1
|
Blackie L, Gaspar P, Mosleh S, Lushchak O, Kong L, Jin Y, Zielinska AP, Cao B, Mineo A, Silva B, Ameku T, Lim SE, Mao Y, Prieto-Godino L, Schoborg T, Varela M, Mahadevan L, Miguel-Aliaga I. The sex of organ geometry. Nature 2024; 630:392-400. [PMID: 38811741 PMCID: PMC11168936 DOI: 10.1038/s41586-024-07463-4] [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: 06/07/2023] [Accepted: 04/24/2024] [Indexed: 05/31/2024]
Abstract
Organs have a distinctive yet often overlooked spatial arrangement in the body1-5. We propose that there is a logic to the shape of an organ and its proximity to its neighbours. Here, by using volumetric scans of many Drosophila melanogaster flies, we develop methods to quantify three-dimensional features of organ shape, position and interindividual variability. We find that both the shapes of organs and their relative arrangement are consistent yet differ between the sexes, and identify unexpected interorgan adjacencies and left-right organ asymmetries. Focusing on the intestine, which traverses the entire body, we investigate how sex differences in three-dimensional organ geometry arise. The configuration of the adult intestine is only partially determined by physical constraints imposed by adjacent organs; its sex-specific shape is actively maintained by mechanochemical crosstalk between gut muscles and vascular-like trachea. Indeed, sex-biased expression of a muscle-derived fibroblast growth factor-like ligand renders trachea sexually dimorphic. In turn, tracheal branches hold gut loops together into a male or female shape, with physiological consequences. Interorgan geometry represents a previously unrecognized level of biological complexity which might enable or confine communication across organs and could help explain sex or species differences in organ function.
Collapse
Affiliation(s)
- Laura Blackie
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Pedro Gaspar
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Salem Mosleh
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Department of Natural Sciences, University of Maryland Eastern Shore, Princess Anne, MD, USA
| | | | - Lingjin Kong
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Yuhong Jin
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Agata P Zielinska
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Boxuan Cao
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Alessandro Mineo
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Bryon Silva
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Tomotsune Ameku
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Shu En Lim
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
| | - Yanlan Mao
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
| | | | - Todd Schoborg
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Marta Varela
- Faculty of Medicine, National Heart & Lung Institute, Imperial College London, London, UK
| | - L Mahadevan
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Departments of Physics and Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Irene Miguel-Aliaga
- MRC Laboratory of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
- The Francis Crick Institute, London, UK.
| |
Collapse
|
2
|
Li XC, Gandara L, Ekelöf M, Richter K, Alexandrov T, Crocker J. Rapid response of fly populations to gene dosage across development and generations. Nat Commun 2024; 15:4551. [PMID: 38811562 PMCID: PMC11137061 DOI: 10.1038/s41467-024-48960-4] [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: 09/06/2023] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Although the effects of genetic and environmental perturbations on multicellular organisms are rarely restricted to single phenotypic layers, our current understanding of how developmental programs react to these challenges remains limited. Here, we have examined the phenotypic consequences of disturbing the bicoid regulatory network in early Drosophila embryos. We generated flies with two extra copies of bicoid, which causes a posterior shift of the network's regulatory outputs and a decrease in fitness. We subjected these flies to EMS mutagenesis, followed by experimental evolution. After only 8-15 generations, experimental populations have normalized patterns of gene expression and increased survival. Using a phenomics approach, we find that populations were normalized through rapid increases in embryo size driven by maternal changes in metabolism and ovariole development. We extend our results to additional populations of flies, demonstrating predictability. Together, our results necessitate a broader view of regulatory network evolution at the systems level.
Collapse
Affiliation(s)
- Xueying C Li
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Lautaro Gandara
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Måns Ekelöf
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kerstin Richter
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Theodore Alexandrov
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit between EMBL and Heidelberg University, Heidelberg, Germany
- BioInnovation Institute, Copenhagen, Denmark
| | - Justin Crocker
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| |
Collapse
|
3
|
Kotov AA, Adashev VE, Kombarov IA, Bazylev SS, Shatskikh AS, Olenina LV. Molecular Insights into Female Hybrid Sterility in Interspecific Crosses between Drosophila melanogaster and Drosophila simulans. Int J Mol Sci 2024; 25:5681. [PMID: 38891872 PMCID: PMC11172174 DOI: 10.3390/ijms25115681] [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: 04/19/2024] [Revised: 05/19/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Species of the genus Drosophila have served as favorite models in speciation studies; however, genetic factors of interspecific reproductive incompatibility are under-investigated. Here, we performed an analysis of hybrid female sterility by crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis and molecular, cellular, and genetic approaches, we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis, and functional defects of oogenesis in hybrids. Premature germline stem cell loss was the most prominent defect of oogenesis in hybrid ovaries. Because of the differential expression of genes encoding piRNA pathway components, rhino and deadlock, the functional RDCmel complex in hybrid ovaries was not assembled. However, the activity of the RDCsim complex was maintained in hybrids independent of the genomic origin of piRNA clusters. Despite the identification of a cohort of overexpressed TEs in hybrid ovaries, we found no evidence that their activity can be considered the main cause of hybrid sterility. We revealed a complicated pattern of Vasa protein expression in the hybrid germline, including partial AT-chX piRNA targeting of the vasasim allele and a significant zygotic delay in vasamel expression. We arrived at the conclusion that the hybrid sterility phenotype was caused by intricate multi-locus differences between the species.
