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Wei Y, Wang X, Ma Z, Xiang P, Liu G, Yin B, Hou L, Shu P, Liu W, Peng X. Sirt6 regulates the proliferation of neural precursor cells and cortical neurogenesis in mice. iScience 2024; 27:108706. [PMID: 38288355 PMCID: PMC10823065 DOI: 10.1016/j.isci.2023.108706] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/07/2023] [Accepted: 12/07/2023] [Indexed: 01/31/2024] Open
Abstract
Sirt6, a member of the class III histone deacetylases (HDACs), functions in the regulation of genomic stability, DNA repair, cancer, metabolism and aging. Sirt6 deficiency is lethal, and newborn SIRT6-null cynomolgus monkeys show unfinished brain development. After the generation of a cortex-specific Sirt6 conditional knockout mouse model, we investigated the specific deletion of Sirt6 in NPCs at E10.5. This study found that Sirt6 deficiency causes excessive proliferation of neural precursor cells (NPCs) and retards differentiation. The results suggest that endogenous Sirt6 in NPCs regulates histone acetylation and limits stemness-related genes, including Notch1, in order to participate in NPC fate determination. These findings help elucidate Sirt6's role in brain development and in NPC fate determination while providing data on species generality and differentiation.
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Affiliation(s)
- Yufei Wei
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xinhuan Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Zhihua Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Pan Xiang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Gaoao Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Bin Yin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Lin Hou
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Pengcheng Shu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wei Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiaozhong Peng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
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2
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Patterson EL, Richardson A, Bartlett M. Pushing the boundaries of organ identity: Homology of the grass lemma. Am J Bot 2023; 110:e16161. [PMID: 37021711 DOI: 10.1002/ajb2.16161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 05/11/2023]
Affiliation(s)
- Erin L Patterson
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Annis Richardson
- Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Madelaine Bartlett
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
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3
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Sokoloff DD, Fomichev CI, Rudall PJ, Macfarlane TD, Remizowa MV. Evolutionary history of the grass gynoecium. J Exp Bot 2022; 73:4637-4661. [PMID: 35512454 DOI: 10.1093/jxb/erac182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 05/03/2022] [Indexed: 06/14/2023]
Abstract
The grass family (Poaceae) includes cereal crops that provide a key food source for the human population. The food industry uses the starch deposited in the cereal grain, which develops directly from the gynoecium. Morphological interpretation of the grass gynoecium remains controversial. We re-examine earlier hypotheses and studies of morphology and development in the context of more recent analyses of grass phylogenetics and developmental genetics. Taken in isolation, data on gynoecium development in bistigmatic grasses do not contradict its interpretation as a solitary ascidiate carpel. Nevertheless, in the context of other data, this interpretation is untenable. Broad comparative analysis in a modern phylogenetic context clearly demonstrates that the grass gynoecium is pseudomonomerous. A bistigmatic grass gynoecium has two sterile carpels, each producing a stigma, and a fertile carpel that lacks a stigma. To date, studies of grass developmental genetics and developmental morphology have failed to fully demonstrate the composite nature of the grass gynoecium be-cause its complex evolutionary history is hidden by extreme organ integration. It is problematic to interpret the gynoecium of grasses in terms of normal angiosperm gynoecium typology. Even the concept of a carpel becomes misleading in grasses; instead, we recommend the term pistil for descriptive purposes.
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Affiliation(s)
- Dmitry D Sokoloff
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234 Moscow, Russia
| | - Constantin I Fomichev
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234 Moscow, Russia
| | - Paula J Rudall
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Terry D Macfarlane
- Western Australian Herbarium, Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre WA 6983, Australia
| | - Margarita V Remizowa
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234 Moscow, Russia
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4
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Hernández-Coronado M, Dias Araujo PC, Ip PL, Nunes CO, Rahni R, Wudick MM, Lizzio MA, Feijó JA, Birnbaum KD. Plant glutamate receptors mediate a bet-hedging strategy between regeneration and defense. Dev Cell 2022; 57:451-465.e6. [PMID: 35148835 PMCID: PMC8891089 DOI: 10.1016/j.devcel.2022.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 11/10/2021] [Accepted: 01/19/2022] [Indexed: 02/07/2023]
Abstract
Wounding is a trigger for both regeneration and defense in plants, but it is not clear whether the two responses are linked by common activation or regulated as trade-offs. Although plant glutamate-receptor-like proteins (GLRs) are known to mediate defense responses, here, we implicate GLRs in regeneration through dynamic changes in chromatin and transcription in reprogramming cells near wound sites. We show that genetic and pharmacological inhibition of GLR activity increases regeneration efficiency in multiple organ repair systems in Arabidopsis and maize. We show that the GLRs work through salicylic acid (SA) signaling in their effects on regeneration, and mutants in the SA receptor NPR1 are hyper-regenerative and partially resistant to GLR perturbation. These findings reveal a conserved mechanism that regulates a trade-off between defense and regeneration, and they also offer a strategy to improve regeneration in agriculture and conservation.
