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no privacy, a Xenopus tropicalis mutant, is a model of human Hermansky-Pudlak Syndrome and allows visualization of internal organogenesis during tadpole development. Dev Biol 2017; 426:472-486. [DOI: 10.1016/j.ydbio.2016.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/17/2016] [Accepted: 08/17/2016] [Indexed: 11/19/2022]
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2
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Igawa T, Watanabe A, Suzuki A, Kashiwagi A, Kashiwagi K, Noble A, Guille M, Simpson DE, Horb ME, Fujii T, Sumida M. Inbreeding Ratio and Genetic Relationships among Strains of the Western Clawed Frog, Xenopus tropicalis. PLoS One 2015. [PMID: 26222540 PMCID: PMC4519292 DOI: 10.1371/journal.pone.0133963] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.
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Affiliation(s)
- Takeshi Igawa
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- * E-mail:
| | - Ai Watanabe
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Atsushi Suzuki
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Akihiko Kashiwagi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Keiko Kashiwagi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Anna Noble
- School of Biological Sciences, Institute of Biomedical and Biomolecular Science, University of Portsmouth, Portsmouth, United Kingdom
| | - Matt Guille
- School of Biological Sciences, Institute of Biomedical and Biomolecular Science, University of Portsmouth, Portsmouth, United Kingdom
| | - David E. Simpson
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
| | - Marko E. Horb
- Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, United States of America
| | - Tamotsu Fujii
- Department of Health Sciences, Faculty of Human Culture & Science, Prefectural University of Hiroshima, Hiroshima, Japan
| | - Masayuki Sumida
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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Abu-Daya A, Khokha MK, Zimmerman LB. The hitchhiker's guide to Xenopus genetics. Genesis 2012; 50:164-75. [PMID: 22344745 DOI: 10.1002/dvg.22007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/19/2011] [Accepted: 12/23/2011] [Indexed: 01/12/2023]
Abstract
A decade after the human genome sequence, most vertebrate gene functions remain poorly understood, limiting benefits to human health from rapidly advancing genomic technologies. Systematic in vivo functional analysis is ideally suited to the experimentally accessible Xenopus embryo, which combines embryological accessibility with a broad range of transgenic, biochemical, and gain-of-function assays. The diploid X. tropicalis adds loss-of-function genetics and enhanced genomics to this repertoire. In the last decade, diverse phenotypes have been recovered from genetic screens, mutations have been cloned, and reverse genetics in the form of TILLING and targeted gene editing have been established. Simple haploid genetics and gynogenesis and the very large number of embryos produced streamline screening and mapping. Improved genomic resources and the revolution in high-throughput sequencing are transforming mutation cloning and reverse genetic approaches. The combination of loss-of-function mutant backgrounds with the diverse array of conventional Xenopus assays offers a uniquely flexible platform for analysis of gene function in vertebrate development.
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Affiliation(s)
- Anita Abu-Daya
- Division of Developmental Biology, MRC-National Institute for Medical Research, Mill Hill, London, United Kingdom
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Abstract
Xenopus tropicalis was introduced as a model system for genetic, and then genomic research, in the early 1990s, complementing work on the widely used model organism Xenopus laevis. Its shorter generation time and diploid genome has facilitated a number of experimental approaches. It has permitted multigenerational experiments (e.g., preparation of transgenic lines and generation of mutant lines) that have added powerful approaches for research by the Xenopus community. As a diploid animal, its simpler genome was sequenced before X. laevis, and has provided a highly valuable resource indispensable for all Xenopus researchers. As more sophisticated transgenic technologies for manipulating gene expression are developed, and mutations, particularly null mutations, are identified in widely studied genes involved in critical cellular and developmental processes, researchers will increasingly turn to X. tropicalis for definitive analysis of complex genetic pathways. This chapter describes the historical and conceptual development of X. tropicalis as a genetic and genomic model system for higher vertebrate development.
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Affiliation(s)
- Robert M Grainger
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
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Harland RM, Grainger RM. Xenopus research: metamorphosed by genetics and genomics. Trends Genet 2011; 27:507-15. [PMID: 21963197 PMCID: PMC3601910 DOI: 10.1016/j.tig.2011.08.003] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/25/2011] [Accepted: 08/25/2011] [Indexed: 01/18/2023]
Abstract
Research using Xenopus takes advantage of large, abundant eggs and readily manipulated embryos in addition to conserved cellular, developmental and genomic organization with mammals. Research on Xenopus has defined key principles of gene regulation and signal transduction, embryonic induction, morphogenesis and patterning as well as cell cycle regulation. Genomic and genetic advances in this system, including the development of Xenopus tropicalis as a genetically tractable complement to the widely used Xenopus laevis, capitalize on the classical strengths and wealth of achievements. These attributes provide the tools to tackle the complex biological problems of the new century, including cellular reprogramming, organogenesis, regeneration, gene regulatory networks and protein interactions controlling growth and development, all of which provide insights into a multitude of human diseases and their potential treatments.