Collapse
Affiliation(s)
- Alexei A. Kotov
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Vladimir E. Adashev
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Ilia A. Kombarov
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Sergei S. Bazylev
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Aleksei S. Shatskikh
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Ludmila V. Olenina
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| |
Collapse
|
4
|
Palumbo RJ, Yang Y, Feigon J, Hanes SD. Catalytic activity of the Bin3/MePCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster. Genetics 2024; 226:iyad203. [PMID: 37982586 PMCID: PMC10763541 DOI: 10.1093/genetics/iyad203] [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: 05/31/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
Methylphosphate Capping Enzyme (MePCE) monomethylates the gamma phosphate at the 5' end of the 7SK noncoding RNA, a modification thought to protect 7SK from degradation. 7SK serves as a scaffold for assembly of a snRNP complex that inhibits transcription by sequestering the positive elongation factor P-TEFb. While much is known about the biochemical activity of MePCE in vitro, little is known about its functions in vivo, or what roles-if any-there are for regions outside the conserved methyltransferase domain. Here, we investigated the role of Bin3, the Drosophila ortholog of MePCE, and its conserved functional domains in Drosophila development. We found that bin3 mutant females had strongly reduced rates of egg-laying, which was rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 promotes fecundity by repressing P-TEFb. bin3 mutants also exhibited neuromuscular defects, analogous to a patient with MePCE haploinsufficiency. These defects were also rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 and MePCE have conserved roles in promoting neuromuscular function by repressing P-TEFb. Unexpectedly, we found that a Bin3 catalytic mutant (Bin3Y795A) could still bind and stabilize 7SK and rescue all bin3 mutant phenotypes, indicating that Bin3 catalytic activity is dispensable for 7SK stability and snRNP function in vivo. Finally, we identified a metazoan-specific motif (MSM) outside of the methyltransferase domain and generated mutant flies lacking this motif (Bin3ΔMSM). Bin3ΔMSM mutant flies exhibited some-but not all-bin3 mutant phenotypes, suggesting that the MSM is required for a 7SK-independent, tissue-specific function of Bin3.
Collapse
Affiliation(s)
- Ryan J Palumbo
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Steven D Hanes
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Palumbo RJ, Hanes SD. Catalytic activity of the Bin3/MEPCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543302. [PMID: 37333392 PMCID: PMC10274667 DOI: 10.1101/2023.06.01.543302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Methylphosphate Capping Enzyme (MEPCE) monomethylates the gamma phosphate at the 5' end of the 7SK noncoding RNA, a modification thought to protect 7SK from degradation. 7SK serves as a scaffold for assembly of a snRNP complex that inhibits transcription by sequestering the positive elongation factor P-TEFb. While much is known about the biochemical activity of MEPCE in vitro, little is known about its functions in vivo, or what roles- if any-there are for regions outside the conserved methyltransferase domain. Here, we investigated the role of Bin3, the Drosophila ortholog of MEPCE, and its conserved functional domains in Drosophila development. We found that bin3 mutant females had strongly reduced rates of egg-laying, which was rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 promotes fecundity by repressing P-TEFb. bin3 mutants also exhibited neuromuscular defects, analogous to a patient with MEPCE haploinsufficiency. These defects were also rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 and MEPCE have conserved roles in promoting neuromuscular function by repressing P-TEFb. Unexpectedly, we found that a Bin3 catalytic mutant (Bin3Y795A) could still bind and stabilize 7SK and rescue all bin3 mutant phenotypes, indicating that Bin3 catalytic activity is dispensable for 7SK stability and snRNP function in vivo. Finally, we identified a metazoan-specific motif (MSM) outside of the methyltransferase domain and generated mutant flies lacking this motif (Bin3ΔMSM). Bin3ΔMSM mutant flies exhibited some-but not all-bin3 mutant phenotypes, suggesting that the MSM is required for a 7SK-independent, tissue-specific function of Bin3.
