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Bedell VM, Dubey P, Lee HB, Bailey DS, Anderson JL, Jamieson-Lucy A, Xiao R, Leonard EV, Falk MJ, Pack MA, Mullins M, Farber SA, Eckenhoff RG, Ekker SC. Zebrafishology, study design guidelines for rigorous and reproducible data using zebrafish. Commun Biol 2025; 8:739. [PMID: 40360750 PMCID: PMC12075475 DOI: 10.1038/s42003-025-07496-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 01/08/2025] [Indexed: 05/15/2025] Open
Abstract
The zebrafish (Danio rerio) is one of the most widely used research model organisms funded by the United States' National Institutes of Health, second only to the mouse. Here, we discuss the advantages and unique qualities of this model organism. Additionally, we discuss key aspects of experimental design and statistical approaches that apply to studies using the zebrafish model organism. Finally, we list critical details that should be considered in the design of zebrafish experiments to enhance rigor and data reproducibility. These guidelines are designed to aid new researchers, journal editors, and manuscript reviewers in supporting the publication of the highest-quality zebrafish research.
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Affiliation(s)
- Victoria M Bedell
- Department of Anesthesiology and Critical Care, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Priya Dubey
- Department of Anesthesiology and Critical Care, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Han B Lee
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Dondra S Bailey
- Department of Natural Sciences, Coppin State University, Baltimore, MD, USA
| | - Jennifer L Anderson
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Allison Jamieson-Lucy
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rui Xiao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Elvin V Leonard
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marni J Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael A Pack
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mary Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Steven A Farber
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Roderic G Eckenhoff
- Department of Anesthesiology and Critical Care, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephen C Ekker
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Department of Molecular Biosciences and Dell Medical School Department of Pediatrics, University of Texas, Austin, TX, USA
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Wilson ML, Romano SN, Khatri N, Aharon D, Liu Y, Kaufman OH, Draper BW, Marlow FL. Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios. Nat Commun 2024; 15:5248. [PMID: 38898112 PMCID: PMC11187175 DOI: 10.1038/s41467-024-49613-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024] Open
Abstract
Reproductive success relies on proper establishment and maintenance of biological sex. In many animals, including mammals, the primary gonad is initially ovary biased. We previously showed the RNA binding protein (RNAbp), Rbpms2, is required for ovary fate in zebrafish. Here, we identified Rbpms2 targets in oocytes (Rbpms2-bound oocyte RNAs; rboRNAs). We identify Rbpms2 as a translational regulator of rboRNAs, which include testis factors and ribosome biogenesis factors. Further, genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway, specifically through the mTorc1-activating Gap activity towards Rags 2 (Gator2) component, Missing oocyte (Mios). Cumulatively, our findings indicate that early gonocytes are in a dual poised, bipotential state in which Rbpms2 acts as a binary fate-switch. Specifically, Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2-mediated checkpoint, thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis.
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Affiliation(s)
- Miranda L Wilson
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020, New York, NY, USA
| | - Shannon N Romano
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020, New York, NY, USA
| | - Nitya Khatri
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020, New York, NY, USA
| | - Devora Aharon
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020, New York, NY, USA
| | - Yulong Liu
- Department of Molecular and Cellular Biology. University of California. 1 Shields Ave, Davis, CA, USA
| | - Odelya H Kaufman
- Department of Developmental and Molecular Biology. Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bruce W Draper
- Department of Molecular and Cellular Biology. University of California. 1 Shields Ave, Davis, CA, USA
| | - Florence L Marlow
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020, New York, NY, USA.
- Department of Developmental and Molecular Biology. Albert Einstein College of Medicine, Bronx, NY, USA.
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Wilson ML, Romano SN, Khatri N, Aharon D, Liu Y, Kaufman OH, Draper BW, Marlow FL. Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component, Mios. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577235. [PMID: 38328218 PMCID: PMC10849709 DOI: 10.1101/2024.01.25.577235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Reproductive success relies on proper establishment and maintenance of biological sex. In many animals, including mammals, the primary gonad is initially ovary in character. We previously showed the RNA binding protein (RNAbp), Rbpms2, is required for ovary fate in zebrafish. Here, we identified Rbpms2 targets in oocytes (Rbpms2-bound oocyte RNAs; rboRNAs). We identify Rbpms2 as a translational regulator of rboRNAs, which include testis factors and ribosome biogenesis factors. Further, genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway, specifically through the mTorc1-activating Gap activity towards Rags 2 (Gator2) component, Missing oocyte (Mios). Cumulatively, our findings indicate that early gonocytes are in a dual poised, bipotential state in which Rbpms2 acts as a binary fate-switch. Specifically, Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2-mediated checkpoint, thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis.
