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Perlee S, Ma Y, Hunter MV, Swanson JB, Ming Z, Xia J, Lionnet T, McGrail M, White RM. Identifying in vivo genetic dependencies of melanocyte and melanoma development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586101. [PMID: 38562693 PMCID: PMC10983904 DOI: 10.1101/2024.03.22.586101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The advent of large-scale sequencing in both development and disease has identified large numbers of candidate genes that may be linked to important phenotypes. Validating the function of these candidates in vivo is challenging, due to low efficiency and low throughput of most model systems. We have developed a rapid, scalable system for assessing the role of candidate genes using zebrafish. We generated transgenic zebrafish in which Cas9 was knocked-in to the endogenous mitfa locus, a master transcription factor of the melanocyte lineage. We used this system to identify both cell-autonomous and non-cell autonomous regulators of normal melanocyte development. We then applied this to the melanoma setting to demonstrate that loss of genes required for melanocyte survival can paradoxically promote more aggressive phenotypes, highlighting that in vitro screens can mask in vivo phenotypes. Our high-efficiency genetic approach offers a versatile tool for exploring developmental processes and disease mechanisms that can readily be applied to other cell lineages.
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2
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Khatiwada B, Jones JL, Zhao D, Gasperini RJ, McComish BJ, Burdon KP. Comparison of baseline cataract rates in AB and TL wildtype zebrafish strains. Exp Eye Res 2024; 243:109908. [PMID: 38657787 DOI: 10.1016/j.exer.2024.109908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/27/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Zebrafish are an outstanding model for assessing the involvement of genes in paediatric cataracts. Gene discovery for cataracts is enhanced by manipulation of the genome of zebrafish embryos and comparing the phenotypes of mutant progeny with the wildtype embryos. However, wildtype laboratory fish can also develop cataracts, potentially confounding the results. In this study, we compared the baseline cataract rate between two commonly used wildtype laboratory strains, AB and TL, and also an outbred transgenic line with mCherry reporter. We assessed a total of 805 lens images of fish at 4 days post-fertilisation for cataracts and scored each cataract observed as mild, moderate or severe. We found that the AB strain had a cataract rate of 16.2%, TL had 8.9%, and mCherry had 0.7% and these rates were significantly different. We found that TL strain had a lower rate of mild cataracts than AB fish, however, the rate of moderate and severe phenotypes in the AB and the TL strain was similar. Overall, we showed that the baseline cataract rate varies significantly between the strains housed in a single facility and conclude that baseline rates of cataracts should be assessed when planning experiments to assess the genetic causes of cataracts.
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Affiliation(s)
- Bibek Khatiwada
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Johanna L Jones
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Duran Zhao
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Bennet J McComish
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia.
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3
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Paull GC, Lee CJ, Tyler CR. Beyond compliance: harmonising research and husbandry practices to improve experimental reproducibility using fish models. Biol Rev Camb Philos Soc 2024; 99:253-264. [PMID: 37817305 DOI: 10.1111/brv.13020] [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: 05/30/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/12/2023]
Abstract
Reproducibility in animal research is impacted by the environment, by husbandry practices in the laboratory and by the animals' provenance. These factors, however, are often not adequately considered by researchers. A disconnect between researchers and animal care staff can result in inappropriate housing and husbandry decisions for scientific studies with those animals. This is especially the case for the research in neuro-behaviour, epigenetics, and the impact of climate change, as heritable phenotypic, behavioural or physiological changes are known to result from the animals' environmental housing, husbandry, provenance and prior experience. This can lead to greater variation (even major differences) in data outcomes among studies, driving scientific uncertainties. Herein, we illustrate some of the endpoints measured in fish studies known to be intrinsically linked to the environment and husbandry conditions and assess the significance of housing and husbandry practice decisions for research adopting these endpoints for different fish species. We highlight the different priorities and challenges faced by researchers and animal care staff and how harmonising their activities and building greater understanding of how husbandry practices affect the fish will improve reproducibility in research outcomes. We furthermore illustrate how improving engagement between stakeholders, including regulatory bodies, can better underpin fish husbandry decisions and where researchers could help to drive best husbandry practices through their own research with fish models.