Collapse
Affiliation(s)
- Ryan J Palumbo
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, 4283 Weiskotten Hall, Syracuse, New York, 13210
| | - Steven D Hanes
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, 4283 Weiskotten Hall, Syracuse, New York, 13210
| |
Collapse
|
7
|
Jamil M, Ahmad S, Ran Y, Ma S, Cao F, Lin X, Yan R. Argonaute1 and Gawky Are Required for the Development and Reproduction of Melon fly, Zeugodacus cucurbitae. Front Genet 2022; 13:880000. [PMID: 35812742 PMCID: PMC9260231 DOI: 10.3389/fgene.2022.880000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/04/2022] [Indexed: 11/18/2022] Open
Abstract
Argonaute family genes encode a highly conserved group of proteins that have been associated with RNA silencing in both animals and plants. This study investigates the importance of microRNA biogenesis key regulators Argonaute1 (Ago1) and Gawky genes in the post-embryonic and ovarian development of the melon fly, Zeugodacus cucurbitae. The expression levels of these genes were mapped in all developmental stages and different adult tissues. Their roles in development were investigated using RNA interference (RNAi) via two different dsRNA delivery techniques. Embryo microinjection and oral feeding of third instar larvae successfully knocked down and greatly reduced the expression level of the target genes. Additionally, ex vivo essays revealed the stability of dsRNA in food was sufficient for gene silencing, although its integrity was affected in midgut. A wide range of phenotypes were observed on pupation, segmentation, pigmentation, and ovarian development. RNAi-mediated silencing of Gawky caused high mortality and loss of body segmentation, while Ago1 knockdown affected ovarian development and pigmentation. Developmental abnormalities and ovarian malformations caused by silencing these genes suggest that these genes are crucial for viability and reproductive capacity of Z. cucurbitae, and may be used as potential target genes in pest management.
Collapse
Affiliation(s)
- Momana Jamil
- School of Life Sciences, Hainan University, Haikou, China
| | - Shakil Ahmad
- School of Plant Protection, Hainan University, Haikou, China
| | - Yingqiao Ran
- School of Plant Protection, Hainan University, Haikou, China
| | - Siya Ma
- School of Life Sciences, Hainan University, Haikou, China
| | - Fengqin Cao
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Plant Protection, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Lab, Sanya, China
| | - Xianwu Lin
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Plant Protection, Hainan University, Haikou, China
- *Correspondence: Xianwu Lin, ; Rihui Yan,
| | - Rihui Yan
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Plant Protection, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Lab, Sanya, China
- *Correspondence: Xianwu Lin, ; Rihui Yan,
| |
Collapse
|
8
|
Vasudevan D, Katow H, Huang HW, Tang G, Ryoo HD. A Protein-trap allele reveals roles for Drosophila ATF4 in photoreceptor degeneration, oogenesis and wing development. Dis Model Mech 2021; 15:273766. [PMID: 34919148 PMCID: PMC8938396 DOI: 10.1242/dmm.049119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/08/2021] [Indexed: 11/20/2022] Open
Abstract
Metazoans have evolved various quality control mechanisms to cope with cellular stress inflicted by external and physiological conditions. ATF4 is a major effector of the Integrated Stress Response (ISR), an evolutionarily conserved pathway that mediates adaptation to various cellular stressors. Loss of function of Drosophila ATF4, encoded by the gene cryptocephal (crc), results in lethality during pupal development. The roles of crc in Drosophila disease models and in adult tissue homeostasis thus remain poorly understood. Here, we report that a protein-trap MiMIC insertion in the crc locus generates a crc-GFP fusion protein that allows visualization of crc activity in vivo. This allele also acts as a hypomorphic mutant that uncovers previously unknown roles for crc. Specifically, the crc protein-trap line shows crc-GFP induction in a Drosophila model for Retinitis Pigmentosa (RP). This crc allele renders flies more vulnerable to amino acid deprivation and age-dependent retinal degeneration. These mutants also show defects in wing veins and oocyte maturation. Together, our data reveal previously unknown roles for crc in development, cellular homeostasis and photoreceptor survival.
