltimore, MD 2120, USA
| | - Enoch Ng’oma
- Division of Biology, University of Missouri, 226 Tucker Hall, Columbia, MO 65211, USA
| | - Kevin M Middleton
- Division of Biology, University of Missouri, 222 Tucker Hall, Columbia, MO 65211, USA
| | - Elizabeth G King
- Division of Biology, University of Missouri, 401 Tucker Hall, Columbia, MO 65211, USA
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Li M, Macro J, Meadows K, Mishra D, Martin D, Olson S, Huggins BJ, Graveley BR, Li JYH, Rogina B. Late-life shift in caloric intake affects fly metabolism and longevity. Proc Natl Acad Sci U S A 2023; 120:e2311019120. [PMID: 38064506 PMCID: PMC10723134 DOI: 10.1073/pnas.2311019120] [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: 06/29/2023] [Accepted: 10/05/2023] [Indexed: 12/17/2023] Open
Abstract
The prevalence of obesity is increasing in older adults and contributes to age-related decline. Caloric restriction (CR) alleviates obesity phenotypes and delays the onset of age-related changes. However, how late in life organisms benefit from switching from a high-(H) to a low-calorie (L) diet is unclear. We transferred male flies from a H to a L (HL) diet or vice versa (LH) at different times during life. Both shifts immediately change fly rate of aging even when applied late in life. HL shift rapidly reduces fly mortality rate to briefly lower rate than in flies on a constant L diet, and extends lifespan. Transcriptomic analysis uncovers that flies aged on H diet have acquired increased stress response, which may have temporal advantage over flies aged on L diet and leads to rapid decrease in mortality rate after HL switch. Conversely, a LH shift increases mortality rate, which is temporarily higher than in flies aged on a H diet, and shortens lifespan. Unexpectedly, more abundant transcriptomic changes accompanied LH shift, including increase in ribosome biogenesis, stress response and growth. These changes reflect protection from sudden release of ROS, energy storage, and use of energy to growth, which all likely contribute to higher mortality rate. As the beneficial effects of CR on physiology and lifespan are conserved across many organisms, our study provides framework to study underlying mechanisms of CR interventions that counteract the detrimental effects of H diets and reduce rate of aging even when initiated later in life.
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Affiliation(s)
- Michael Li
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT06030
| | - Jacob Macro
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT06030
| | - Kali Meadows
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT06030
| | - Dushyant Mishra
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT06030
| | - Dominique Martin
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT06030
| | - Sara Olson
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT06030
- Institute for Systems Genomics, School of Medicine, University of Connecticut Health Center, Farmington, CT06030
| | - Billy Joe Huggins
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT06030
| | - Brenton R. Graveley
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT06030
- Institute for Systems Genomics, School of Medicine, University of Connecticut Health Center, Farmington, CT06030
| | - James Y. H. Li
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT06030
- Institute for Systems Genomics, School of Medicine, University of Connecticut Health Center, Farmington, CT06030
| | - Blanka Rogina
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT06030
- Institute for Systems Genomics, School of Medicine, University of Connecticut Health Center, Farmington, CT06030
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Williams-Simon PA, Oster C, Moaton JA, Ghidey R, Ng'oma E, Middleton KM, Zars T, King EG. Naturally segregating genetic variants contribute to thermal tolerance in a D. melanogaster model system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.547110. [PMID: 37461510 PMCID: PMC10350013 DOI: 10.1101/2023.07.06.547110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Thermal tolerance is a fundamental physiological complex trait for survival in many species. For example, everyday tasks such as foraging, finding a mate, and avoiding predation, are highly dependent on how well an organism can tolerate extreme temperatures. Understanding the general architecture of the natural variants of the genes that control this trait is of high importance if we want to better comprehend how this trait evolves in natural populations. Here, we take a multipronged approach to further dissect the genetic architecture that controls thermal tolerance in natural populations using the Drosophila Synthetic Population Resource (DSPR) as a model system. First, we used quantitative genetics and Quantitative Trait Loci (QTL) mapping to identify major effect regions within the genome that influences thermal tolerance, then integrated RNA-sequencing to identify differences in gene expression, and lastly, we used the RNAi system to 1) alter tissue-specific gene expression and 2) functionally validate our findings. This powerful integration of approaches not only allows for the identification of the genetic basis of thermal tolerance but also the physiology of thermal tolerance in a natural population, which ultimately elucidates thermal tolerance through a fitness-associated lens.