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Affiliation(s)
- Gregory C Paull
- Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Carole J Lee
- Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Charles R Tyler
- Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
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4
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Shin M, Yin HM, Shih YH, Nozaki T, Portman D, Toles B, Kolb A, Luk K, Isogai S, Ishida K, Hanasaka T, Parsons MJ, Wolfe SA, Burns CE, Burns CG, Lawson ND. Generation and application of endogenously floxed alleles for cell-specific knockout in zebrafish. Dev Cell 2023; 58:2614-2626.e7. [PMID: 37633272 PMCID: PMC10840978 DOI: 10.1016/j.devcel.2023.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 05/30/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
The zebrafish is amenable to a variety of genetic approaches. However, lack of conditional deletion alleles limits stage- or cell-specific gene knockout. Here, we applied an existing protocol to establish a floxed allele for gata2a but failed to do so due to off-target integration and incomplete knockin. To address these problems, we applied simultaneous co-targeting with Cas12a to insert loxP sites in cis, together with transgenic counterscreening and comprehensive molecular analysis, to identify off-target insertions and confirm targeted knockins. We subsequently used our approach to establish endogenously floxed alleles of foxc1a, rasa1a, and ruvbl1, each in a single generation. We demonstrate the utility of these alleles by verifying Cre-dependent deletion, which yielded expected phenotypes in each case. Finally, we used the floxed gata2a allele to demonstrate an endothelial autonomous requirement in lymphatic valve development. Together, our results provide a framework for routine generation and application of endogenously floxed alleles in zebrafish.
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Affiliation(s)
- Masahiro Shin
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hui-Min Yin
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Yu-Huan Shih
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Takayuki Nozaki
- Technical Support Center for Life Science Research, Iwate Medical University, Shiwa, Iwate 028-3694, Japan
| | - Daneal Portman
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Benjamin Toles
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Amy Kolb
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Kevin Luk
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Sumio Isogai
- Department of Medical Education, Iwate Medical University, Shiwa, Iwate 028-3694, Japan
| | - Kinji Ishida
- Technical Support Center for Life Science Research, Iwate Medical University, Shiwa, Iwate 028-3694, Japan
| | - Tomohito Hanasaka
- Technical Support Center for Life Science Research, Iwate Medical University, Shiwa, Iwate 028-3694, Japan
| | - Michael J Parsons
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Scot A Wolfe
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Caroline E Burns
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - C Geoffrey Burns
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Nathan D Lawson
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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5
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Hodorovich DR, Lindsley PM, Berry AA, Burton DF, Marsden KC. Morphological and sensorimotor phenotypes in a zebrafish CHARGE syndrome model are domain-dependent. GENES, BRAIN, AND BEHAVIOR 2023:e12839. [PMID: 36717082 DOI: 10.1111/gbb.12839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/22/2022] [Accepted: 01/20/2023] [Indexed: 02/01/2023]
Abstract
CHARGE syndrome is a heterogeneous disorder characterized by a spectrum of defects affecting multiple tissues and behavioral difficulties such as autism, attention-deficit/hyperactivity disorder, obsessive-compulsive disorder, anxiety, and sensory deficits. Most CHARGE cases arise from de novo, loss-of-function mutations in chromodomain-helicase-DNA-binding-protein-7 (CHD7). CHD7 is required for processes such as neuronal differentiation and neural crest cell migration, but how CHD7 affects neural circuit function to regulate behavior is unclear. To investigate the pathophysiology of behavioral symptoms in CHARGE, we established a mutant chd7 zebrafish line that recapitulates multiple CHARGE phenotypes including ear, cardiac, and craniofacial defects. Using a panel of behavioral assays, we found that chd7 mutants have specific auditory and visual behavior deficits that are independent of defects in sensory structures. Mauthner cell-dependent short-latency acoustic startle responses are normal in chd7 mutants, while Mauthner-independent long-latency responses are reduced. Responses to sudden decreases in light are also reduced in mutants, while responses to sudden increases in light are normal, suggesting that the retinal OFF pathway may be affected. Furthermore, by analyzing multiple chd7 alleles we observed that the penetrance of morphological and behavioral phenotypes is influenced by genetic background but that it also depends on the mutation location, with a chromodomain mutation causing the highest penetrance. This pattern is consistent with analysis of a CHARGE patient dataset in which symptom penetrance was highest in subjects with mutations in the CHD7 chromodomains. These results provide new insight into the heterogeneity of CHARGE and will inform future work to define CHD7-dependent neurobehavioral mechanisms.
