1
|
Abstract
Genetic effects on complex traits may depend on context, such as age, sex, environmental exposures or social settings. However, it is often unclear if the extent of context dependency, or Gene-by-Environment interaction (GxE), merits more involved models than the additive model typically used to analyze data from genome-wide association studies (GWAS). Here, we suggest considering the utility of GxE models in GWAS as a tradeoff between bias and variance parameters. In particular, We derive a decision rule for choosing between competing models for the estimation of allelic effects. The rule weighs the increased estimation noise when context is considered against the potential bias when context dependency is ignored. In the empirical example of GxSex in human physiology, the increased noise of context-specific estimation often outweighs the bias reduction, rendering GxE models less useful when variants are considered independently. However, we argue that for complex traits, the joint consideration of context dependency across many variants mitigates both noise and bias. As a result, polygenic GxE models can improve both estimation and trait prediction. Finally, we exemplify (using GxDiet effects on longevity in fruit flies) how analyses based on independently ascertained "top hits" alone can be misleading, and that considering polygenic patterns of GxE can improve interpretation.
Collapse
|
2
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
3
|
Doyle T, Jimenez-Guri E, Hawkes WLS, Massy R, Mantica F, Permanyer J, Cozzuto L, Hermoso Pulido T, Baril T, Hayward A, Irimia M, Chapman JW, Bass C, Wotton KR. Genome-wide transcriptomic changes reveal the genetic pathways involved in insect migration. Mol Ecol 2022; 31:4332-4350. [PMID: 35801824 PMCID: PMC9546057 DOI: 10.1111/mec.16588] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022]
Abstract
Insects are capable of extraordinary feats of long‐distance movement that have profound impacts on the function of terrestrial ecosystems. The ability to undertake these movements arose multiple times through the evolution of a suite of traits that make up the migratory syndrome, however the underlying genetic pathways involved remain poorly understood. Migratory hoverflies (Diptera: Syrphidae) are an emerging model group for studies of migration. They undertake seasonal movements in huge numbers across large parts of the globe and are important pollinators, biological control agents and decomposers. Here, we assembled a high‐quality draft genome of the marmalade hoverfly (Episyrphus balteatus). We leveraged this genomic resource to undertake a genome‐wide transcriptomic comparison of actively migrating Episyrphus, captured from a high mountain pass as they flew south to overwinter, with the transcriptomes of summer forms which were non‐migratory. We identified 1543 genes with very strong evidence for differential expression. Interrogation of this gene set reveals a remarkable range of roles in metabolism, muscle structure and function, hormonal regulation, immunity, stress resistance, flight and feeding behaviour, longevity, reproductive diapause and sensory perception. These features of the migrant phenotype have arisen by the integration and modification of pathways such as insulin signalling for diapause and longevity, JAK/SAT for immunity, and those leading to octopamine production and fuelling to boost flight capabilities. Our results provide a powerful genomic resource for future research, and paint a comprehensive picture of global expression changes in an actively migrating insect, identifying key genomic components involved in this important life‐history strategy.
Collapse
Affiliation(s)
- Toby Doyle
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Eva Jimenez-Guri
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Will L S Hawkes
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Richard Massy
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jon Permanyer
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Toni Hermoso Pulido
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Alex Hayward
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Jason W Chapman
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, United Kingdom.,Environment and Sustainability Institute, University of Exeter, Cornwall Campus, Penryn, United Kingdom.,Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Karl R Wotton
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| |
Collapse
|
4
|
Rihani K, Sachse S. Shedding Light on Inter-Individual Variability of Olfactory Circuits in Drosophila. Front Behav Neurosci 2022; 16:835680. [PMID: 35548690 PMCID: PMC9084309 DOI: 10.3389/fnbeh.2022.835680] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/29/2022] [Indexed: 12/25/2022] Open
Abstract
Inter-individual differences in behavioral responses, anatomy or functional properties of neuronal populations of animals having the same genotype were for a long time disregarded. The majority of behavioral studies were conducted at a group level, and usually the mean behavior of all individuals was considered. Similarly, in neurophysiological studies, data were pooled and normalized from several individuals. This approach is mostly suited to map and characterize stereotyped neuronal properties between individuals, but lacks the ability to depict inter-individual variability regarding neuronal wiring or physiological characteristics. Recent studies have shown that behavioral biases and preferences to olfactory stimuli can vary significantly among individuals of the same genotype. The origin and the benefit of these diverse “personalities” is still unclear and needs to be further investigated. A perspective taken into account the inter-individual differences is needed to explore the cellular mechanisms underlying this phenomenon. This review focuses on olfaction in the vinegar fly Drosophila melanogaster and summarizes previous and recent studies on odor-guided behavior and the underlying olfactory circuits in the light of inter-individual variability. We address the morphological and physiological variabilities present at each layer of the olfactory circuitry and attempt to link them to individual olfactory behavior. Additionally, we discuss the factors that might influence individuality with regard to olfactory perception.