Collapse
Affiliation(s)
- Deepika Vasudevan
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA.,Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Hidetaka Katow
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | | | - Grace Tang
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Hyung Don Ryoo
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
| |
Collapse
|
9
|
Bestetti I, Barbieri C, Sironi A, Specchia V, Yatsenko SA, De Donno MD, Caslini C, Gentilini D, Crippa M, Larizza L, Marozzi A, Rajkovic A, Toniolo D, Bozzetti MP, Finelli P. Targeted whole exome sequencing and Drosophila modelling to unveil the molecular basis of primary ovarian insufficiency. Hum Reprod 2021; 36:2975-2991. [PMID: 34480478 PMCID: PMC8523209 DOI: 10.1093/humrep/deab192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 07/29/2021] [Indexed: 11/25/2022] Open
Abstract
STUDY QUESTION Can a targeted whole exome sequencing (WES) on a cohort of women showing a primary ovarian insufficiency (POI) phenotype at a young age, combined with a study of copy number variations, identify variants in candidate genes confirming their deleterious effect on ovarian function? SUMMARY ANSWER This integrated approach has proved effective in identifying novel candidate genes unveiling mechanisms involved in POI pathogenesis. WHAT IS KNOWN ALREADY POI, a condition occurring in 1% of women under 40 years of age, affects women’s fertility leading to a premature loss of ovarian reserve. The genetic causes of POI are highly heterogeneous and several determinants contributing to its prominent oligogenic inheritance pattern still need to be elucidated. STUDY DESIGN, SIZE, DURATION WES screening for pathogenic variants of 41 Italian women with non-syndromic primary and early secondary amenorrhoea occurring before age 25 was replicated on another 60 POI patients, including 35 French and 25 American women, to reveal statistically significant shared variants. PARTICIPANTS/MATERIALS, SETTING, METHODS The Italian POI patients’ DNA were processed by targeted WES including 542 RefSeq genes expressed or functioning during distinct reproductive or ovarian processes (e.g. DNA repair, meiosis, oocyte maturation, folliculogenesis and menopause). Extremely rare variants were filtered and selected by means of a Fisher Exact test using several publicly available datasets. A case-control Burden test was applied to highlight the most significant genes using two ad-hoc control female cohorts. To support the obtained data, the identified genes were screened on a novel cohort of 60 Caucasian POI patients and the same case-control analysis was carried out. Comparative analysis of the human identified genes was performed on mouse and Drosophila melanogaster by analysing the orthologous genes in their ovarian phenotype, and two of the selected genes were fruit fly modelled to explore their role in fertility. MAIN RESULTS AND THE ROLE OF CHANCE The filtering steps applied to search for extremely rare pathogenic variants in the Italian cohort revealed 64 validated single-nucleotide variants/Indels in 59 genes in 30 out of 41 screened women. Burden test analysis highlighted 13 ovarian genes as being the most enriched and significant. To validate these findings, filtering steps and Burden analysis on the second cohort of Caucasian patients yielded 11 significantly enriched genes. Among them, AFP, DMRT3, MOV10, FYN and MYC were significant in both patient cohorts and hence were considered strong candidates for POI. Mouse and Drosophila comparative analysis evaluated a conserved role through the evolution of several candidates, and functional studies using a Drosophila model, when applicable, supported the conserved role of the MOV10 armitage and DMRT3 dmrt93B orthologues in female fertility. LARGE SCALE DATA The datasets for the Italian cohort generated during the current study are publicly available at ClinVar database (http://www.ncbi.nlm.nih.gov/clinvar/): accession numbers SCV001364312 to SCV001364375. LIMITATIONS, REASONS FOR CAUTION This is a targeted WES analysis hunting variants in candidate genes previously identified by different genomic approaches. For most of the investigated sporadic cases, we could not track the parental inheritance, due to unavailability of the parents’ DNA samples; in addition, we might have overlooked additional rare variants in novel candidate POI genes extracted from the exome data. On the contrary, we might have considered some inherited variants whose clinical significance is uncertain and might not be causative for the patients’ phenotype. Additionally, as regards the Drosophila model, it will be extremely important in the future to have more mutants or RNAi strains available for each candidate gene in order to validate their role in POI pathogenesis. WIDER IMPLICATIONS OF THE FINDINGS The genomic, statistical, comparative and functional approaches integrated in our study convincingly support the extremely heterogeneous oligogenic nature of POI, and confirm the maintenance across the evolution of some key genes safeguarding fertility and successful reproduction. Two principal classes of genes were identified: (i) genes primarily involved in meiosis, namely in synaptonemal complex formation, asymmetric division and oocyte maturation and (ii) genes safeguarding cell maintenance (piRNA and DNA repair pathways). STUDY FUNDING/COMPETING INTEREST(S) This work was supported by Italian Ministry of Health grants ‘Ricerca Corrente’ (08C621_2016 and 08C924_2019) provided to IRCCS Istituto Auxologico Italiano, and by ‘Piano Sostegno alla Ricerca’ (PSR2020_FINELLI_LINEA_B) provided by the University of Milan; M.P.B. was supported by Telethon-Italy (grant number GG14181). There are no conflicts of interest.
Collapse
Affiliation(s)
- I Bestetti
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
| | - C Barbieri
- Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milan, Italy
| | - A Sironi
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
| | - V Specchia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - S A Yatsenko
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, PA, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - M D De Donno
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - C Caslini
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
| | - D Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.,Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - M Crippa
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
| | - L Larizza
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - A Marozzi
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
| | - A Rajkovic
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San, Francisco, San Francisco, CA, USA.,Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - D Toniolo
- Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milan, Italy
| | - M P Bozzetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - P Finelli
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
| |
Collapse
|
10
|
Tarikere S, Ylla G, Extavour CG. Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster. G3 (BETHESDA, MD.) 2021; 12:6364899. [PMID: 34849771 PMCID: PMC9210308 DOI: 10.1093/g3journal/jkab305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022]
Abstract
The survival and evolution of a species is a function of the number of offspring it can produce. In insects, the number of eggs that an ovary can produce is a major determinant of reproductive capacity. Insect ovaries are made up of tubular egg-producing subunits called ovarioles, whose number largely determines the number of eggs that can be potentially laid. Ovariole number in Drosophila is directly determined by the number of cellular structures called terminal filaments, which are stacks of cells that assemble in the larval ovary. Elucidating the developmental and regulatory mechanisms of terminal filament formation is thus key to understanding the regulation of insect reproduction through ovariole number regulation. We systematically measured mRNA expression of all cells in the larval ovary at the beginning, middle, and end of terminal filament formation. We also separated somatic and germ line cells during these stages and assessed their tissue-specific gene expression during larval ovary development. We found that the number of differentially expressed somatic genes is highest during the late stages of terminal filament formation and includes many signaling pathways that govern ovary development. We also show that germ line tissue, in contrast, shows greater differential expression during early stages of terminal filament formation, and highly expressed germ line genes at these stages largely control cell division and DNA repair. We provide a tissue-specific and temporal transcriptomic dataset of gene expression in the developing larval ovary as a resource to study insect reproduction.
