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Gomez A, Gonzalez S, Oke A, Luo J, Duong JB, Esquerra RM, Zimmerman T, Capponi S, Fung JC, Nystul TG. A high-throughput method for quantifying Drosophila fecundity. bioRxiv 2024:2024.03.27.587093. [PMID: 38585877 PMCID: PMC10996622 DOI: 10.1101/2024.03.27.587093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Measurements of Drosophila fecundity are used in a wide variety of studies, such as investigations of stem cell biology, nutrition, behavior, and toxicology. In addition, because fecundity assays are performed on live flies, they are suitable for longitudinal studies such as investigations of aging or prolonged chemical exposure. However, standard Drosophila fecundity assays have been difficult to perform in a high-throughput manner because experimental factors such as the physiological state of the flies and environmental cues must be carefully controlled to achieve consistent results. In addition, exposing flies to a large number of different experimental conditions (such as chemical additives in the diet) and manually counting the number of eggs laid to determine the impact on fecundity is time-consuming. We have overcome these challenges by combining a new multiwell fly culture strategy with a novel 3D-printed fly transfer device to rapidly and accurately transfer flies from one plate to another; the RoboCam, a low-cost, custom built robotic camera to capture images of the wells automatically; and an image segmentation pipeline to automatically identify and quantify eggs. We show that this method is compatible with robust and consistent egg laying throughout the assay period; and demonstrate that the automated pipeline for quantifying fecundity is very accurate (r2 = 0.98 for the correlation between the automated egg counts and the ground truth) In addition, we show that this method can be used to efficiently detect the effects on fecundity induced by dietary exposure to chemicals. Taken together, this strategy substantially increases the efficiency and reproducibility of high throughput egg laying assays that require exposing flies to multiple different media conditions.
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Affiliation(s)
- Andreana Gomez
- University of California, San Francisco, Department of Anatomy
| | - Sergio Gonzalez
- San Francisco State University, Department of Biology
- Center for Cellular Construction, San Francisco, CA
| | - Ashwini Oke
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
| | - Jiayu Luo
- San Francisco State University, Department of Biology
- Center for Cellular Construction, San Francisco, CA
| | - Johnny B Duong
- Center for Cellular Construction, San Francisco, CA
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
| | - Raymond M Esquerra
- Center for Cellular Construction, San Francisco, CA
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
| | - Thomas Zimmerman
- Center for Cellular Construction, San Francisco, CA
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
| | - Sara Capponi
- Center for Cellular Construction, San Francisco, CA
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
| | - Jennifer C Fung
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
- University of California, San Francisco EaRTH Center
| | - Todd G Nystul
- University of California, San Francisco, Department of Anatomy
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
- University of California, San Francisco EaRTH Center
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2
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Barghi N, Ramirez-Lanzas C. A high throughput method for egg size measurement in Drosophila. Sci Rep 2023; 13:3791. [PMID: 36882448 DOI: 10.1038/s41598-023-30472-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
Life-history traits are used as proxies of fitness in insects including Drosophila. Egg size is an adaptive and ecologically important trait potentially with genetic variation across different populations. However, the low throughput of manual measurement of egg size has hampered the widespread use of this trait in evolutionary biology and population genetics. We established a method for accurate and high throughput measurement of Drosophila egg size using large particle flow cytometry (LPFC). The size estimates using LPFC are accurate and highly correlated with the manual measurements. The measurement of egg size is high throughput (average of 214 eggs measured per minute) and viable eggs of a specific size can be sorted rapidly (average of 70 eggs per minute). Sorting by LPFC does not reduce the survival of eggs making it a suitable approach for sorting eggs for downstream analyses. This protocol can be applied to any organism within the detectable size range (10-1500 µm) of the large particle flow cytometers. We discuss the potential applications of this method and provide recommendations for optimizing the protocol for other organisms.