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Affiliation(s)
- Richard M Harland
- Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California Berkeley, CA 94720, USA
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Khokha MK, Krylov V, Reilly MJ, Gall JG, Bhattacharya D, Cheung CYJ, Kaufman S, Lam DK, Macha J, Ngo C, Prakash N, Schmidt P, Tlapakova T, Trivedi T, Tumova L, Abu-Daya A, Geach T, Vendrell E, Ironfield H, Sinzelle L, Sater AK, Wells DE, Harland RM, Zimmerman LB. Rapid gynogenetic mapping of Xenopus tropicalis mutations to chromosomes. Dev Dyn 2009; 238:1398-46. [PMID: 19441086 DOI: 10.1002/dvdy.21965] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Pilot forward genetic screens in Xenopus tropicalis have isolated over 60 recessive mutations. Here we present a simple method for mapping mutations to chromosomes using gynogenesis and centromeric markers. When coupled with available genomic resources, gross mapping facilitates evaluation of candidate genes as well as higher resolution linkage studies. Using gynogenesis, we have mapped the genetic locations of the 10 X. tropicalis centromeres, and performed fluorescence in situ hybridization to validate these locations cytologically. We demonstrate the use of this very small set of centromeric markers to map mutations efficiently to specific chromosomes. Developmental Dynamics 238:1398-1406, 2009. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Mustafa K Khokha
- Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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7
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Zimmermann AL, King EA, Dengler E, Scogin SR, Powell WH. An aryl hydrocarbon receptor repressor from Xenopus laevis: function, expression, and role in dioxin responsiveness during frog development. Toxicol Sci 2008; 104:124-34. [PMID: 18385208 DOI: 10.1093/toxsci/kfn066] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Xenopus laevis and other frogs are extremely insensitive to the toxicity of xenobiotic ligands of the aryl hydrocarbon receptor (AHR), including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Premetamorphic life stages are especially insensitive, and they are reported to be refractory to induction of Cytochrome P4501As, which are readily induced in older animals. The AHR repressor (AHRR) is a member of the AHR gene family. AHRR expression is induced by TCDD; it then represses AHR in an apparent negative feedback loop. In this study, we sought to test the hypothesis that constitutive AHRR expression underlies the lack of TCDD responsiveness in frog early life stages. We determined the sequence of an AHRR complimentary DNA encoding an 85.3-kDa protein sharing 52-55% identity with the bHLH/PAS domains of other AHRRs. In transient transfection assays, X. laevis AHRR inhibited TCDD-induced reporter gene expression mediated by either X. laevis AHR paralog, AHR1alpha or AHR1beta. AHRR messenger RNA was expressed at low levels in embryos (Nieuwkoop-Faber stage 33-38; approximately 52 h.p.f.) and was induced approximately twofold following TCDD exposure (42 ng/g wet weight). In contrast, AHRR exhibited higher constitutive expression and was induced more than threefold in tadpoles at stage 52-55 (prometamorphic; approximately 4 weeks postfertilization) and in isolated viscera of stage 62 tadpoles (in the metamorphic climax; approximately 7 weeks postfertilization). Although the magnitude of induction was smaller, the temporal pattern of AHRR expression and inducibility resembled that of CYP1A6. Thus, attenuated transcriptional activation of AHR target genes and low TCDD toxicity in X. laevis embryos cannot be explained by constitutive, high-level expression of AHRR.
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Viczian AS, Bang AG, Harris WA, Zuber ME. Expression of Xenopus laevis Lhx2 during eye development and evidence for divergent expression among vertebrates. Dev Dyn 2006; 235:1133-41. [PMID: 16470628 DOI: 10.1002/dvdy.20708] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Members of the LIM homeodomain (LIM-HD) family of proteins are double zinc-finger containing transcription factors with important functions in pattern formation and cell lineage determination. The LIM-HD family member Lhx2 is required for normal eye, liver, and central nervous system formation. Lhx2(-/-) mice lack eyes, and experiments in Xenopus predict that Lhx2 forms a regulatory network with other eye field transcription factors to specify the eye field during eye formation. Here, we describe the structure and developmental expression pattern of the Xenopus laevis homologue, XLhx2. We show that XLhx2 shares significant amino acid sequence identity with other vertebrate Lhx2 proteins and Drosophila apterous (ap). The expression patterns of XLhx2 in the early neural plate and during eye development are consistent with a role in eye field specification and retinal differentiation. Despite highly similar expression patterns in the mouse and Xenopus central nervous system, divergent expression patterns were also observed. Phylogenetic analysis confirmed the identity of the isolated cDNA as a Xenopus ortholog of Lhx2. Therefore, in spite of structural similarities, the mouse and Xenopus Lhx2 expression patterns differ, suggesting potential functional differences in these species.