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Affiliation(s)
- Marcela Hernández-Coronado
- New York University, Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York, NY 10003, USA
| | - Poliana Coqueiro Dias Araujo
- New York University, Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York, NY 10003, USA
| | - Pui-Leng Ip
- New York University, Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York, NY 10003, USA
| | - Custódio O Nunes
- University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD 20742, USA
| | - Ramin Rahni
- New York University, Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York, NY 10003, USA
| | - Michael M Wudick
- University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD 20742, USA
| | - Michael A Lizzio
- University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD 20742, USA
| | - José A Feijó
- University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD 20742, USA
| | - Kenneth D Birnbaum
- New York University, Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York, NY 10003, USA.
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5
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Senger K, Yuan W, Sagolla M, Doerr J, Bolon B, Ziai J, Sun K, Warming S, Roose‐Girma M, Zhang N, Tam L, Newman RJ, Chaudhuri S, Antony A, Goldstein LD, Durinck S, Jaiswal BS, Lafkas D, Modrusan Z, Seshagiri S. Embryonic lethality and defective mammary gland development of activator-function impaired conditional knock-in Erbb3 V943R mice. Adv Genet (Hoboken) 2020; 2:e10036. [PMID: 36618440 PMCID: PMC9744554 DOI: 10.1002/ggn2.10036] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 01/11/2023]
Abstract
ERBB3 is a pseudokinase domain-containing member of the ERBB family of receptor tyrosine kinases (RTKs). Following ligand binding, ERBB receptors homo- or hetero-dimerize, leading to a head-to-tail arrangement of the intracellular kinase domains, where the "receiver" kinase domain of one ERBB is activated by the "activator" domain of the other ERBB in the dimer. In ERBB3, a conserved valine at codon 943 (V943) in the kinase C-terminal domain has been shown to be important for its function as an "activator" kinase in vitro. Here we report a knock-in mouse model where we have modified the endogenous Erbb3 allele to allow for tissue-specific conditional expression of Erbb3 V943R (Erbb3 CKI-V943R ). Additionally, we generated an Erbb3 D850N (Erbb3 CKI-D850N ) conditional knock-in mouse model where the conserved aspartate in the DFG motif of the pseudokinase domain was mutated to abolish any potential residual kinase activity. While Erbb3 D850N/D850N animals developed normally, homozygous Erbb3 V943R/V943R expression during development resulted in embryonic lethality. Further, tissue specific expression of Erbb3 V943R/V943R in the mammary gland epithelium following its activation using MMTV-Cre resulted in delayed elongation of the ductal network during puberty. Single-cell RNA-seq analysis of Erbb3 V943R/V943R mammary glands showed a reduction in a specific subset of fibrinogen-producing luminal epithelial cells.
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Affiliation(s)
- Kate Senger
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Wenlin Yuan
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Meredith Sagolla
- Department of PathologyGenentechSouth San FranciscoCaliforniaUSA
| | - Jonas Doerr
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | | | - James Ziai
- Department of PathologyGenentechSouth San FranciscoCaliforniaUSA
| | - Kai‐Hui Sun
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Soren Warming
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Merone Roose‐Girma
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Na Zhang
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Lucinda Tam
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Robert J. Newman
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Subhra Chaudhuri
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | | | - Leonard D. Goldstein
- Department of Bioinformatics and Computational BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Steffen Durinck
- Department of Bioinformatics and Computational BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Bijay S. Jaiswal
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Daniel Lafkas
- Department of Immunology DiscoveryGenentechSouth San FranciscoCaliforniaUSA
| | - Zora Modrusan
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Somasekar Seshagiri
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA,SciGenom Research FoundationBangaloreKarnatakaIndia
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6
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Fowler DA, Larsson HCE. The benefits differential equations bring to limb development. Wiley Interdiscip Rev Dev Biol 2019; 9:e364. [PMID: 31637866 DOI: 10.1002/wdev.364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/22/2019] [Accepted: 09/07/2019] [Indexed: 11/07/2022]
Abstract
Systems biology is a large field, offering a number of advantages to a variety of biological disciplines. In limb development, differential-equation based models can provide insightful hypotheses about the gene/protein interactions and tissue differentiation events that form the core of limb development research. Differential equations are like any other communicative tool, with misuse and limitations that can come along with their advantages. Every theory should be critically analyzed to best ascertain whether they reflect the reality in biology as well they claim. Differential equation-based models have consistent features which researchers have drawn upon to aid in more realistic descriptions and hypotheses. Nine features are described that highlight these trade-offs. The advantages range from more detailed descriptions of gene interactions and their consequence and the capacity to model robustness to the incorporation of tissue size and shape. The drawbacks come with the added complication that additional genes and signaling pathways that require additional terms within the mathematical model. They also come in the translation between the mathematical terms of the model, values and matrices, to the real world of genes, proteins, and tissues that constitute limb development. A critical analysis is necessary to ensure that these models effectively expand the understanding of the origins of a diversity of limb anatomy, from evolution to teratology. This article is categorized under: Vertebrate Organogenesis > Musculoskeletal and Vascular Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Establishment of Spatial and Temporal Patterns > Repeating Patterns and Lateral Inhibition.