Collapse
Affiliation(s)
- Karen Rihani
- Research Group Olfactory Coding, Max Planck Institute for Chemical Ecology, Jena, Germany
- Max Planck Center Next Generation Insect Chemical Ecology, Jena, Germany
| | - Silke Sachse
- Research Group Olfactory Coding, Max Planck Institute for Chemical Ecology, Jena, Germany
- Max Planck Center Next Generation Insect Chemical Ecology, Jena, Germany
- *Correspondence: Silke Sachse,
| |
Collapse
|
5
|
Abstract
Among individuals, behavioral differences result from the well-known interplay of nature and nurture. Minute differences in the genetic code can lead to differential gene expression and function, dramatically affecting developmental processes and adult behavior. Environmental factors, epigenetic modifications, and gene expression and function are responsible for generating stochastic behaviors. In the last decade, the advent of high-throughput sequencing has facilitated studying the genetic basis of behavior and individuality. We can now study the genomes of multiple individuals and infer which genetic variations might be responsible for the observed behavior. In addition, the development of high-throughput behavioral paradigms, where multiple isogenic animals can be analyzed in various environmental conditions, has again facilitated the study of the influence of genetic and environmental variations in animal personality. Mainly, Drosophila melanogaster has been the focus of a great effort to understand how inter-individual behavioral differences emerge. The possibility of using large numbers of animals, isogenic populations, and the possibility of modifying neuronal function has made it an ideal model to search for the origins of individuality. In the present review, we will focus on the recent findings that try to shed light on the emergence of individuality with a particular interest in D. melanogaster.
Collapse
|
6
|
Behl T, Kaur I, Sehgal A, Singh S, Zengin G, Negrut N, Nistor-Cseppento DC, Pavel FM, Corb Aron RA, Bungau S. Exploring the Genetic Conception of Obesity via the Dual Role of FoxO. Int J Mol Sci 2021; 22:ijms22063179. [PMID: 33804729 PMCID: PMC8003860 DOI: 10.3390/ijms22063179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022] Open
Abstract
Obesity or overweight are not superficial problems, constituting a pressing issue. The obesity index has almost tripled since 1975, which is an alarming state. Most of the individuals are currently becoming overweight or have inappropriate body mass index (BMI) conditions. Obesity is characterized by increased fat accumulation and thus poses a higher health risk. There is increased size and volume of fat cells in the body, which usually accounts for obesity. Many investigations have been carried out in this area, such as behavioral improvements, dietary changes, chemical involvements, etc., but presently no such goals are established to manage these health concerns. Based on previous literature reports and our interpretation, the current review indicates the involvement of various transcriptional and transporter functions in modifying the above-mentioned health conditions. Various transcriptional factors such as Forkhead box O1 (FoxO1) impart a significant effect on the physiology and pathology of metabolic dysfunction such as obesity. FoxO1 plays a dual role whether in the progression or suppression of metabolic processes depending on its targets. Thus, in the current study, will be discussed the dual role of FoxO1 in metabolic conditions (such as obesity), also summarizing the role of various other transcriptional factors involved in obesity.
Collapse
Affiliation(s)
- Tapan Behl
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
- Correspondence: (T.B.); (S.B.); Tel.: +40-726-776-588 (S.B.)
| | - Ishnoor Kaur
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
| | - Aayush Sehgal
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
| | - Sukhbir Singh
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
| | - Gokhan Zengin
- Department of Biology, Faculty of Science, Selcuk University Campus, Konya 42130, Turkey;
| | - Nicoleta Negrut
- Department of Psycho-Neuroscience and Recovery, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (N.N.); (D.C.N.-C.)
| | - Delia Carmen Nistor-Cseppento
- Department of Psycho-Neuroscience and Recovery, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (N.N.); (D.C.N.-C.)
| | - Flavia Maria Pavel
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (F.M.P.); (R.A.C.A.)
| | - Raluca Anca Corb Aron
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (F.M.P.); (R.A.C.A.)
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania
- Correspondence: (T.B.); (S.B.); Tel.: +40-726-776-588 (S.B.)
| |
Collapse
|