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Affiliation(s)
- Andrea S Viczian
- Departments of Ophthalmology and Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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Goda T, Abu-Daya A, Carruthers S, Clark MD, Stemple DL, Zimmerman LB. Genetic screens for mutations affecting development of Xenopus tropicalis. PLoS Genet 2006; 2:e91. [PMID: 16789825 PMCID: PMC1475704 DOI: 10.1371/journal.pgen.0020091] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 04/28/2006] [Indexed: 11/18/2022] Open
Abstract
We present here the results of forward and reverse genetic screens for chemically-induced mutations in Xenopus tropicalis. In our forward genetic screen, we have uncovered 77 candidate phenotypes in diverse organogenesis and differentiation processes. Using a gynogenetic screen design, which minimizes time and husbandry space expenditures, we find that if a phenotype is detected in the gynogenetic F2 of a given F1 female twice, it is highly likely to be a heritable abnormality (29/29 cases). We have also demonstrated the feasibility of reverse genetic approaches for obtaining carriers of mutations in specific genes, and have directly determined an induced mutation rate by sequencing specific exons from a mutagenized population. The Xenopus system, with its well-understood embryology, fate map, and gain-of-function approaches, can now be coupled with efficient loss-of-function genetic strategies for vertebrate functional genomics and developmental genetics.
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Affiliation(s)
- Tadahiro Goda
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Anita Abu-Daya
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Samantha Carruthers
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthew D Clark
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek L Stemple
- Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- * To whom correspondence should be addressed. E-mail: (DLS); (LBZ)
| | - Lyle B Zimmerman
- Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
- * To whom correspondence should be addressed. E-mail: (DLS); (LBZ)
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Abstract
Research using Xenopus laevis has made enormous contributions to our understanding of vertebrate development, control of the eukaryotic cell cycle and the cytoskeleton. One limitation, however, has been the lack of systematic genetic studies in Xenopus to complement molecular and cell biological investigations. Work with the closely related diploid frog Xenopus tropicalis is beginning to address this limitation. Here, we review the resources that will make genetic studies using X. tropicalis a reality.
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Affiliation(s)
- Samantha Carruthers
- Vertebrate Development and Genetics, The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
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Grammer TC, Khokha MK, Lane MA, Lam K, Harland RM. Identification of mutants in inbred Xenopus tropicalis. Mech Dev 2005; 122:263-72. [PMID: 15763207 DOI: 10.1016/j.mod.2004.11.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2004] [Revised: 10/08/2004] [Accepted: 11/04/2004] [Indexed: 12/01/2022]
Abstract
Xenopus tropicalis offers the potential for genetic analysis in an amphibian. In order to take advantage of this potential, we have been inbreeding strains of frogs for future mutagenesis. While inbreeding a population of Nigerian frogs, we identified three mutations in the genetic background of this strain. These mutations are all recessive embryonic lethals. We show that multigenerational mutant analysis is feasible and demonstrate that mutations can be identified, propagated, and readily characterized using hybrid, dihybrid, and even trihybrid crosses. In addition, we are optimizing conditions to raise frogs rapidly and present our protocols for X. tropicalis husbandry. We find that males mature faster than females (currently 4 versus 6 months to sexual maturity). Here we document our progress in developing X. tropicalis as a genetic model organism and demonstrate the utility of the frog to study the genetics of early vertebrate development.
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Affiliation(s)
- Timothy C Grammer
- Department of Molecular and Cell Biology and the Center for Integrative Genomics, University of California, 142 LSA, Berkeley, CA 94720-3204, USA
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12
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Noramly S, Zimmerman L, Cox A, Aloise R, Fisher M, Grainger RM. A gynogenetic screen to isolate naturally occurring recessive mutations in Xenopus tropicalis. Mech Dev 2005; 122:273-87. [PMID: 15763208 DOI: 10.1016/j.mod.2004.11.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Revised: 10/27/2004] [Accepted: 11/04/2004] [Indexed: 10/25/2022]
Abstract
In the rapidly developing, diploid amphibian Xenopus tropicalis, genetics can be married to the already powerful tools of the amphibian system to overcome a disability that has hampered Xenopus laevis as a model organism: the difficulties inherent in conducting genetic analyses in a tetraploid organism with a longer generation time. We describe here a gynogenetic screen to uncover naturally occurring recessive mutations in wild X. tropicalis populations, a procedure that is both faster and easier than conventional genetic screens traditionally employed in model organisms to dissect early developmental pathways. During the first round of our screen, gynogenetic diploids from over 160 females comprising four different wild-caught populations were examined. Forty-two potential mutant phenotypes were isolated during this round of gynogenesis. From this group, we describe 10 lines that have genetically heritable recessive mutations. A wide range of developmental defects were obtained in this screen, encompassing effects limited to individual organs as well phenotypes characterized by more global changes in tadpole body morphology. The frequency of recessive mutations detected in our screen appears lower than that seen in other vertebrate genetic screens, but given constraints on the screening procedure used here, is likely to be consistent with rates seen in other animals, and clearly illustrates how wild-caught animals can be a productive source of developmental mutations for experimental study. The development of genetic strategies for the Xenopus system, together with new genomic resources, existing technologies for transgenesis, and other means for manipulating gene expression, as well as the power of performing embryonic manipulations, will provide an impressive set of tools for resolving complex cell and developmental phenomena in the future.