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Affiliation(s)
- Donald A Fowler
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
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7
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Abstract
Human gonadal development is regulated by the temporospatial expression of many different genes with critical dosage effects. Subsequent sex steroid hormone production requires several consecutive enzymatic steps and functional hormone receptors. Disruption of this complex process can result in atypical sex development and lead to conditions referred to as differences (disorders) of sex development (DSD). With the advent of massively parallel sequencing technologies, in silico protein modeling and innovative tools for the generation of animal models, new genes and pathways have been implicated in the pathogenesis of these conditions. Here, we provide an overview of the currently known DSD genes and mechanisms involved in the process of gonadal and phenotypical sex development and highlight phenotypic findings that may trigger further diagnostic investigations.
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Affiliation(s)
- Dorien Baetens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium; Division of Pediatric Endocrinology, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University, Ghent, Belgium
| | - Hannah Verdin
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Martine Cools
- Division of Pediatric Endocrinology, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University, Ghent, Belgium.
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8
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Hehmeyer J. Two potential evolutionary origins of the fruiting bodies of the dictyostelid slime moulds. Biol Rev Camb Philos Soc 2019; 94:1591-1604. [PMID: 30989827 DOI: 10.1111/brv.12516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 11/29/2022]
Abstract
Dictyostelium discoideum and the other dictyostelid slime moulds ('social amoebae') are popular model organisms best known for their demonstration of sorocarpic development. In this process, many cells aggregate to form a multicellular unit that ultimately becomes a fruiting body bearing asexual spores. Several other unrelated microorganisms undergo comparable processes, and in some it is evident that their multicellular development evolved from the differentiation process of encystation. While it has been argued that the dictyostelid fruiting body had similar origins, it has also been proposed that dictyostelid sorocarpy evolved from the unicellular fruiting process found in other amoebozoan slime moulds. This paper reviews the developmental biology of the dictyostelids and other relevant organisms and reassesses the two hypotheses on the evolutionary origins of dictyostelid development. Recent advances in phylogeny, genetics, and genomics and transcriptomics indicate that further research is necessary to determine whether or not the fruiting bodies of the dictyostelids and their closest relatives, the myxomycetes and protosporangids, are homologous.
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9
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Pitchers W, Nye J, Márquez EJ, Kowalski A, Dworkin I, Houle D. A Multivariate Genome-Wide Association Study of Wing Shape in Drosophila melanogaster. Genetics 2019; 211:1429-47. [PMID: 30792267 DOI: 10.1534/genetics.118.301342] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/03/2019] [Indexed: 02/02/2023] Open
Abstract
Due to the complexity of genotype-phenotype relationships, simultaneous analyses of genomic associations with multiple traits will be more powerful and informative than a series of univariate analyses. However, in most cases, studies of genotype-phenotype relationships have been analyzed only one trait at a time. Here, we report the results of a fully integrated multivariate genome-wide association analysis of the shape of the Drosophila melanogaster wing in the Drosophila Genetic Reference Panel. Genotypic effects on wing shape were highly correlated between two different laboratories. We found 2396 significant SNPs using a 5% false discovery rate cutoff in the multivariate analyses, but just four significant SNPs in univariate analyses of scores on the first 20 principal component axes. One quarter of these initially significant SNPs retain their effects in regularized models that take into account population structure and linkage disequilibrium. A key advantage of multivariate analysis is that the direction of the estimated phenotypic effect is much more informative than a univariate one. We exploit this fact to show that the effects of knockdowns of genes implicated in the initial screen were on average more similar than expected under a null model. A subset of SNP effects were replicable in an unrelated panel of inbred lines. Association studies that take a phenomic approach, considering many traits simultaneously, are an important complement to the power of genomics.