Collapse
Affiliation(s)
- Shreeharsha Tarikere
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Guillem Ylla
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA,Corresponding author:
| |
Collapse
|
11
|
Spierer AN, Mossman JA, Smith SP, Crawford L, Ramachandran S, Rand DM. Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila. PLoS Genet 2021; 17:e1008887. [PMID: 33735180 PMCID: PMC7971549 DOI: 10.1371/journal.pgen.1008887] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 01/26/2021] [Indexed: 12/28/2022] Open
Abstract
The winged insects of the order Diptera are colloquially named for their most recognizable phenotype: flight. These insects rely on flight for a number of important life history traits, such as dispersal, foraging, and courtship. Despite the importance of flight, relatively little is known about the genetic architecture of flight performance. Accordingly, we sought to uncover the genetic modifiers of flight using a measure of flies’ reaction and response to an abrupt drop in a vertical flight column. We conducted a genome wide association study (GWAS) using 197 of the Drosophila Genetic Reference Panel (DGRP) lines, and identified a combination of additive and marginal variants, epistatic interactions, whole genes, and enrichment across interaction networks. Egfr, a highly pleiotropic developmental gene, was among the most significant additive variants identified. We functionally validated 13 of the additive candidate genes’ (Adgf-A/Adgf-A2/CG32181, bru1, CadN, flapper (CG11073), CG15236, flippy (CG9766), CREG, Dscam4, form3, fry, Lasp/CG9692, Pde6, Snoo), and introduce a novel approach to whole gene significance screens: PEGASUS_flies. Additionally, we identified ppk23, an Acid Sensing Ion Channel (ASIC) homolog, as an important hub for epistatic interactions. We propose a model that suggests genetic modifiers of wing and muscle morphology, nervous system development and function, BMP signaling, sexually dimorphic neural wiring, and gene regulation are all important for the observed differences flight performance in a natural population. Additionally, these results represent a snapshot of the genetic modifiers affecting drop-response flight performance in Drosophila, with implications for other insects. Insect flight is a widely recognizable phenotype of many winged insects, hence the name: flies. While fruit flies, or Drosophila melanogaster, are a genetically tractable model, flight performance is a highly integrative phenotype, and therefore challenging to identify comprehensively which genetic modifiers contribute to its genetic architecture. Accordingly, we screened 197 Drosophila Genetic Reference Panel lines for their ability to react and respond to an abrupt drop. Using several computational approaches, we identified additive, marginal, and epistatic variants, as well as whole genes and altered sub-networks of gene-gene and protein-protein interaction networks that contribute to variation in flight performance. More generally, we demonstrate the benefits of employing multiple methodologies to elucidate the genetic architecture of complex traits. Many variants and genes mapped to regions of the genome that affect neurodevelopment, wing and muscle development, and regulation of gene expression. We also introduce PEGASUS_flies, a Drosophila-adapted version of the PEGASUS platform first used in human studies, to infer gene-level significance of association based on the gene’s distribution of individual variant P-values. Our results contribute to the debate over the relative importance of individual, additive factors and epistatic, or higher order, interactions, in the mapping of genotype to phenotype.
Collapse
Affiliation(s)
- Adam N Spierer
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Jim A Mossman
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Samuel Pattillo Smith
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- Microsoft Research New England, Cambridge, Massachusetts, United States of America
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| |
Collapse
|
12
|
Kumar T, Blondel L, Extavour CG. Topology-driven protein-protein interaction network analysis detects genetic sub-networks regulating reproductive capacity. eLife 2020; 9:54082. [PMID: 32901612 PMCID: PMC7550192 DOI: 10.7554/elife.54082] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 09/01/2020] [Indexed: 12/23/2022] Open
Abstract
Understanding the genetic regulation of organ structure is a fundamental problem in developmental biology. Here, we use egg-producing structures of insect ovaries, called ovarioles, to deduce systems-level gene regulatory relationships from quantitative functional genetic analysis. We previously showed that Hippo signalling, a conserved regulator of animal organ size, regulates ovariole number in Drosophila melanogaster. To comprehensively determine how Hippo signalling interacts with other pathways in this regulation, we screened all known signalling pathway genes, and identified Hpo-dependent and Hpo-independent signalling requirements. Network analysis of known protein-protein interactions among screen results identified independent gene regulatory sub-networks regulating one or both of ovariole number and egg laying. These sub-networks predict involvement of previously uncharacterised genes with higher accuracy than the original candidate screen. This shows that network analysis combining functional genetic and large-scale interaction data can predict function of novel genes regulating development.