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dSec16 Acting in Insulin-like Peptide Producing Cells Controls Energy Homeostasis in Drosophila. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010081. [PMID: 36676030 PMCID: PMC9862641 DOI: 10.3390/life13010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 12/29/2022]
Abstract
Many studies show that genetics play a major contribution to the onset of obesity. Human genome-wide association studies (GWASs) have identified hundreds of genes that are associated with obesity. However, the majority of them have not been functionally validated. SEC16B has been identified in multiple obesity GWASs but its physiological role in energy homeostasis remains unknown. Here, we use Drosophila to determine the physiological functions of dSec16 in energy metabolism. Our results showed that global RNAi of dSec16 increased food intake and triglyceride (TAG) levels. Furthermore, this TAG increase was observed in flies with a specific RNAi of dSec16 in insulin-like peptide producing cells (IPCs) with an alteration of endocrine peptides. Together, our study demonstrates that dSec16 acting in IPCs controls energy balance and advances the molecular understanding of obesity.
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Drosophila suzukii energetic pathways are differently modulated by nutritional geometry in males and females. Sci Rep 2022; 12:21194. [PMID: 36476948 PMCID: PMC9729594 DOI: 10.1038/s41598-022-25509-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
As a polyphagous pest, Drosophila suzukii has a variety of host fruits available for feeding and oviposition, but how the nutritional geometry of different hosts influences its metabolism is still poorly understood. This work aimed to evaluate how D. suzukii metabolic and transcriptional pathways are influenced by feeding on different host fruits, and how sex influences these responses. Adult flies were allowed to feed on five different fruit-based media. Lipids, glucose, glycogen, and energy pathways-associated gene expression, were quantified. Females showed an energetic metabolism easily adaptable to the food's nutritional characteristics; in contrast, males' energetic metabolism was particularly influenced by food, predominantly those fed on raspberry media who showed changes in glucose levels and in the expression of genes associated with metabolic pathways, suggesting activation of gluconeogenesis and trehaloneogenesis as a result of nutritional deficiency. Here we present novel insight into how D. suzukii's energetic pathways are modulated depending on fruits' nutritional geometry and sex. While the females showed high adaptability in their energetic metabolism to the diet, males were more feeding-sensitive. These findings might be used not only to control this pest population but to better advise producers to invest in less suitable fruits based on the hosts' nutritional geometry.
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Phenotyping of Drosophila melanogaster—A Nutritional Perspective. Biomolecules 2022; 12:biom12020221. [PMID: 35204721 PMCID: PMC8961528 DOI: 10.3390/biom12020221] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 02/01/2023] Open
Abstract
The model organism Drosophila melanogaster was increasingly applied in nutrition research in recent years. A range of methods are available for the phenotyping of D. melanogaster, which are outlined in the first part of this review. The methods include determinations of body weight, body composition, food intake, lifespan, locomotor activity, reproductive capacity and stress tolerance. In the second part, the practical application of the phenotyping of flies is demonstrated via a discussion of obese phenotypes in response to high-sugar diet (HSD) and high-fat diet (HFD) feeding. HSD feeding and HFD feeding are dietary interventions that lead to an increase in fat storage and affect carbohydrate-insulin homeostasis, lifespan, locomotor activity, reproductive capacity and stress tolerance. Furthermore, studies regarding the impacts of HSD and HFD on the transcriptome and metabolome of D. melanogaster are important for relating phenotypic changes to underlying molecular mechanisms. Overall, D. melanogaster was demonstrated to be a valuable model organism with which to examine the pathogeneses and underlying molecular mechanisms of common chronic metabolic diseases in a nutritional context.