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Affiliation(s)
- Dana R Hodorovich
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Patrick M Lindsley
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.,University of Virginia School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Austen A Berry
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.,Biogen, Durham, NC, USA
| | - Derek F Burton
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.,Washington University, St. Louis, MO, USA
| | - Kurt C Marsden
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.,Washington University, St. Louis, MO, USA
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6
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Evolutionary conservation of maternal RNA localization in fishes and amphibians revealed by TOMO-Seq. Dev Biol 2022; 489:146-160. [PMID: 35752299 DOI: 10.1016/j.ydbio.2022.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/18/2022] [Accepted: 06/19/2022] [Indexed: 11/24/2022]
Abstract
Asymmetrical localization of biomolecules inside the egg, results in uneven cell division and establishment of many biological processes, cell types and the body plan. However, our knowledge about evolutionary conservation of localized transcripts is still limited to a few models. Our goal was to compare localization profiles along the animal-vegetal axis of mature eggs from four vertebrate models, two amphibians (Xenopus laevis, Ambystoma mexicanum) and two fishes (Acipenser ruthenus, Danio rerio) using the spatial expression method called TOMO-Seq. We revealed that RNAs of many known important transcripts such as germ layer determinants, germ plasm factors and members of key signalling pathways, are localized in completely different profiles among the models. It was also observed that there was a poor correlation between the vegetally localized transcripts but a relatively good correlation between the animally localized transcripts. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model.
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7
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The phylogenetic position of zebrafish (Danio rerio) from south african pet shops. Mol Biol Rep 2022; 49:7327-7336. [PMID: 35596052 DOI: 10.1007/s11033-022-07522-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Zebrafish (Danio rerio), a small freshwater fish that originates from India, Bangladesh, Nepal, Bhutan and northern Myanmar, have been widely used as a model organism for studies of developmental biology and genetics. The current study aimed to determine the origin of South African pet shop stock that are currently being used to establish a laboratory population founded from diverse sources available locally. METHODS AND RESULTS Zebrafish DNA was extracted from 65 specimens housed at the University of the Free State (UFS) Department of Genetics. For phylogenetic analysis, cytb sequences were generated from all samples. A further 178 sequences were downloaded from the GenBank database, including sequences of an outgroup species (Danio kyathit). Five microsatellite markers were used to further assess the genetic diversity of the UFS zebrafish specimens. A maximum likelihood analysis was performed for the cytb data. Results of the phylogenetic analyses divided the sequences into three major genetic groups, which was congruent with a previous study on laboratory zebrafish provenance. The SA pet shop fish grouped with the lines from the northern and north-eastern regions of India. High levels of microsatellite genetic diversity were observed for the pet shop sourced population, correlating to what has previously been observed in zebrafish. CONCLUSION These results can be used to guide the future development of laboratory lines suited to the needs at the UFS.
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8
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Gonçalves C, Kareklas K, Teles MC, Varela SAM, Costa J, Leite RB, Paixão T, Oliveira RF. Phenotypic architecture of sociality and its associated genetic polymorphisms in zebrafish. GENES, BRAIN, AND BEHAVIOR 2022; 21:e12809. [PMID: 35524578 PMCID: PMC9744564 DOI: 10.1111/gbb.12809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 12/11/2022]
Abstract
Sociality relies on motivational and cognitive components that may have evolved independently, or may have been linked by phenotypic correlations driven by a shared selective pressure for increased social competence. Furthermore, these components may be domain-specific or of general-domain across social and non-social contexts. Here, we used zebrafish to test if the motivational and cognitive components of social behavior are phenotypically linked and if they are domain specific or of general domain. The behavioral phenotyping of zebrafish in social and equivalent non-social tests shows that the motivational (preference) and cognitive (memory) components of sociality: (1) are independent from each other, hence not supporting the occurrence of a sociality syndrome; and (2) are phenotypically linked to non-social traits, forming two general behavioral modules, suggesting that sociality traits have been co-opted from general-domain motivational and cognitive traits. Moreover, the study of the association between single nucleotide polymorphisms (SNPs) and each behavioral module further supports this view, since several SNPs from a list of candidate "social" genes, are statistically associated with the motivational, but not with the cognitive, behavioral module. Together, these results support the occurrence of general-domain motivational and cognitive behavioral modules in zebrafish, which have been co-opted for the social domain.