Collapse
Affiliation(s)
- Tarun Kumar
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Leo Blondel
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| |
Collapse
|
13
|
Serrato-Capuchina A, Wang J, Earley E, Peede D, Isbell K, Matute DR. Paternally Inherited P-Element Copy Number Affects the Magnitude of Hybrid Dysgenesis in Drosophila simulans and D. melanogaster. Genome Biol Evol 2020; 12:808-826. [PMID: 32339225 PMCID: PMC7313671 DOI: 10.1093/gbe/evaa084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) are repetitive regions of DNA that are able to self-replicate and reinsert themselves throughout host genomes. Since the discovery of TEs, a prevalent question has been whether increasing TE copy number has an effect on the fitness of their hosts. P-elements (PEs) in Drosophila are a well-studied TE that has strong phenotypic effects. When a female without PEs (M) is crossed to a male with them (P), the resulting females are often sterile, a phenomenon called hybrid dysgenesis (HD). Here, we used short- and long-read sequencing to infer the number of PEs in the genomes of dozens of isofemale lines from two Drosophila species and measured whether the magnitude of HD was correlated with the number of PEs in the paternal genome. Consistent with previous reports, we find evidence for a positive correlation between the paternal PE copy number and the magnitude of HD in progeny from ♀M × ♂ P crosses for both species. Other crosses are not affected by the number of PE copies. We also find that the correlation between the strength of HD and PE copy number differs between species, which suggests that there are genetic differences that might make some genomes more resilient to the potentially deleterious effects of TEs. Our results suggest that PE copy number interacts with other factors in the genome and the environment to cause HD and that the importance of these interactions is species specific.
Collapse
Affiliation(s)
| | - Jeremy Wang
- Genetics Department, University of North Carolina, Chapel Hill
| | - Eric Earley
- Genomics in Public Health and Medicine RTI International, Research Triangle Park, North Carolina
| | - David Peede
- Biology Department, University of North Carolina, Chapel Hill
| | - Kristin Isbell
- Biology Department, University of North Carolina, Chapel Hill
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill
| |
Collapse
|
14
|
Flatt T. Life-History Evolution and the Genetics of Fitness Components in Drosophila melanogaster. Genetics 2020; 214:3-48. [PMID: 31907300 PMCID: PMC6944413 DOI: 10.1534/genetics.119.300160] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/03/2019] [Indexed: 12/28/2022] Open
Abstract
Life-history traits or "fitness components"-such as age and size at maturity, fecundity and fertility, age-specific rates of survival, and life span-are the major phenotypic determinants of Darwinian fitness. Analyzing the evolution and genetics of these phenotypic targets of selection is central to our understanding of adaptation. Due to its simple and rapid life cycle, cosmopolitan distribution, ease of maintenance in the laboratory, well-understood evolutionary genetics, and its versatile genetic toolbox, the "vinegar fly" Drosophila melanogaster is one of the most powerful, experimentally tractable model systems for studying "life-history evolution." Here, I review what has been learned about the evolution and genetics of life-history variation in D. melanogaster by drawing on numerous sources spanning population and quantitative genetics, genomics, experimental evolution, evolutionary ecology, and physiology. This body of work has contributed greatly to our knowledge of several fundamental problems in evolutionary biology, including the amount and maintenance of genetic variation, the evolution of body size, clines and climate adaptation, the evolution of senescence, phenotypic plasticity, the nature of life-history trade-offs, and so forth. While major progress has been made, important facets of these and other questions remain open, and the D. melanogaster system will undoubtedly continue to deliver key insights into central issues of life-history evolution and the genetics of adaptation.
Collapse
Affiliation(s)
- Thomas Flatt
- Department of Biology, University of Fribourg, CH-1700, Switzerland
| |
Collapse
|
15
|
Sarikaya DP, Church SH, Lagomarsino LP, Magnacca KN, Montgomery SL, Price DK, Kaneshiro KY, Extavour CG. Reproductive Capacity Evolves in Response to Ecology through Common Changes in Cell Number in Hawaiian Drosophila. Curr Biol 2019; 29:1877-1884.e6. [PMID: 31130459 DOI: 10.1016/j.cub.2019.04.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/01/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023]
Abstract
Lifetime reproductive capacity is a critical fitness component. In insects, female reproductive capacity is largely determined by the number of ovarioles, the egg-producing subunits of the ovary [e.g., 1]. Recent work has provided insights into ovariole number regulation in Drosophila melanogaster. However, whether mechanisms discovered under laboratory conditions explain evolutionary variation in natural populations is an outstanding question. We investigated potential effects of ecology on the developmental processes underlying ovariole number evolution among Hawaiian Drosophila, a large adaptive radiation wherein the highest and lowest ovariole numbers of the family have evolved within 25 million years. Previous studies proposed that ovariole number correlated with oviposition substrate [2-4] but sampled largely one clade of these flies and were limited by a provisional phylogeny and the available comparative methods. We test this hypothesis by applying phylogenetic modeling to an expanded sampling of ovariole numbers and substrate types and show support for these predictions across all major groups of Hawaiian Drosophila, wherein ovariole number variation is best explained by adaptation to specific substrates. Furthermore, we show that oviposition substrate evolution is linked to changes in the allometric relationship between body size and ovariole number. Finally, we provide evidence that the major changes in ovarian cell number that regulate D. melanogaster ovariole number also regulate ovariole number in Hawaiian drosophilids. Thus, we provide evidence that this remarkable adaptive radiation is linked to evolutionary changes in a key reproductive trait regulated at least partly by variation in the same developmental parameters that operate in the model species D. melanogaster.