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Schwab DB, Casasa S, Moczek AP. On the Reciprocally Causal and Constructive Nature of Developmental Plasticity and Robustness. Front Genet 2019; 9:735. [PMID: 30687394 PMCID: PMC6335315 DOI: 10.3389/fgene.2018.00735] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 08/30/2018] [Accepted: 12/22/2018] [Indexed: 01/29/2023] Open
Abstract
Exposure to environmental variation is a characteristic feature of normal development, one that organisms can respond to during their lifetimes by actively adjusting or maintaining their phenotype in order to maximize fitness. Plasticity and robustness have historically been studied by evolutionary biologists through quantitative genetic and reaction norm approaches, while more recent efforts emerging from evolutionary developmental biology have begun to characterize the molecular and developmental genetic underpinnings of both plastic and robust trait formation. In this review, we explore how our growing mechanistic understanding of plasticity and robustness is beginning to force a revision of our perception of both phenomena, away from our conventional view of plasticity and robustness as opposites along a continuum and toward a framework that emphasizes their reciprocal, constructive, and integrative nature. We do so in three sections. Following an introduction, the first section looks inward and reviews the genetic, epigenetic, and developmental mechanisms that enable organisms to sense and respond to environmental conditions, maintaining and adjusting trait formation in the process. In the second section, we change perspective and look outward, exploring the ways in which organisms reciprocally shape their environments in ways that influence trait formation, and do so through the lens of behavioral plasticity, niche construction, and host-microbiota interactions. In the final section, we revisit established plasticity and robustness concepts in light of these findings, and highlight research opportunities to further advance our understanding of the causes, mechanisms, and consequences of these ubiquitous, and interrelated, phenomena.
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Juriloff DM, Harris MJ. Insights into the Etiology of Mammalian Neural Tube Closure Defects from Developmental, Genetic and Evolutionary Studies. J Dev Biol 2018; 6:E22. [PMID: 30134561 DOI: 10.3390/jdb6030022] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 02/06/2023] Open
Abstract
The human neural tube defects (NTD), anencephaly, spina bifida and craniorachischisis, originate from a failure of the embryonic neural tube to close. Human NTD are relatively common and both complex and heterogeneous in genetic origin, but the genetic variants and developmental mechanisms are largely unknown. Here we review the numerous studies, mainly in mice, of normal neural tube closure, the mechanisms of failure caused by specific gene mutations, and the evolution of the vertebrate cranial neural tube and its genetic processes, seeking insights into the etiology of human NTD. We find evidence of many regions along the anterior–posterior axis each differing in some aspect of neural tube closure—morphology, cell behavior, specific genes required—and conclude that the etiology of NTD is likely to be partly specific to the anterior–posterior location of the defect and also genetically heterogeneous. We revisit the hypotheses explaining the excess of females among cranial NTD cases in mice and humans and new developments in understanding the role of the folate pathway in NTD. Finally, we demonstrate that evidence from mouse mutants strongly supports the search for digenic or oligogenic etiology in human NTD of all types.
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12
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Chomicki G, Coiro M, Renner SS. Evolution and ecology of plant architecture: integrating insights from the fossil record, extant morphology, developmental genetics and phylogenies. Ann Bot 2017; 120:855-891. [PMID: 29165551 PMCID: PMC5710528 DOI: 10.1093/aob/mcx113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 10/03/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND In contrast to most animals, plants have an indeterminate body plan, which allows them to add new body parts during their lifetime. A plant's realized modular construction is the result of exogenous constraints and endogenous processes. This review focuses on endogenous processes that shape plant architectures and their evolution. SCOPE The phylogenetic distribution of plant growth forms across the phylogeny implies that body architectures have originated and been lost repeatedly, being shaped by a limited set of genetic pathways. We (1) synthesize concepts of plant architecture, so far captured in 23 models; (2) extend them to the fossil record; (3) summarize what is known about their developmental genetics; (4) use a phylogenetic approach in several groups to infer how plant architecture has changed and by which intermediate steps; and (5) discuss which macroecological factors may constrain the geographic and ecological distribution of plant architectures. CONCLUSIONS Dichotomously branching Paleozoic plants already encompassed a considerable diversity of growth forms, here captured in 12 new architectural models. Plotting the frequency of branching types through time based on an analysis of 58 927 land plant fossils revealed a decrease in dichotomous branching throughout the Devonian and Carboniferous, mirrored by an increase in other branching types including axillary branching. We suggest that the evolution of seed plant megaphyllous leaves enabling axillary branching contributed to the demise of dichotomous architectures. The developmental-genetic bases for key architectural traits underlying sympodial vs. monopodial branching, rhythmic vs. continuous growth, and axillary branching and its localization are becoming well understood, while the molecular basis of dichotomous branching and plagiotropy remains elusive. Three phylogenetic case studies of architecture evolution in conifers, Aloe and monocaulous arborescent vascular plants reveal relationships between architectural models and show that some are labile in given groups, whereas others are widely conserved, apparently shaped by ecological factors, such as intercepted sunlight, temperature, humidity and seasonality.