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Langmüller AM, Champer J, Lapinska S, Xie L, Metzloff M, Champer SE, Liu J, Xu Y, Du J, Clark AG, Messer PW. Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations. eLife 2022; 11:e71809. [PMID: 36135925 PMCID: PMC9545523 DOI: 10.7554/elife.71809] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 provides a highly efficient and flexible genome editing technology with numerous potential applications ranging from gene therapy to population control. Some proposed applications involve the integration of CRISPR/Cas9 endonucleases into an organism's genome, which raises questions about potentially harmful effects to the transgenic individuals. One example for which this is particularly relevant are CRISPR-based gene drives conceived for the genetic alteration of entire populations. The performance of such drives can strongly depend on fitness costs experienced by drive carriers, yet relatively little is known about the magnitude and causes of these costs. Here, we assess the fitness effects of genomic CRISPR/Cas9 expression in Drosophila melanogaster cage populations by tracking allele frequencies of four different transgenic constructs that allow us to disentangle 'direct' fitness costs due to the integration, expression, and target-site activity of Cas9, from fitness costs due to potential off-target cleavage. Using a maximum likelihood framework, we find that a model with no direct fitness costs but moderate costs due to off-target effects fits our cage data best. Consistent with this, we do not observe fitness costs for a construct with Cas9HF1, a high-fidelity version of Cas9. We further demonstrate that using Cas9HF1 instead of standard Cas9 in a homing drive achieves similar drive conversion efficiency. These results suggest that gene drives should be designed with high-fidelity endonucleases and may have implications for other applications that involve genomic integration of CRISPR endonucleases.
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Affiliation(s)
- Anna M Langmüller
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Institut für Populationsgenetik, Vetmeduni ViennaViennaAustria
- Vienna Graduate School of Population Genetics, Vetmeduni ViennaViennaAustria
| | - Jackson Champer
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking UniversityBeijingChina
| | - Sandra Lapinska
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Lin Xie
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Matthew Metzloff
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Samuel E Champer
- Department of Computational Biology, Cornell UniversityIthacaUnited States
| | - Jingxian Liu
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Yineng Xu
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Jie Du
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking UniversityBeijingChina
| | - Andrew G Clark
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Philipp W Messer
- Department of Computational Biology, Cornell UniversityIthacaUnited States
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Christodoulaki E, Nolte V, Lai WY, Schlötterer C. Natural variation in Drosophila shows weak pleiotropic effects. Genome Biol 2022; 23:116. [PMID: 35578368 PMCID: PMC9109288 DOI: 10.1186/s13059-022-02680-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 04/26/2022] [Indexed: 11/12/2022] Open
Abstract
Background Pleiotropy describes the phenomenon in which a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of issues of inadequate power of analyses. A further challenge is that empirical tests of pleiotropy are restricted to a small subset of all possible phenotypes. To overcome these limitations, we propose a new measurement of pleiotropy that integrates across many phenotypes and multiple generations to improve power. Results We infer pleiotropy from the fitness cost imposed by frequency changes of pleiotropic loci. Mixing Drosophila simulans populations, which adapted independently to the same new environment using different sets of genes, we show that the adaptive frequency changes have been accompanied by measurable fitness costs. Conclusions Unlike previous studies characterizing the molecular basis of pleiotropy, we show that many loci, each of weak effect, contribute to genome-wide pleiotropy. We propose that the costs of pleiotropy are reduced by the modular architecture of gene expression, which facilitates adaptive gene expression changes with low impact on other functions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02680-4.
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Affiliation(s)
- Eirini Christodoulaki
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210, Vienna, Austria
| | - Wei-Yun Lai
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
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Thierry M, Pardikes NA, Rosenbaum B, Ximénez-Embún MG, Hrček J. The presence of multiple parasitoids decreases host survival under warming, but parasitoid performance also decreases. Proc Biol Sci 2022; 289:20220121. [PMID: 35291840 PMCID: PMC8924747 DOI: 10.1098/rspb.2022.0121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Current global changes are reshaping ecological communities and modifying environmental conditions. We need to recognize the combined impact of these biotic and abiotic factors on species interactions, community dynamics and ecosystem functioning. Specifically, the strength of predator-prey interactions often depends on the presence of other natural enemies: it weakens with competition and interference or strengthens with facilitation. Such effects of multiple predators on prey are likely to be affected by changes in the abiotic environment, altering top-down control, a key structuring force in natural and agricultural ecosystems. Here, we investigated how warming alters the effects of multiple predators on prey suppression using a dynamic model coupled with empirical laboratory experiments with Drosophila-parasitoid communities. While multiple parasitoids enhanced top-down control under warming, parasitoid performance generally declined when another parasitoid was present owing to competitive interactions. This could reduce top-down control over multiple generations. Our study highlights the importance of accounting for interactive effects between abiotic and biotic factors to better predict community dynamics in a rapidly changing world and thus better preserve ecosystem functioning and services such as biological control.