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Affiliation(s)
- Selina Noramly
- Department of Biology, University of Virginia, Gilmer Hall, Charlottesville, VA 22904, USA
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McCune AR, Houle D, McMillan K, Annable R, Kondrashov AS. Two classes of deleterious recessive alleles in a natural population of zebrafish, Danio rerio. Proc Biol Sci 2004; 271:2025-33. [PMID: 15451692 PMCID: PMC1691827 DOI: 10.1098/rspb.2004.2787] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Natural populations carry deleterious recessive alleles which cause inbreeding depression. We compared mortality and growth of inbred and outbred zebrafish, Danio rerio, between 6 and 48 days of age. Grandparents of the studied fish were caught in the wild. Inbred fish were generated by brother-sister mating. Mortality was 9% in outbred fish, and 42% in inbred fish, which implies at least 3.6 lethal equivalents of deleterious recessive alleles per zygote. There was no significant inbreeding depression in the growth, perhaps because the surviving inbred fish lived under less crowded conditions. In contrast to alleles that cause embryonic and early larval mortality in the same population, alleles responsible for late larval and early juvenile mortality did not result in any gross morphological abnormalities. Thus, deleterious recessive alleles that segregate in a wild zebrafish population belong to two sharply distinct classes: early-acting, morphologically overt, unconditional lethals; and later-acting, morphologically cryptic, and presumably milder alleles.
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Affiliation(s)
- Amy R McCune
- Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY 14853, USA.
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Abstract
Knowledge of the frequency of lethal mutant alleles in a population is important for our understanding of population genetics and evolution, and yet there have been few attempts to measure their number in wild populations. A new study has revealed unexpectedly low numbers of segregating lethal alleles in two species of fish. More experiments are needed, however, to know whether this result is general.
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Affiliation(s)
- Daniel L Halligan
- Institute of Cell, Animal and Population Biology, University of Edinburgh, EH9 3JT, Edinburgh, UK
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Hirsch N, Zimmerman LB, Grainger RM. Xenopus, the next generation: X. tropicalis genetics and genomics. Dev Dyn 2002; 225:422-33. [PMID: 12454920 DOI: 10.1002/dvdy.10178] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A small, fast-breeding, diploid relative of the frog Xenopus laevis, Xenopus tropicalis, has recently been adopted for research in developmental genetics and functional genomics. X. tropicalis shares advantages of X. laevis as a classic embryologic system, but its simpler genome and shorter generation time make it more convenient for multigenerational genetic, genomic, and transgenic approaches. Its embryos closely resemble those of X. laevis, except for their smaller size, and assays and molecular probes developed in X. laevis can be readily adapted for use in X. tropicalis. Genomic manipulation techniques such as gynogenesis facilitate genetic screens, because they permit the identification of recessive phenotypes after only one generation. Stable transgenic lines can be used both as in vivo reporters to streamline a variety of embryologic and molecular assays, or to experimentally manipulate gene expression through the use of binary constructs such as the GAL4/UAS system. Several mutations have been identified in wild-caught animals and during the course of generating inbred lines. A variety of strategies are discussed for conducting and managing genetic screens, obtaining mutations in specific sequences, achieving homologous recombination, and in developing and taking advantage of the genomic resources for Xenopus tropicalis.
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Affiliation(s)
- Nicolas Hirsch
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904-4328, USA
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Furlow JD, Kanamori A. The transcription factor basic transcription element-binding protein 1 is a direct thyroid hormone response gene in the frog Xenopus laevis. Endocrinology 2002; 143:3295-305. [PMID: 12193541 DOI: 10.1210/en.2002-220126] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Several genes have been identified that are activated or repressed by thyroid hormone in tadpole tissues during metamorphosis of the frog Xenopus laevis. One rapidly and strongly induced gene encodes the Xenopus homolog of basic transcription element-binding protein 1 (xBTEB1), an SP1-related transcription factor. xBTEB1 has similar DNA-binding activity and transcriptional activation properties as mammalian BTEB1. The thyroid hormone-dependent regulation of xBTEB1 was investigated using a modified electrophoretic mobility shift assay to scan genomic DNA for receptor-binding sites. Due to the tetraploid X. laevis genome, xBTEB1 is duplicated, and thyroid hormone regulates both copies. A consensus thyroid hormone response element (TRE) lies far upstream of the transcriptional start site of both genes. The TRE is nested within a 200-bp region of high sequence conservation between these two genes that duplicated millions of years ago. The TRE acts as a strong response element in transfection assays using a heterologous promoter or its native context. Thus, one of the earliest thyroid hormone-induced genes in tadpoles is a transcription factor regulated through an evolutionarily conserved TRE. xBTEB1 is predicted to play an important role in downstream gene regulation leading to the growth and remodeling of tissues at metamorphosis.