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Affiliation(s)
- Guillaume Chomicki
- Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), Munich, Germany
| | - Mario Coiro
- Institute of Systematic Botany, University of Zürich, Zürich, Switzerland
| | - Susanne S Renner
- Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), Munich, Germany
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13
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Zhang N, Khan LA, Membreno E, Jafari G, Yan S, Zhang H, Gobel V. The C. elegans Intestine As a Model for Intercellular Lumen Morphogenesis and In Vivo Polarized Membrane Biogenesis at the Single-cell Level: Labeling by Antibody Staining, RNAi Loss-of-function Analysis and Imaging. J Vis Exp 2017:56100. [PMID: 28994799 PMCID: PMC5628585 DOI: 10.3791/56100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Multicellular tubes, fundamental units of all internal organs, are composed of polarized epithelial or endothelial cells, with apical membranes lining the lumen and basolateral membranes contacting each other and/or the extracellular matrix. How this distinctive membrane asymmetry is established and maintained during organ morphogenesis is still an unresolved question of cell biology. This protocol describes the C. elegans intestine as a model for the analysis of polarized membrane biogenesis during tube morphogenesis, with emphasis on apical membrane and lumen biogenesis. The C. elegans twenty-cell single-layered intestinal epithelium is arranged into a simple bilaterally symmetrical tube, permitting analysis on a single-cell level. Membrane polarization occurs concomitantly with polarized cell division and migration during early embryogenesis, but de novo polarized membrane biogenesis continues throughout larval growth, when cells no longer proliferate and move. The latter setting allows one to separate subcellular changes that simultaneously mediate these different polarizing processes, difficult to distinguish in most polarity models. Apical-, basolateral membrane-, junctional-, cytoskeletal- and endomembrane components can be labeled and tracked throughout development by GFP fusion proteins, or assessed by in situ antibody staining. Together with the organism's genetic versatility, the C. elegans intestine thus provides a unique in vivo model for the visual, developmental, and molecular genetic analysis of polarized membrane and tube biogenesis. The specific methods (all standard) described here include how to: label intestinal subcellular components by antibody staining; analyze genes involved in polarized membrane biogenesis by loss-of-function studies adapted to the typically essential tubulogenesis genes; assess polarity defects during different developmental stages; interpret phenotypes by epifluorescence, differential interference contrast (DIC) and confocal microscopy; quantify visual defects. This protocol can be adapted to analyze any of the often highly conserved molecules involved in epithelial polarity, membrane biogenesis, tube and lumen morphogenesis.
