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Suzuki M, Iida M, Hayashi T, Suzuki KIT. CRISPR-Cas9-Based Functional Analysis in Amphibians: Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl. Methods Mol Biol 2023; 2637:341-357. [PMID: 36773159 DOI: 10.1007/978-1-0716-3016-7_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Amphibians have made many fundamental contributions to our knowledge, from basic biology to biomedical research on human diseases. Current genome editing tools based on the CRISPR-Cas system enable us to perform gene functional analysis in vivo, even in non-model organisms. We introduce here a highly efficient and easy protocol for gene knockout, which can be used in three different amphibians seamlessly: Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl. As it utilizes Cas9 ribonucleoprotein complex (RNP) for injection, this cloning-free method enables researchers to obtain founder embryos with a nearly complete knockout phenotype within a week. To evaluate somatic mutation rate and its correlation to the phenotype of a Cas9 RNP-injected embryo (crispant), we also present accurate and cost-effective genotyping methods using pooled amplicon-sequencing and a user-friendly web-based tool.
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Affiliation(s)
- Miyuki Suzuki
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Midori Iida
- Department of Bioscience and Bioinformatics, School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Fukuoka, Japan
| | - Toshinori Hayashi
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Hiroshima, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Ken-Ichi T Suzuki
- Emerging Model Organisms Facility, Trans-scale Biology Center, National Institute for Basic Biology, Okazaki, Aichi, Japan.
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Melicher D, Bowsher JH, Rinehart JP. Fluctuating temperatures extend longevity in pupae and adult stages of the sepsid Themira biloba. J Therm Biol 2021; 99:102959. [PMID: 34420614 DOI: 10.1016/j.jtherbio.2021.102959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 11/16/2022]
Abstract
Fluctuating Thermal Regimes (FTR), where organisms are held at low temperatures with a brief, daily warm pulse, have been shown to increase longevity in adult insects and improve pupa survival while reducing sublethal effects. We used FTR to extend the longevity and thus generation time of the fly species Themira biloba (Diptera: Sepsidae). T. biloba can be maintained in continuous culture and requires an insecticide-free dung substrate for larval growth and development. Our objective was to decrease labor and consumable materials required to maintain insect species in critical scientific collections using FTR. We extended pupation time from 4 days up to 8 weeks with no increase in mortality, and mean adult longevity was increased from 12 days to 50 days. FTR is a valuable tool for reducing the investment required to maintain rare and exotic insects.
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Affiliation(s)
- Dacotah Melicher
- Bioscience Research Laboratory, U.S. Department of Agriculture/Agricultural Research Station, 1605 Albrecht Boulevard, Fargo, ND, 58105, USA.
| | - Julia H Bowsher
- Department of Biological Sciences, North Dakota State University, 1340 Bolley Drive, 218 Stevens Hall, Fargo, ND, 58102, USA
| | - Joseph P Rinehart
- Bioscience Research Laboratory, U.S. Department of Agriculture/Agricultural Research Station, 1605 Albrecht Boulevard, Fargo, ND, 58105, USA
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3
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Monteiro A. Distinguishing serial homologs from novel traits: Experimental limitations and ideas for improvements. Bioessays 2020; 43:e2000162. [PMID: 33118632 DOI: 10.1002/bies.202000162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/13/2022]
Abstract
One of the central but yet unresolved problems in evolutionary biology concerns the origin of novel complex traits. One hypothesis is that complex traits derive from pre-existing gene regulatory networks (GRNs) reused and modified to specify a novel trait somewhere else in the body. This simple explanation encounters problems when the novel trait that emerges in a body is in a region that is known to harbor a latent or repressed trait that has been silent for millions of years. Is the novel trait merely a re-emerged de-repressed trait or a truly novel trait that emerged via a novel deployment of an old GRN? A couple of new studies sided on opposite sides of this question when investigating the origin of horns in dung beetles and helmets in treehoppers that develop in the first thoracic segment (T1) of their bodies, a segment known to harbor a pair of repressed/modified wings in close relatives. Here, I point to some key limitations of the experimental approaches used and highlight additional experiments that could be done in future to resolve the developmental origin of these and other traits.
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Affiliation(s)
- Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Science Division, Yale-NUS College, Singapore, Singapore
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Temporal flexibility of gene regulatory network underlies a novel wing pattern in flies. Proc Natl Acad Sci U S A 2020; 117:11589-11596. [PMID: 32393634 PMCID: PMC7261121 DOI: 10.1073/pnas.2002092117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Developmental genes can be coopted to generate evolutionary novelties by changing their spatial regulation. However, developmental genes seldom act independently, but rather work in a gene regulatory network (GRN). How is it possible to recruit a single gene from a whole GRN? What are the properties that allow parallel cooptions of the same genes during evolution? Here, we show that a novel engrailed gene expression underlies a novel wing color pattern in flies. We show that cooption is facilitated 1) because of GRN flexibility over development and 2) because every single gene of the GRN has its own functional time window. We suggest these two temporal properties could explain why the same gene can be independently recruited several times during evolution. Organisms have evolved endless morphological, physiological, and behavioral novel traits during the course of evolution. Novel traits were proposed to evolve mainly by orchestration of preexisting genes. Over the past two decades, biologists have shown that cooption of gene regulatory networks (GRNs) indeed underlies numerous evolutionary novelties. However, very little is known about the actual GRN properties that allow such redeployment. Here we have investigated the generation and evolution of the complex wing pattern of the fly Samoaia leonensis. We show that the transcription factor Engrailed is recruited independently from the other players of the anterior–posterior specification network to generate a new wing pattern. We argue that partial cooption is made possible because 1) the anterior–posterior specification GRN is flexible over time in the developing wing and 2) this flexibility results from the fact that every single gene of the GRN possesses its own functional time window. We propose that the temporal flexibility of a GRN is a general prerequisite for its possible cooption during the course of evolution.