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Affiliation(s)
- Mélanie Thierry
- Faculty of Science, University of South Bohemia, Branisovska 31, 37005 Czech Republic,Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Czech Republic
| | - Nicholas A. Pardikes
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Czech Republic
| | - Benjamin Rosenbaum
- Theory in Biodiversity Science, German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany,Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Miguel G. Ximénez-Embún
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Czech Republic
| | - Jan Hrček
- Faculty of Science, University of South Bohemia, Branisovska 31, 37005 Czech Republic,Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Czech Republic
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Langmüller AM, Nolte V, Galagedara R, Poupardin R, Dolezal M, Schlötterer C. Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature. BMC Biol 2020; 18:157. [PMID: 33121485 PMCID: PMC7597021 DOI: 10.1186/s12915-020-00882-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/28/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Insect pest control programs often use periods of insecticide treatment with intermittent breaks, to prevent fixing of mutations conferring insecticide resistance. Such mutations are typically costly in an insecticide-free environment, and their frequency is determined by the balance between insecticide treatment and cost of resistance. Ace, a key gene in neuronal signaling, is a prominent target of many insecticides and across several species, three amino acid replacements (I161V, G265A, and F330Y) provide resistance against several insecticides. Because temperature disturbs neuronal signaling homeostasis, we reasoned that the cost of insecticide resistance could be modulated by ambient temperature. RESULTS Experimental evolution of a natural Drosophila simulans population at hot and cold temperature regimes uncovered a surprisingly strong effect of ambient temperature. In the cold temperature regime, the resistance mutations were strongly counter selected (s = - 0.055), but in a hot environment, the fitness costs of resistance mutations were reduced by almost 50% (s = - 0.031). We attribute this unexpected observation to the advantage of the reduced enzymatic activity of resistance mutations in hot environments. CONCLUSION We show that fitness costs of insecticide resistance genes are temperature-dependent and suggest that the duration of insecticide-free periods need to be adjusted for different climatic regions to reflect these costs. We suggest that such environment-dependent fitness effects may be more common than previously assumed and pose a major challenge for modeling climate change.
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Affiliation(s)
- Anna Maria Langmüller
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Ruwansha Galagedara
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Rodolphe Poupardin
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- Present Address: Paracelsus Medical University Salzburg, Strubergasse 21, 5020, Salzburg, Austria
| | - Marlies Dolezal
- Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Lee SH, Min KJ. Drosophila melanogaster as a model system in the study of pharmacological interventions in aging. Translational Medicine of Aging 2019. [DOI: 10.1016/j.tma.2019.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Abstract
The ability to quantify fecundity is critically important to a wide range of experimental applications, particularly in widely-used model organisms such as Drosophila melanogaster. However, the standard method of manually counting eggs is time consuming and limits the feasibility of large-scale experiments. We develop a predictive model to automate the counting of eggs from images of eggs removed from the media surface and washed onto dark filter paper. Our method uses the simple relationship between the white area in an image and the number of eggs present to create a predictive model that performs well even at high egg densities where clumping can complicate the individual identification of eggs. A cross-validation approach demonstrates our method performs well, with a correlation between predicted and manually counted values of 0.88. We show how this method can be applied to a large data set where egg densities vary widely.
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Affiliation(s)
- Enoch Ng'oma
- a Division of Biological Sciences , University of Missouri , Columbia , MO , USA
| | - Elizabeth G King
- a Division of Biological Sciences , University of Missouri , Columbia , MO , USA
| | - Kevin M Middleton
- b Department of Pathology and Anatomical Sciences , University of Missouri School of Medicine , Columbia , MO , USA
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