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Affiliation(s)
- Nan Zhang
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital, Harvard Medical School; College of Life Sciences, Jilin University
| | - Liakot A Khan
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital, Harvard Medical School
| | - Edward Membreno
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital, Harvard Medical School
| | - Gholamali Jafari
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital, Harvard Medical School
| | - Siyang Yan
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital, Harvard Medical School
| | - Hongjie Zhang
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital, Harvard Medical School; Faculty of Health Sciences, University of Macau;
| | - Verena Gobel
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital, Harvard Medical School;
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14
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Flynn JR, Conn VL, Boyle KA, Hughes DI, Watanabe M, Velasquez T, Goulding MD, Callister RJ, Graham BA. Anatomical and Molecular Properties of Long Descending Propriospinal Neurons in Mice. Front Neuroanat 2017; 11:5. [PMID: 28220062 PMCID: PMC5292581 DOI: 10.3389/fnana.2017.00005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 11/07/2016] [Accepted: 01/19/2017] [Indexed: 11/13/2022] Open
Abstract
Long descending propriospinal neurons (LDPNs) are interneurons that form direct connections between cervical and lumbar spinal circuits. LDPNs are involved in interlimb coordination and are important mediators of functional recovery after spinal cord injury (SCI). Much of what we know about LDPNs comes from a range of species, however, the increased use of transgenic mouse lines to better define neuronal populations calls for a more complete characterisation of LDPNs in mice. In this study, we examined the cell body location, inhibitory neurotransmitter phenotype, developmental provenance, morphology and synaptic inputs of mouse LDPNs throughout the cervical and upper thoracic spinal cord. LDPNs were retrogradely labelled from the lumbar spinal cord to map cell body locations throughout the cervical and upper thoracic segments. Ipsilateral LDPNs were distributed throughout the dorsal, intermediate and ventral grey matter as well as the lateral spinal nucleus and lateral cervical nucleus. In contrast, contralateral LDPNs were more densely concentrated in the ventromedial grey matter. Retrograde labelling in GlyT2GFP and GAD67GFP mice showed the majority of inhibitory LDPNs project either ipsilaterally or adjacent to the midline. Additionally, we used several transgenic mouse lines to define the developmental provenance of LDPNs and found that V2b positive neurons form a subset of ipsilaterally projecting LDPNs. Finally, a population of Neurobiotin (NB) labelled LDPNs were assessed in detail to examine morphology and plot the spatial distribution of contacts from a variety of neurochemically distinct axon terminals. These results provide important baseline data in mice for future work on their role in locomotion and recovery from SCI.
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Affiliation(s)
- Jamie R Flynn
- School of Biomedical Sciences and Pharmacy, University of NewcastleCallaghan, NSW, Australia; Hunter Medical Research InstituteNewcastle, NSW, Australia
| | - Victoria L Conn
- Institute of Neuroscience and Psychology, University of Glasgow Glasgow, UK
| | - Kieran A Boyle
- Institute of Neuroscience and Psychology, University of Glasgow Glasgow, UK
| | - David I Hughes
- Institute of Neuroscience and Psychology, University of Glasgow Glasgow, UK
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University School of Medicine Sapporo, Japan
| | - Tomoko Velasquez
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies La Jolla, CA, USA
| | - Martyn D Goulding
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies La Jolla, CA, USA
| | - Robert J Callister
- School of Biomedical Sciences and Pharmacy, University of NewcastleCallaghan, NSW, Australia; Hunter Medical Research InstituteNewcastle, NSW, Australia
| | - Brett A Graham
- School of Biomedical Sciences and Pharmacy, University of NewcastleCallaghan, NSW, Australia; Hunter Medical Research InstituteNewcastle, NSW, Australia
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15
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Di Stilio VS, Melzer R, Hall JC. Editorial: A Broader View for Plant EvoDevo: Novel Approaches for Diverse Model Systems. Front Plant Sci 2017; 8:61. [PMID: 28184231 PMCID: PMC5266680 DOI: 10.3389/fpls.2017.00061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 01/11/2017] [Indexed: 06/06/2023]
Affiliation(s)
| | - Rainer Melzer
- School of Biology and Environmental Science, University College DublinDublin, Ireland
| | - Jocelyn C. Hall
- Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada
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16
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Renner SS. Pathways for making unisexual flowers and unisexual plants:Moving beyond the "two mutations linked on one chromosome" model. Am J Bot 2016; 103:587-9. [PMID: 26993970 DOI: 10.3732/ajb.1600029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 02/11/2016] [Indexed: 05/20/2023]
Affiliation(s)
- Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger-Str. 67 80638 Munich, Germany
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17
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Stroebele E, Erives A. Integration of Orthogonal Signaling by the Notch and Dpp Pathways in Drosophila. Genetics 2016; 203:219-40. [PMID: 26975664 DOI: 10.1534/genetics.116.186791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/08/2016] [Indexed: 11/18/2022] Open
Abstract
The transcription factor Suppressor of Hairless and its coactivator, the Notch intracellular domain, are polyglutamine (pQ)-rich factors that target enhancer elements and interact with other locally bound pQ-rich factors. To understand the functional repertoire of such enhancers, we identify conserved regulatory belts with binding sites for the pQ-rich effectors of both Notch and BMP/Dpp signaling, and the pQ-deficient tissue selectors Apterous (Ap), Scalloped (Sd), and Vestigial (Vg). We find that the densest such binding site cluster in the genome is located in the BMP-inducible nab locus, a homolog of the vertebrate transcriptional cofactors NAB1/NAB2 We report three major findings. First, we find that this nab regulatory belt is a novel enhancer driving dorsal wing margin expression in regions of peak phosphorylated Mad in wing imaginal discs. Second, we show that Ap is developmentally required to license the nab dorsal wing margin enhancer (DWME) to read out Notch and Dpp signaling in the dorsal compartment. Third, we find that the nab DWME is embedded in a complex of intronic enhancers, including a wing quadrant enhancer, a proximal wing disc enhancer, and a larval brain enhancer. This enhancer complex coordinates global nab expression via both tissue-specific activation and interenhancer silencing. We suggest that DWME integration of BMP signaling maintains nab expression in proliferating margin descendants that have divided away from Notch-Delta boundary signaling. As such, uniform expression of genes like nab and vestigial in proliferating compartments would typically require both boundary and nonboundary lineage-specific enhancers.