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Affiliation(s)
- J David Furlow
- Section of Neurobiology, Physiology, and Behavior, University of California, Davis, California 95616-8519, USA.
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McCune AR, Fuller RC, Aquilina AA, Dawley RM, Fadool JM, Houle D, Travis J, Kondrashov AS. A low genomic number of recessive lethals in natural populations of bluefin killifish and zebrafish. Science 2002; 296:2398-401. [PMID: 12089444 DOI: 10.1126/science.1071757] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Despite the importance of selection against deleterious mutations in natural populations, reliable estimates of the genomic numbers of mutant alleles in wild populations are scarce. We found that, in wild-caught bluefin killifish Lucania goodei (Fundulidae) and wild-caught zebrafish Danio rerio (Cyprinidae), the average numbers of recessive lethal alleles per individual are 1.9 (95% confidence limits 1.3 to 2.6) and 1.4 (95% confidence limits 1.0 to 2.0), respectively. These results, together with data on several Drosophila species and on Xenopus laevis, show that phylogenetically distant animals with different genome sizes and numbers of genes carry similar numbers of lethal mutations.
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Affiliation(s)
- Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
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Abstract
Much of our knowledge about the mechanisms of vertebrate early development comes from studies using Xenopus laevis. The recent development of a remarkably efficient method for generating transgenic embryos is now allowing study of late development and organogenesis in Xenopus embryos. Possibilities are also emerging for genomic studies using the closely related diploid frog Xenopus tropicalis.
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Affiliation(s)
- C W Beck
- Developmental Biology Programme, School of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.
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19
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Affiliation(s)
- E Amaya
- Wellcome/CRC Institute, Cambridge, UK
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20
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Gervasi C, Szaro BG. Sequence and expression patterns of two forms of the middle molecular weight neurofilament protein (NF-M) of Xenopus laevis. BRAIN RESEARCH. MOLECULAR BRAIN RESEARCH 1997; 48:229-42. [PMID: 9332720 DOI: 10.1016/s0169-328x(97)00096-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The middle molecular weight neurofilament protein (NF-M) is relevant to our understanding of vertebrate neurofilaments in growing axons, both because it exists in all vertebrates and because it undergoes characteristic changes in its phosphorylation state during axonal development. Indeed, all vertebrate neurofilament proteins are believed to have originated by gene duplication from an ancestral, NF-M-like protein. The role of NF-M in axonal development has been studied extensively in the frog, Xenopus laevis, through the use of monoclonal antibodies. To acquire a better understanding of the relationship of X. laevis NF-M to that of other vertebrates and to obtain additional reagents to study and perturb neurofilaments in developing axons, we isolated cDNA clones from the nervous system. These clones encoded two forms of NF-M, which exhibited 93% amino acid identity overall and 94%, 96% and 90% identity over their head, rod, and tail domains, respectively. Synonymous nucleotide substitution rates between the two forms tied their origin to an ancestral duplication of the Xenopus genome, which occurred approximately 30 million years ago. Non-synonymous substitution rates indicated that the tail domain is evolving more rapidly than the rod domain. Both forms shared structural features in common with other vertebrate NF-Ms but had only a single example of the KSP phosphorylation motif that is repeated multiple times in the NF-Ms of bird, goldfish and mammal. In post-metamorphic frogs, the NF-M(1) transcript was consistently expressed at higher levels than that of NF-M(2), although their anatomical patterns of expression were qualitatively similar. During development, however, only NF-M(2) was detectable in retinal ganglion cells through stage 42. We speculate that the differences observed between these two forms may represent early stages of protein diversification akin to what occurred after the gene duplications that gave rise to other vertebrate neurofilament proteins.
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Affiliation(s)
- C Gervasi
- Department of Biological Sciences, University at Albany, State University of New York 12222, USA
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21
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Denver RJ, Pavgi S, Shi YB. Thyroid hormone-dependent gene expression program for Xenopus neural development. J Biol Chem 1997; 272:8179-88. [PMID: 9079635 DOI: 10.1074/jbc.272.13.8179] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Although thyroid hormone (TH) plays a significant role in vertebrate neural development, the molecular basis of TH action on the brain is poorly understood. Using polymerase chain reaction-based subtractive hybridization we isolated 34 cDNAs for TH-regulated genes in the diencephalon of Xenopus tadpoles. Northern blots verified that the mRNAs are regulated by TH and are expressed during metamorphosis. Kinetic analyses showed that most of the genes are up-regulated by TH within 4-8 h and 13 are regulated by TH only in the brain. All cDNA fragments were sequenced and the identities of seven were determined through homology with known genes; an additional five TH-regulated genes were identified by hybridization with known cDNA clones. These include five transcription factors (including two members of the steroid receptor superfamily), a TH-converting deiodinase, two metabolic enzymes, a protein disulfide isomerase-like protein that may bind TH, a neural-specific cytoskeletal protein, and two hypophysiotropic neuropeptides. This is the first successful attempt to isolate a large number of TH-target genes in the developing vertebrate brain. The gene identities allow predictions about the gene regulatory networks underlying TH action on the brain, and the cloned cDNAs provide tools for understanding the basic molecular mechanisms underlying neural cell differentiation.