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Affiliation(s)
- Miranda L. Wilson
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020 New York, NY 10029-6574
| | - Shannon N. Romano
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020 New York, NY 10029-6574
| | - Nitya Khatri
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020 New York, NY 10029-6574
| | - Devora Aharon
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020 New York, NY 10029-6574
| | - Yulong Liu
- Department of Molecular and Cellular Biology. University of California. 1 Shields Ave, Davis, CA 95616
| | - Odelya H. Kaufman
- Department of Developmental and Molecular Biology. Albert Einstein College of Medicine. 1300 Morris Park Avenue, Bronx, NY 10461
| | - Bruce W. Draper
- Department of Molecular and Cellular Biology. University of California. 1 Shields Ave, Davis, CA 95616
| | - Florence L. Marlow
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020 New York, NY 10029-6574
- Department of Developmental and Molecular Biology. Albert Einstein College of Medicine. 1300 Morris Park Avenue, Bronx, NY 10461
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Wei Y, Wang J, Qu R, Zhang W, Tan Y, Sha Y, Li L, Yin T. Genetic mechanisms of fertilization failure and early embryonic arrest: a comprehensive review. Hum Reprod Update 2024; 30:48-80. [PMID: 37758324 DOI: 10.1093/humupd/dmad026] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/07/2023] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND Infertility and pregnancy loss are longstanding problems. Successful fertilization and high-quality embryos are prerequisites for an ongoing pregnancy. Studies have proven that every stage in the human reproductive process is regulated by multiple genes and any problem, at any step, may lead to fertilization failure (FF) or early embryonic arrest (EEA). Doctors can diagnose the pathogenic factors involved in FF and EEA by using genetic methods. With the progress in the development of new genetic technologies, such as single-cell RNA analysis and whole-exome sequencing, a new approach has opened up for us to directly study human germ cells and reproductive development. These findings will help us to identify the unique mechanism(s) that leads to FF and EEA in order to find potential treatments. OBJECTIVE AND RATIONALE The goal of this review is to compile current genetic knowledge related to FF and EEA, clarifying the mechanisms involved and providing clues for clinical diagnosis and treatment. SEARCH METHODS PubMed was used to search for relevant research articles and reviews, primarily focusing on English-language publications from January 1978 to June 2023. The search terms included fertilization failure, early embryonic arrest, genetic, epigenetic, whole-exome sequencing, DNA methylation, chromosome, non-coding RNA, and other related keywords. Additional studies were identified by searching reference lists. This review primarily focuses on research conducted in humans. However, it also incorporates relevant data from animal models when applicable. The results were presented descriptively, and individual study quality was not assessed. OUTCOMES A total of 233 relevant articles were included in the final review, from 3925 records identified initially. The review provides an overview of genetic factors and mechanisms involved in the human reproductive process. The genetic mutations and other genetic mechanisms of FF and EEA were systematically reviewed, for example, globozoospermia, oocyte activation failure, maternal effect gene mutations, zygotic genome activation abnormalities, chromosome abnormalities, and epigenetic abnormalities. Additionally, the review summarizes progress in treatments for different gene defects, offering new insights for clinical diagnosis and treatment. WIDER IMPLICATIONS The information provided in this review will facilitate the development of more accurate molecular screening tools for diagnosing infertility using genetic markers and networks in human reproductive development. The findings will also help guide clinical practice by identifying appropriate interventions based on specific gene mutations. For example, when an individual has obvious gene mutations related to FF, ICSI is recommended instead of IVF. However, in the case of genetic defects such as phospholipase C zeta1 (PLCZ1), actin-like7A (ACTL7A), actin-like 9 (ACTL9), and IQ motif-containing N (IQCN), ICSI may also fail to fertilize. We can consider artificial oocyte activation technology with ICSI to improve fertilization rate and reduce monetary and time costs. In the future, fertility is expected to be improved or restored by interfering with or supplementing the relevant genes.
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Affiliation(s)
- Yiqiu Wei
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jingxuan Wang
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Rui Qu
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weiqian Zhang
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yiling Tan
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yanwei Sha
- Department of Andrology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, China
| | - Lin Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Tailang Yin
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
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Luo M, Yi Y, Huang S, Dai S, Xie L, Liu K, Zhang S, Jiang T, Wang T, Yao B, Wang H, Xu D. Gestational dexamethasone exposure impacts hippocampal excitatory synaptic transmission and learning and memory function with transgenerational effects. Acta Pharm Sin B 2023; 13:3708-3727. [PMID: 37719378 PMCID: PMC10501875 DOI: 10.1016/j.apsb.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/20/2023] [Accepted: 05/06/2023] [Indexed: 09/19/2023] Open
Abstract
The formation of learning and memory is regulated by synaptic plasticity in hippocampal neurons. Here we explored how gestational exposure to dexamethasone, a synthetic glucocorticoid commonly used in clinical practice, has lasting effects on offspring's learning and memory. Adult offspring rats of prenatal dexamethasone exposure (PDE) displayed significant impairments in novelty recognition and spatial learning memory, with some phenotypes maintained transgenerationally. PDE impaired synaptic transmission of hippocampal excitatory neurons in offspring of F1 to F3 generations, and abnormalities of neurotransmitters and receptors would impair synaptic plasticity and lead to impaired learning and memory, but these changes failed to carry over to offspring of F5 and F7 generations. Mechanistically, altered hippocampal miR-133a-3p-SIRT1-CDK5-NR2B signaling axis in PDE multigeneration caused inhibition of excitatory synaptic transmission, which might be related to oocyte-specific high expression and transmission of miR-133a-3p. Together, PDE affects hippocampal excitatory synaptic transmission, with lasting consequences across generations, and CDK5 in offspring's peripheral blood might be used as an early-warning marker for fetal-originated learning and memory impairment.
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Affiliation(s)
- Mingcui Luo
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
| | - Yiwen Yi
- Department of Pharmacology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
| | - Songqiang Huang
- Department of Pharmacology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
| | - Shiyun Dai
- Department of Pharmacology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
| | - Lulu Xie
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan 430071, China
| | - Kexin Liu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Shuai Zhang
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
| | - Tao Jiang
- Department of Pharmacology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
| | - Tingting Wang
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
| | - Baozhen Yao
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan 430071, China
| | - Hui Wang
- Department of Pharmacology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
| | - Dan Xu
- Department of Obstetrics, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
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