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18
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Yang D, Li M, Liu Y, Chang L, Cheng H, Chen J, Chai S. Identification of Quantitative Trait Loci and Water Environmental Interactions for Developmental Behaviors of Leaf Greenness in Wheat. Front Plant Sci 2016; 7:273. [PMID: 27014298 PMCID: PMC4782216 DOI: 10.3389/fpls.2016.00273] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/21/2016] [Indexed: 05/30/2023]
Abstract
The maintenance of leaf greenness in wheat, highly responsible for yield potential and resistance to drought stress, has been proved to be quantitatively inherited and susceptible to interact with environments by traditional genetic analysis. In order to further dissect the developmental genetic behaviors of flag leaf greenness under terminal drought, unconditional and conditional QTL mapping strategies were performed with a mixed linear model in 120 F8-derived recombinant inbred lines (RILs) from two Chinese common wheat cultivars (Longjian 19 × Q9086) in different water environments. A total of 65 additive QTLs (A-QTLs) and 42 pairs of epistatic QTLs (AA-QTLs) were identified as distribution on almost all 21 chromosomes except 5A, explaining from 0.24 to 3.29 % of the phenotypic variation. Of these, 22 A-QTLs and 25 pairs of AA-QTLs were common in two sets of mapping methods but the others differed. These putative QTLs were essentially characteristic of time- and environmentally-dependent expression patterns. Indeed some loci were expressed at two or more stages, while no single QTL was continually active through whole measuring duration. More loci were detected in early growth periods but most of QTL × water environment interactions (QEIs) happened in mid-anaphase, where drought stress was more conducted with negative regulation on QTL expressions. Compared to other genetic components, epistatic effects and additive QEIs effects could be predominant in regulating phenotypic variations during the ontogeny of leaf greenness. Several QTL cluster regions were suggestive of tight linkage or expression pleiotropy in the inheritance of these traits. Some reproducibly-expressed QTLs or common loci consistent with previously detected would be useful to the genetic improvement of staygreen types in wheat through MAS, especially in water-deficit environments.
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Affiliation(s)
- Delong Yang
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Mengfei Li
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Yuan Liu
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Lei Chang
- School of Agronomy, Gansu Agricultural UniversityLanzhou, China
| | - Hongbo Cheng
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Jingjing Chen
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural UniversityLanzhou, China
| | - Shouxi Chai
- School of Agronomy, Gansu Agricultural UniversityLanzhou, China
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19
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Kramer EM. A stranger in a strange land: the utility and interpretation of heterologous expression. Front Plant Sci 2015; 6:734. [PMID: 26442047 PMCID: PMC4569974 DOI: 10.3389/fpls.2015.00734] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/29/2015] [Indexed: 05/29/2023]
Abstract
One of the major goals of the modern study of evodevo is to understand the evolution of gene function across a range of contexts, including sub/neofunctionalization, co-option of genetic modules, and the evolution of morphological novelty. To these ends, comparative studies of gene expression can be useful for constructing hypotheses, but cannot provide direct evidence of functional evolution. Unfortunately, determining endogenous gene function in non-model species is often not an option. Faced with this dilemma, a common approach is to use heterologous expression (HE) in genetically tractable model species as a proxy for functional analyses. Such experiments have important limitations, however, and require caution in the interpretation of their results. How do we dissociate biochemical function from its original genomic context? In the end, what does HE actually tell us? Here, I argue that HE only sheds light on specific types of biochemical conservation, but can be useful when experiments are carefully interpreted.