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Affiliation(s)
- R J Denver
- Department of Biology, The University of Michigan, Ann Arbor, Michigan 48109, USA.
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22
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Eliceiri B, Brown D. Quantitation of endogenous thyroid hormone receptors alpha and beta during embryogenesis and metamorphosis in Xenopus laevis. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(19)51106-1] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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23
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Shi Y, Brown D. The earliest changes in gene expression in tadpole intestine induced by thyroid hormone. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(20)80730-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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24
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Fischer L, Catz D, Kelley D. An androgen receptor mRNA isoform associated with hormone-induced cell proliferation. Proc Natl Acad Sci U S A 1993; 90:8254-8. [PMID: 7690145 PMCID: PMC47327 DOI: 10.1073/pnas.90.17.8254] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The larynx of male Xenopus laevis undergoes an androgen-driven developmental transformation that enables the adult to produce his complex mate attraction song. During the early postmetamorphic period, androgen directs proliferation and differentiation of laryngeal muscle and cartilage. To explore the cellular and molecular basis of androgen control, we have cloned an androgen receptor cDNA from juvenile larynx. Here we identify two androgen receptor mRNA isoforms, alpha and beta, differing within the A/B, or hypervariable, domain. Northern blot analyses reveal that the beta isoform is transiently expressed during early juvenile stages, whereas the alpha transcript is expressed throughout postmetamorphic life. Using in situ hybridization and [3H]thymidine autoradiography, we examined the expression of androgen receptor mRNA isoforms during androgen-evoked cell proliferation and differentiation. The alpha and beta transcripts are coexpressed in proliferating tissues of the juvenile larynx; in postmitotic differentiated tissues, only the alpha transcript is expressed. Because androgen receptor beta mRNA is specifically expressed during hormone-evoked cell proliferation, we propose that this developmentally regulated mRNA isoform is required for the masculine program of cell addition within the developing vocal organ.
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Affiliation(s)
- L Fischer
- Department of Biological Sciences, Columbia University, New York, NY 10027
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25
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Buckbinder L, Brown DD. Expression of the Xenopus laevis prolactin and thyrotropin genes during metamorphosis. Proc Natl Acad Sci U S A 1993; 90:3820-4. [PMID: 7683408 PMCID: PMC46397 DOI: 10.1073/pnas.90.9.3820] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The cDNAs encoding Xenopus laevis prolactin (PRL) and the alpha and beta subunits of thyroid-stimulating hormone (TSH alpha and TSH beta, respectively) have been cloned from a pituitary library. Results of developmental RNA blot analysis contradict the long-held biological role for PRL as a juvenilizing hormone in amphibia. The pituitary gland of a premetamorphic tadpole expresses PRL mRNA at very low levels. The abundance of PRL mRNA increases late in metamorphosis as a response to thyroid hormone (TH), suggesting that PRL is more likely to have a function in the frog than in the tadpole. TSH alpha and -beta mRNA levels increase through prometamorphosis; this rise does not appear to be regulated directly by TH. At climax, both TH and TSH mRNA levels drop. The sequential morphological changes that characterize prometamorphosis depend upon the gradual increase of endogenous TH, which peaks at climax. This increase in TH in turn depends upon the lack of a traditional thyroid-pituitary negative-feedback loop throughout prometamorphosis.
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Affiliation(s)
- L Buckbinder
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21210
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26
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Saha MS, Grainger RM. Early opsin expression in Xenopus embryos precedes photoreceptor differentiation. BRAIN RESEARCH. MOLECULAR BRAIN RESEARCH 1993; 17:307-18. [PMID: 8510503 DOI: 10.1016/0169-328x(93)90016-i] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The visual pigment which serves as the first step in the phototransduction cycle in vertebrate rod cells consists of a retinal chromophore which is linked to the transmembrane protein, opsin. Opsin genes have been isolated from a number of different organisms and studies have shown opsin to be developmentally regulated with both mRNA and protein expression associated with the morphological differentiation of photoreceptor cells. Due to its potential utility as a marker for rod photoreceptor determination in studies of retinal tissue interactions, and because no amphibian opsin genes have as yet been cloned, we isolated cDNA clones of the Xenopus laevis opsin gene. Sequence analysis shows that within the coding region Xenopus opsin shares a high degree of identity with other rod opsin genes, except at the C-terminal where it more closely resembles the mammalian color opsins. A developmental analysis, on the other hand, reveals that Xenopus opsin transcripts are detectable in a retina-specific fashion early in retinal development. Using in situ hybridization we find that Xenopus opsin mRNA is initially restricted to a few isolated cells in the presumptive photoreceptor layer which express the gene at relatively high levels. This suggests that rod photoreceptor determination occurs in single cells, and that the mechanisms controlling opsin expression in Xenopus are initiated well before any evidence of morphological differentiation.