Collapse
Affiliation(s)
- Didem P Sarikaya
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA.
| | - Samuel H Church
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA
| | - Laura P Lagomarsino
- Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | | | | | - Donald K Price
- Biology Department, University of Hawai'i at Hilo, 200 W. Kawili St., Hilo, HI 96720, USA
| | - Kenneth Y Kaneshiro
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, 1993 East-West Rd., Manoa, HI 96822, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA.
| |
Collapse
|
16
|
Singh S, Nandy B, Tapadia MG. Complex effects of Ayurvedic formulation: Guduchi and Madhuyashti on different components of life history may elude the elixir effect. J Genet 2018; 97:1253-1261. [PMID: 30555074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Formulations from the traditional Indian medicine, Ayurveda, have long been considered to have potent life-style enhancing effects, possibly by their effect(s) on key life-history attributes. Although several studies have reported beneficial effects of these formulations on different components of life history, few have investigated their concurrent influence on various life-history traits. Here, we report the results of an investigation showing the effect of two well-known Ayurvedic formulations, Guduchi and Madhuyashti, on fecundity and longevity of Drosophila melanogaster. Flies were either grown (i.e., larval exposure) and/or maintained (i.e., adult exposure) on standard food supplemented with 0.5% Guduchi or 0.5% Madhuyashti. It was observed that the longevity of adult flies of both sexes was not affected on feeding Guduchifood, but fecundity of the females was greatly enhanced. Fecundity was also found to be affected by the adult food and whether their mates were grown on Guduchi or normal food. Madhuyashti, on the other hand, significantly reduced mean longevity and had a stimulatory effect on female fecundity. This fecundity enhancing effect however seemed to be mediated through its effect on the males. Interestingly, much of these effects interacted with age in a complex way, making it difficult to generalize the overall effect of these formulations on the reproductive output of the flies. Ourstudy underlines the importance of evaluating the interacting effects of these (and similar) formulations on a range of life-history traits in a holistic way to understand their utility better.
Collapse
Affiliation(s)
- Surabhi Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221 005, India
| | | | | |
Collapse
|
17
|
The Sleep Inbred Panel, a Collection of Inbred Drosophila melanogaster with Extreme Long and Short Sleep Duration. G3-GENES GENOMES GENETICS 2018; 8:2865-2873. [PMID: 29991508 PMCID: PMC6118319 DOI: 10.1534/g3.118.200503] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Understanding how genomic variation causes differences in observable phenotypes remains a major challenge in biology. It is difficult to trace the sequence of events originating from genomic variants to changes in transcriptional responses or protein modifications. Ideally, one would conduct experiments with individuals that are at either extreme of the trait of interest, but such resources are often not available. Further, advances in genome editing will enable testing of candidate polymorphisms individually and in combination. Here we have created a resource for the study of sleep with 39 inbred lines of Drosophila-the Sleep Inbred Panel (SIP). SIP lines have stable long- and short-sleeping phenotypes developed from naturally occurring polymorphisms. These lines are fully sequenced, enabling more accurate targeting for genome editing and transgenic constructs. This panel facilitates the study of intermediate transcriptional and proteomic correlates of sleep, and supports genome editing studies to verify polymorphisms associated with sleep duration.
Collapse
|
18
|
Potdar S, Daniel DK, Thomas FA, Lall S, Sheeba V. Sleep deprivation negatively impacts reproductive output in Drosophila melanogaster. ACTA ACUST UNITED AC 2018; 221:jeb.174771. [PMID: 29361608 DOI: 10.1242/jeb.174771] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022]
Abstract
Most animals sleep or exhibit a sleep-like state, yet the adaptive significance of this phenomenon remains unclear. Although reproductive deficits are associated with lifestyle-induced sleep deficiencies, how sleep loss affects reproductive physiology is poorly understood, even in model organisms. We aimed to bridge this mechanistic gap by impairing sleep in female fruit flies and testing its effect on egg output. We found that sleep deprivation by feeding caffeine or by mechanical perturbation resulted in decreased egg output. Transient activation of wake-promoting dopaminergic neurons decreased egg output in addition to sleep levels, thus demonstrating a direct negative impact of sleep deficit on reproductive output. Similarly, loss-of-function mutation in dopamine transporter fumin (fmn) led to both significant sleep loss and lowered fecundity. This demonstration of a direct relationship between sleep and reproductive fitness indicates a strong driving force for the evolution of sleep.