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Mansourian S, Fandino RA, Riabinina O. Progress in the use of genetic methods to study insect behavior outside Drosophila. CURRENT OPINION IN INSECT SCIENCE 2019; 36:45-56. [PMID: 31494407 DOI: 10.1016/j.cois.2019.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/20/2019] [Accepted: 08/02/2019] [Indexed: 06/10/2023]
Abstract
In the span of a decade we have seen a rapid progress in the application of genetic tools and genome editing approaches in 'non-model' insects. It is now possible to target sensory receptor genes and neurons, explore their functional roles and manipulate behavioral responses in these insects. In this review, we focus on the latest examples from Diptera, Lepidoptera and Hymenoptera of how applications of genetic tools advanced our understanding of diverse behavioral phenomena. We further discuss genetic methods that could be applied to study insect behavior in the future.
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Affiliation(s)
| | - Richard A Fandino
- Mass Spectrometry Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany.
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Eberhard WG, Lehmann GUC. Demonstrating sexual selection by cryptic female choice on male genitalia: What is enough? Evolution 2019; 73:2415-2435. [PMID: 31599962 DOI: 10.1111/evo.13863] [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: 06/07/2019] [Revised: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 01/07/2023]
Abstract
Rapid divergence in external genital structures occurs in nearly all animal groups that practice internal insemination; explaining this pattern is a major challenge in evolutionary biology. The hypothesis that species-specific differences in male genitalia evolved under sexual selection as courtship devices to influence cryptic female choice (CFC) has been slow to be accepted. Doubts may stem from its radical departure from previous ideas, observational difficulties because crucial events occur hidden within the female's body, and alternative hypotheses involving biologically important phenomena such as speciation, sperm competition, and male-female conflicts of interest. We assess the current status of the CFC hypothesis by reviewing data from two groups in which crucial predictions have been especially well-tested, Glossina tsetse flies and Roeseliana (formerly Metrioptera) roeselii bushcrickets. Eighteen CFC predictions have been confirmed in Glossina and 19 in Roeseliana. We found data justifying rejection of alternative hypotheses, but none that contradicted CFC predictions. The number and extent of tests confirming predictions of the CFC hypothesis in these species is greater than that for other generally accepted hypotheses regarding the functions of nongenital structures. By this criterion, it is reasonable to conclude that some genital structures in both groups likely involved sexual selection by CFC.
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Affiliation(s)
- William G Eberhard
- Smithsonian Tropical Research Institute, Universidad de Costa Rica, and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Gerlind U C Lehmann
- Evolutionary Ecology, Department of Biology, Humboldt University Berlin, 10117, Berlin, Germany
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Connahs H, Tlili S, van Creij J, Loo TYJ, Banerjee TD, Saunders TE, Monteiro A. Activation of butterfly eyespots by Distal-less is consistent with a reaction-diffusion process. Development 2019; 146:dev169367. [PMID: 30992277 PMCID: PMC6526720 DOI: 10.1242/dev.169367] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 04/05/2019] [Indexed: 01/08/2023]
Abstract
Eyespots on the wings of nymphalid butterflies represent colorful examples of pattern formation, yet the developmental origins and mechanisms underlying eyespot center differentiation are still poorly understood. Using CRISPR-Cas9 we re-examine the function of Distal-less (Dll) as an activator or repressor of eyespots, a topic that remains controversial. We show that the phenotypic outcome of CRISPR mutations depends upon which specific exon is targeted. In Bicyclus anynana, exon 2 mutations are associated with both missing and ectopic eyespots, and also exon skipping. Exon 3 mutations, which do not lead to exon skipping, produce only null phenotypes, including missing eyespots, lighter wing coloration and loss of scales. Reaction-diffusion modeling of Dll function, using Wnt and Dpp as candidate morphogens, accurately replicates these complex crispant phenotypes. These results provide new insight into the function of Dll as a potential activator of eyespot development, scale growth and melanization, and suggest that the tuning of Dll expression levels can generate a diversity of eyespot phenotypes, including their appearance on the wing.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Heidi Connahs
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Sham Tlili
- Mechanobiology Institute, National University of Singapore, Singapore 117411
| | - Jelle van Creij
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Tricia Y J Loo
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Tirtha Das Banerjee
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Timothy E Saunders
- Department of Biological Sciences, National University of Singapore, Singapore 117558
- Mechanobiology Institute, National University of Singapore, Singapore 117411
- Institute of Molecular and Cell Biology, A*Star, Proteos, Singapore 138673
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore 117558
- Yale-NUS College, Singapore 138527
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The people behind the papers – Heidi Connahs, Sham Tlili, Timothy Saunders and Antónia Monteiro. Development 2019; 146:146/9/dev179366. [DOI: 10.1242/dev.179366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Butterfly eyespots are striking examples of animal patterning, but their developmental origins are still relatively poorly understood. A new paper in Development – the result of a collaboration between two Singapore-based labs – now combines CRISPR-Cas9 gene targeting with theoretical modelling to address the role of the Distal-less transcription factor in eyespot patterning. We caught up with co-first authors Heidi Connahs and Sham Tlili, and their respective supervisors Timothy Saunders (Assistant Professor at the Mechanobiology Institute, National University of Singapore) and Antónia Monteiro (Associate Professor at the Department of Biological Sciences, National University of Singapore and Yale-NUS College) to find out more about the story.
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