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Affiliation(s)
- M S Saha
- Department of Biology University of Virginia Charlottesville 22903
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27
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Droin A. Genetic and experimental studies on a new pigment mutant in Xenopus laevis. THE JOURNAL OF EXPERIMENTAL ZOOLOGY 1992; 264:196-205. [PMID: 1431781 DOI: 10.1002/jez.1402640212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
White lethal (wl) is a recessive mutation affecting the differentiation of the three types of chromatophores in Xenopus laevis and eventually leading to the death of the mutants around stage 50. Melanophores appear at st. 33 but differentiate abnormally, remaining pale grey, and do not proliferate after st. 41. The rare xanthophores present contain only a few differentiated pterinosomes, and the iridophores consist of noniridescent white dots. When the albino gene (ap) is combined with wl, melanophores do not differentiate. Reciprocal heterotopic and orthotopic trunk neural crest grafts have shown that the defect is intrinsic to the neural crest cells but is not due, in the case of melanophores, to a tyrosinase deficiency as revealed by the dopa reaction. The mode of action of the gene, the abnormal pattern, and lethality are discussed.
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Affiliation(s)
- A Droin
- Station de Zoologie expérimentale, Université de Genève, Switzerland
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29
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Genomic organization and alternative promoter usage of the two thyroid hormone receptor beta genes in Xenopus laevis. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)48345-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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30
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Androgen receptor expression and sexual differentiation of effectors for courtship song in Xenopus laevis. ACTA ACUST UNITED AC 1991. [DOI: 10.1016/1044-5765(91)90056-t] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Affiliation(s)
- R Tompkins
- Department of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana 70118
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32
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Abstract
The Xenopus laevis genome encodes two genes for the alpha (TR alpha) and two genes for the beta (TR beta) thyroid hormone receptors. The two TR alpha genes closely resemble their rat, human, and chicken counterparts. No alternatively spliced TR alpha cDNA clones were found in the 5' untranslated region (5' UTR). In contrast, complex alternative splicing of TR beta mRNA occurs within the 5' UTR as well as possible alternative transcriptional start sites. As many as eight exons encoding mainly the 5' UTR are alternatively spliced, giving rise to at least two amino termini for each of the two TR beta proteins. The 5' UTR of transcripts from both TR alpha and TR beta genes contain multiple AUG sequences with short open reading frames suggesting translational control mechanisms might play a role in expression of TR genes.
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33
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Shi YB, Brown DD. Developmental and thyroid hormone-dependent regulation of pancreatic genes in Xenopus laevis. Genes Dev 1990; 4:1107-13. [PMID: 2210372 DOI: 10.1101/gad.4.7.1107] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have isolated and sequenced a cDNA encoding Xenopus laevis pancreatic trypsin, which has approximately 70% amino acid sequence identity to mammalian trypsinogen. Northern blotting analysis shows that the trypsin gene is activated just before the tadpole starts to feed, reaches peak activity in the swimming tadpole (premetamorphosis), and is then repressed during prometamorphosis, attaining its lowest activity at the climax of metamorphosis. The same gene is then activated again in frogs but to a much lower level. The pattern of the changes in trypsin gene expression is followed by at least two other pancreas-specific genes and marks the remodeling of the pancreas of the animal at metamorphosis. Thyroid hormone, which is the causative agent of metamorphosis, can down-regulate trypsin gene expression prematurely.
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Affiliation(s)
- Y B Shi
- Department of Embryology, Carnegie Institution of Washington, Baltimore, Maryland 21210
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34
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35
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Shiokawa K, Tashiro K, Nakakura N, Fu Y, Atsuchi Y, Nakazato S, Tsuzaki Y, Ikenishi K. A possible maternal-effect mutant of Xenopus laevis: II. Studies of RNA synthesis in dissociated embryonic cells. CELL DIFFERENTIATION AND DEVELOPMENT : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF DEVELOPMENTAL BIOLOGISTS 1988; 25:47-55. [PMID: 2461791 DOI: 10.1016/0922-3371(88)90054-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Embryos from a female of Xenopus laevis (designated as no. 65) arrest development at gastrulation and are assumed to be ova-deficient mutant. We dissociated these embryos and studied RNA synthesis at different stages. The cells from the ova-deficient embryos reaggregated quite actively as wild-type embryo cells until the late gastrula stage. RNA synthesis was normal at the early blastula stage but greatly inhibited by the late blastula (stage 9.5) stage, when the synthesis of DNA and protein was still not inhibited appreciably. Thus, inhibition in RNA synthesis appears to be the first manifestation of the maternal defect that occurs before the gastrulation arrest.