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Phillips MA, Arnold KR, Vue Z, Beasley HK, Garza-Lopez E, Marshall AG, Morton DJ, McReynolds MR, Barter TT, Hinton A. Combining Metabolomics and Experimental Evolution Reveals Key Mechanisms Underlying Longevity Differences in Laboratory Evolved Drosophila melanogaster Populations. Int J Mol Sci 2022; 23:ijms23031067. [PMID: 35162994 PMCID: PMC8835531 DOI: 10.3390/ijms23031067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/22/2022] Open
Abstract
Experimental evolution with Drosophila melanogaster has been used extensively for decades to study aging and longevity. In recent years, the addition of DNA and RNA sequencing to this framework has allowed researchers to leverage the statistical power inherent to experimental evolution to study the genetic basis of longevity itself. Here, we incorporated metabolomic data into to this framework to generate even deeper insights into the physiological and genetic mechanisms underlying longevity differences in three groups of experimentally evolved D. melanogaster populations with different aging and longevity patterns. Our metabolomic analysis found that aging alters mitochondrial metabolism through increased consumption of NAD+ and increased usage of the TCA cycle. Combining our genomic and metabolomic data produced a list of biologically relevant candidate genes. Among these candidates, we found significant enrichment for genes and pathways associated with neurological development and function, and carbohydrate metabolism. While we do not explicitly find enrichment for aging canonical genes, neurological dysregulation and carbohydrate metabolism are both known to be associated with accelerated aging and reduced longevity. Taken together, our results provide plausible genetic mechanisms for what might be driving longevity differences in this experimental system. More broadly, our findings demonstrate the value of combining multiple types of omic data with experimental evolution when attempting to dissect mechanisms underlying complex and highly polygenic traits such as aging.
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Affiliation(s)
- Mark A. Phillips
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA;
| | - Kenneth R. Arnold
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA; (K.R.A.); (T.T.B.)
| | - Zer Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Z.V.); (H.K.B.); (A.G.M.)
| | - Heather K. Beasley
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Z.V.); (H.K.B.); (A.G.M.)
- Department of Biochemistry, Cancer Biology, Neuroscience, and Pharmacology, Meharry Medical College, Nashville, TN 37208, USA
| | - Edgar Garza-Lopez
- Hinton and Garza-Lopez Family Consulting Company, Iowa City, IA 52246, USA;
| | - Andrea G. Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Z.V.); (H.K.B.); (A.G.M.)
| | - Derrick J. Morton
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - Melanie R. McReynolds
- Department of Biochemistry and Molecular Biology, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA;
| | - Thomas T. Barter
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA; (K.R.A.); (T.T.B.)
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Z.V.); (H.K.B.); (A.G.M.)
- Hinton and Garza-Lopez Family Consulting Company, Iowa City, IA 52246, USA;
- Correspondence:
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Karpova EK, Komyshev EG, Genaev MA, Adonyeva NV, Afonnikov DA, Eremina MA, Gruntenko NE. Quantifying Drosophila adults with the use of a smartphone. Biol Open 2020; 9:bio054452. [PMID: 32917765 PMCID: PMC7561479 DOI: 10.1242/bio.054452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/02/2020] [Indexed: 11/24/2022] Open
Abstract
A method for automation of imago quantifying and fecundity assessment in Drosophila with the use of mobile devices running Android operating system is proposed. The traditional manual method of counting the progeny takes a long time and limits the opportunity of making large-scale experiments. Thus, the development of computerized methods that would allow us to automatically make a quantitative estimate of Drosophilamelanogaster fecundity is an urgent requirement. We offer a modification of the mobile application SeedCounter that analyzes images of objects placed on a standard sheet of paper for an automatic calculation of D. melanogaster offspring or quantification of adult flies in any other kind of experiment. The relative average error in estimates of the number of flies by mobile app is about 2% in comparison with the manual counting and the processing time is six times shorter. Study of the effects of imaging conditions on accuracy of flies counting showed that lighting conditions do not significantly affect this parameter, and higher accuracy can be achieved using high-resolution smartphone cameras (8 Mpx and more). These results indicate the high accuracy and efficiency of the method suggested.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Evgenia K Karpova
- Laboratory of Stress Genetics, Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Evgenii G Komyshev
- Laboratory of Stress Genetics, Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Mikhail A Genaev
- Laboratory of Stress Genetics, Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Laboratory of Evolutionary Bioinformatics and Theoretical Genetics, Department of Natural Sciences, Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Natalya V Adonyeva
- Laboratory of Stress Genetics, Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Dmitry A Afonnikov
- Laboratory of Stress Genetics, Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Margarita A Eremina
- Laboratory of Stress Genetics, Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Nataly E Gruntenko
- Laboratory of Stress Genetics, Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
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