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Affiliation(s)
- Elena M. Kramer
- *Correspondence: Elena M. Kramer, Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA,
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Rice C, Beekman D, Liu L, Erives A. The Nature, Extent, and Consequences of Genetic Variation in the opa Repeats of Notch in Drosophila. G3 (Bethesda) 2015; 5:2405-19. [PMID: 26362765 DOI: 10.1534/g3.115.021659] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyglutamine (pQ) tracts are abundant in proteins co-interacting on DNA. The lengths of these pQ tracts can modulate their interaction strengths. However, pQ tracts >40 residues are pathologically prone to amyloidogenic self-assembly. Here, we assess the extent and consequences of variation in the pQ-encoding opa repeats of Notch in Drosophila melanogaster. We use Sanger sequencing to genotype opa sequences (5′-CAX repeats), which have resisted assembly using short sequence reads. While most sampled lines carry the major allele opa31 encoding Q13HQ17 or the opa32 allele encoding Q13HQ18, many lines carry rare alleles encoding pQ tracts >32 residues: opa33a (Q14HQ18), opa33b (Q15HQ17), opa34 (Q16HQ17), opa35a1/opa35a2 (Q13HQ21), opa36 (Q13HQ22), and opa37 (Q13HQ23). Only one rare allele encodes a tract <31 residues: opa23 (Q13–Q10). This opa23 allele shortens the pQ tract while simultaneously eliminating the interrupting histidine. We introgressed these opa variant alleles into common backgrounds and measured the frequency of Notch-type phenotypes. Homozygotes for the short and long opa alleles have defects in embryonic survival and sensory bristle organ patterning, and sometimes show wing notching. Consistent with functional differences between Notch opa variants, we find that a scute inversion carrying the rare opa33b allele suppresses the bristle patterning defect caused by achaete/scute insufficiency, while an equivalent scute inversion carrying opa31 manifests the patterning defect. Our results demonstrate the existence of potent pQ variants of Notch and the need for long read genotyping of key repeat variables underlying gene regulatory networks.
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21
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Meagher TR. Linking the evolution of gender variation to floral development. Ann Bot 2007; 100:165-76. [PMID: 17416913 PMCID: PMC2735311 DOI: 10.1093/aob/mcm035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 11/22/2006] [Accepted: 01/17/2007] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS In the present review, I have endeavoured to conduct a joint assessment of the thinking underlying the evolutionary genetics of gender polymorphism and the developmental genetics of gender determination. It is my hope, through highlighting the historical development of ideas in two related but somewhat disparate sets of scientific literature, to encourage a synthetic perspective that integrates the two. SCOPE An overview is provided of various theories on the evolution of sex polymorphism and examples of evidence that has been brought to bear in support of them. Current knowledge on floral development is summarized, with an emphasis on gender variation. Finally, an attempt is made to integrate the two perspectives with the hope that it will encourage future research at the interface. CONCLUSIONS Evolutionary models of gender evolution have, of necessity, posited genetic effects that are relatively simple in their impacts. Emerging insights from developmental genetics have demonstrated that the underlying reality is a more complex matrix of interacting factors. The study of gender variation in plants is poised for significant advance through the integration of these two perspectives. Bringing genomic tools to bear on population-level processes, we may finally develop a comprehensive perspective on the evolution of floral gender.
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Affiliation(s)
- Thomas R Meagher
- Centre for Evolution Genes & Genomics, School of Biology, Sir Harold Mitchell Building, University of St Andrews, St Andrews, Fife KY16 9TH, UK.
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22
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Garen A, Gehring W. Repair of the lethal developmental defect in deep orange embryos of Drosophila by injection of normal egg cytoplasm. Proc Natl Acad Sci U S A 1972; 69:2982-5. [PMID: 4628097 PMCID: PMC389689 DOI: 10.1073/pnas.69.10.2982] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The eggs produced by deep orange females (dor/dor) of Drosophila melanogaster have a defect that causes early death of the deep orange embryos derived from these eggs. Ovaries transplanted from deep orange females to normal female hosts continue to produce defective eggs, showing that the dor mutation directly affects an ovarian function. In heterozygous embryos (dor(+)/dor) derived from eggs of deep orange females, the presence of a paternal dor(+) gene enables normal development to occur in about half of the embryos. Thus, the egg defect caused by the dor mutation is repairable after fertilization by the action of a dor(+) gene. The deep orange egg defect has also been repaired by injection of cytoplasm from unfertilized normal eggs into deep orange embryos at the syncitial preblastoderm stage of development. About one-third of the injected deep orange embryos were able to continue their development to an advanced stage of embryogenesis. This developmental response can serve as a bioassay for the identification of the defective component in eggs of deep orange females.
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