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Affiliation(s)
- K Shiokawa
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
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36
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Krotoski DM, Fraser SE, Bronner-Fraser M. Mapping of neural crest pathways in Xenopus laevis using inter- and intra-specific cell markers. Dev Biol 1988; 127:119-32. [PMID: 2452101 DOI: 10.1016/0012-1606(88)90194-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This study examines the pathways of migration followed by neural crest cells in Xenopus embryos using two recently described cell marking techniques. The first is an interspecific chimera created by grafting Xenopus borealis cells into Xenopus laevis hosts. The cells of these closely related species can be distinguished by their nuclear dimorphism. The second type of marker is created by microinjection of lysinated dextrans into fertilized eggs which can then be used for intraspecific grafting. These recently developed fluorescent dyes are fixable and identifiable in both living and fixed embryos. After grafting labeled donor neural tubes into unlabeled host embryos, the distribution of neural crest cells at various stages after grafting was used to define the pathways of neural crest migration. To control for possible grafting artifacts, fluorescent lysinated dextran was injected into a single blastomere which gives rise to a large number of neural crest cells, thereby labeling the neural crest without grafting. By all three techniques, Xenopus neural crest cells were observed along two predominant pathways in the trunk. The majority of neural crest cells were observed along a "ventral" route, between the neural tube and somite, the notochord and somite, and along the dorsal mesentery. A second group of neural crest cells was observed "dorsally" where they populated the dorsal fin. A third minor "lateral" pathway was observed primarily in borealis/laevis chimerae and in blastomere-injected embryos; some neural crest cells were observed underneath the ectoderm lateral to the neural tube. Along the rostrocaudal axis, neural crest cells were not continuously distributed but were primarily located across from the caudal two-thirds of the somite. Fewer than 3% of the neural crest cells were observed across from the rostral third of each somite. When grafted to ventral locations, neural crest cells were not able to migrate dorsally but migrated laterally along the dorsal mesentery. Labeled neural crest cells gave rise to cells of the spinal, sympathetic, and enteric ganglia as well as to adrenal chromaffin cells, Schwann cells, pigment cells, mesenchymal cells of the dorsal fin, and some cells in the integuments and in the region of the pronephros. These results show that the neural crest migratory pathways in Xenopus differ from those in the avian embryo. In avians NC cells migrate as a closely associated sheet of cells while in Xenopus they migrate as individual cells. Both species exhibit a metamerism in the neural crest cell distribution pattern along the rostrocaudal axis.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- D M Krotoski
- Developmental Biology Center, University of California Irvine 92717
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37
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Magrassi L, Graziadei PP. Single olfactory organ associated with prosencephalic malformation and cyclopia in a Xenopus laevis tadpole. Brain Res 1987; 412:386-90. [PMID: 3111639 DOI: 10.1016/0006-8993(87)91148-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A cyclops Xenopus laevis tadpole with a single olfactory organ is described. At a stage comparable to 48, the telencephalon was severely atrophic and only the region where the olfactory fibres terminated appeared to have the cytoarchitecture of the olfactory bulb. In this animal the central nervous system (CNS) appeared normally developed only posterior to the preoptic area. The hypothesis of a diencephalic origin of the region where the olfactory fibres terminated is discussed in the light of our previous results of olfactory placode transplantation. By analogy between this case and other malformations (cyclopia, holoprosencephaly) in higher vertebrates and humans, the need is emphasized for a more precise anatomical description of the olfactory input in related malformations.
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Taylor W, Jackson IJ, Siegel N, Kumar A, Brown DD. The developmental expression of the gene for TFIIIA in Xenopus laevis. Nucleic Acids Res 1986; 14:6185-95. [PMID: 3755818 PMCID: PMC311630 DOI: 10.1093/nar/14.15.6185] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The sequence of the trans-acting positive transcription factor TFIIIA has been deduced by sequencing cDNA and genomic DNA clones. Using DNA from a homozygous diploid animal we show that there is one gene for TFIIIA per haploid genome of X. laevis. Protein sequencing of proteolytic fragments of TFIIIA orients the protein in its interaction with the internal control region (ICR) of the 5S RNA gene. The protein lies along the DNA with its carboxyl terminus at the 5' end of the ICR and its amino terminus at the 3' end. The developmental pattern of TFIIIA and its mRNA during oogenesis and embryogenesis are consistent with the idea that the abundance of TFIIIA plays an essential role in the developmental change in 5S RNA gene expression. The change to almost exclusive somatic 5S RNA gene expression by gastrulation occurs using either the TFIIIA that was synthesized by oocyte and/or TFIIIA synthesized from maternal mRNA.
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