Collapse
Affiliation(s)
- Sheetal Potdar
- Behavioural Neurogenetics Laboratory, Evolutionary and Integrative Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Danita K Daniel
- Behavioural Neurogenetics Laboratory, Evolutionary and Integrative Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Femi A Thomas
- Behavioural Neurogenetics Laboratory, Evolutionary and Integrative Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Shraddha Lall
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Vasu Sheeba
- Behavioural Neurogenetics Laboratory, Evolutionary and Integrative Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India .,Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| |
Collapse
|
19
|
Wu KJ, Kumar S, Serrano Negron YL, Harbison ST. Genotype Influences Day-to-Day Variability in Sleep in Drosophila melanogaster. Sleep 2018; 41:zsx205. [PMID: 29228366 PMCID: PMC6018780 DOI: 10.1093/sleep/zsx205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/27/2017] [Indexed: 12/22/2022] Open
Abstract
Patterns of sleep often vary among individuals. But sleep and activity may also vary within an individual, fluctuating in pattern across time. One possibility is that these daily fluctuations in sleep are caused by the underlying genotype of the individual. However, differences attributable to genetic causes are difficult to distinguish from environmental factors in outbred populations such as humans. We therefore employed Drosophila as a model of intra-individual variability in sleep using previously collected sleep and activity data from the Drosophila Genetic Reference Panel, a collection of wild-derived inbred lines. Individual flies had significant daily fluctuations in their sleep patterns, and these fluctuations were heritable. Using the standard deviation of sleep parameters as a metric, we conducted a genome-wide association study. We found 663 polymorphisms in 104 genes associated with daily fluctuations in sleep. We confirmed the effects of 12 candidate genes on the standard deviation of sleep parameters. Our results suggest that daily fluctuations in sleep patterns are due in part to gene activity.
Collapse
Affiliation(s)
- Katherine J Wu
- Laboratory of Systems Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Shailesh Kumar
- Laboratory of Systems Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Yazmin L Serrano Negron
- Laboratory of Systems Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Susan T Harbison
- Laboratory of Systems Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| |
Collapse
|
20
|
O'Hanlon KN, Dam RA, Archambeault SL, Berg CA. Two Drosophilids exhibit distinct EGF pathway patterns in oogenesis. Dev Genes Evol 2018; 228:31-48. [PMID: 29264645 PMCID: PMC5805658 DOI: 10.1007/s00427-017-0601-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
Abstract
Deciphering the evolution of morphological structures is a remaining challenge in the field of developmental biology. The respiratory structures of insect eggshells, called the dorsal appendages, provide an outstanding system for exploring these processes since considerable information is known about their patterning and morphogenesis in Drosophila melanogaster and dorsal appendage number and morphology vary widely across Drosophilid species. We investigated the patterning differences that might facilitate morphogenetic differences between D. melanogaster, which produces two oar-like structures first by wrapping and then elongating the tubes via cell intercalation and cell crawling, and Scaptodrosophila lebanonensis, which produces a variable number of appendages simply by cell intercalation and crawling. Analyses of BMP pathway components thickveins and P-Mad demonstrate that anterior patterning is conserved between these species. In contrast, EGF signaling exhibits significant differences. Transcripts for the ligand encoded by gurken localize similarly in the two species, but this morphogen creates a single dorsolateral primordium in S. lebanonensis as defined by activated MAP kinase and the downstream marker broad. Expression patterns of pointed, argos, and Capicua, early steps in the EGF pathway, exhibit a heterochronic shift in S. lebanonensis relative to those seen in D. melanogaster. We demonstrate that the S. lebanonensis Gurken homolog is active in D. melanogaster but is insufficient to alter downstream patterning responses, indicating that Gurken-EGF receptor interactions do not distinguish the two species' patterning. Altogether, these results differentiate EGF signaling patterns between species and shed light on how changes to the regulation of patterning genes may contribute to different tube-forming mechanisms.
Collapse
Affiliation(s)
- Kenley N O'Hanlon
- Department of Genome Sciences, University of Washington, 3720 15th AVE NE, Seattle, WA, 98195-5065, USA
| | - Rachel A Dam
- Molecular and Cellular Biology Program, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195-7275, USA
| | - Sophie L Archambeault
- Molecular and Cellular Biology Program, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195-7275, USA
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Celeste A Berg
- Department of Genome Sciences, University of Washington, 3720 15th AVE NE, Seattle, WA, 98195-5065, USA.
- Molecular and Cellular Biology Program, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195-7275, USA.
| |
Collapse
|