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Affiliation(s)
- Claúdia Gonçalves
- Integrative Behavioural Biology LaboratoryGulbenkian Institute of ScienceOeirasPortugal
| | - Kyriacos Kareklas
- Integrative Behavioural Biology LaboratoryGulbenkian Institute of ScienceOeirasPortugal
| | - Magda C. Teles
- Integrative Behavioural Biology LaboratoryGulbenkian Institute of ScienceOeirasPortugal
| | - Susana A. M. Varela
- Integrative Behavioural Biology LaboratoryGulbenkian Institute of ScienceOeirasPortugal
| | - João Costa
- Integrative Behavioural Biology LaboratoryGulbenkian Institute of ScienceOeirasPortugal
| | - Ricardo B. Leite
- Integrative Behavioural Biology LaboratoryGulbenkian Institute of ScienceOeirasPortugal
| | - Tiago Paixão
- Integrative Behavioural Biology LaboratoryGulbenkian Institute of ScienceOeirasPortugal
| | - Rui F. Oliveira
- Integrative Behavioural Biology LaboratoryGulbenkian Institute of ScienceOeirasPortugal,Department of BiosciencesISPA‐Instituto UniversitárioLisbonPortugal,Champalimaud Neuroscience Program, Champalimaud FoundationLisbonPortugal
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9
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Marcos S, Parejo M, Estonba A, Alberdi A. Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100065. [PMID: 36620197 PMCID: PMC9744478 DOI: 10.1002/ggn2.202100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/05/2022] [Indexed: 01/11/2023]
Abstract
Metagenomic datasets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two-step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low-depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low- and high-depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.
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Affiliation(s)
- Sofia Marcos
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Melanie Parejo
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Andone Estonba
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Antton Alberdi
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
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10
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Mundy PC, Mendieta R, Lein PJ. Diisopropylfluorophosphate (DFP) volatizes and cross-contaminates wells in a common 96-well plate format used in zebrafish larvae toxicology studies. J Pharmacol Toxicol Methods 2022; 115:107173. [DOI: 10.1016/j.vascn.2022.107173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/23/2022] [Accepted: 05/01/2022] [Indexed: 11/27/2022]
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11
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Wallis DJ, La Du J, Thunga P, Elson D, Truong L, Kolluri SK, Tanguay RL, Reif DM. Leveraging a High-Throughput Screening Method to Identify Mechanisms of Individual Susceptibility Differences in a Genetically Diverse Zebrafish Model. FRONTIERS IN TOXICOLOGY 2022; 4:846221. [PMID: 35573279 PMCID: PMC9098949 DOI: 10.3389/ftox.2022.846221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding the mechanisms behind chemical susceptibility differences is key to protecting sensitive populations. However, elucidating gene-environment interactions (GxE) presents a daunting challenge. While mammalian models have proven useful, problems with scalability to an enormous chemical exposome and clinical translation faced by all models remain; therefore, alternatives are needed. Zebrafish (Danio rerio) have emerged as an excellent model for investigating GxE. This study used a combined bioinformatic and experimental approach to probe the mechanisms underlying chemical susceptibility differences in a genetically diverse zebrafish population. Starting from high-throughput screening (HTS) data, a genome-wide association study (GWAS) using embryonic fish exposed to 0.6 μM Abamectin revealed significantly different effects between individuals. A hypervariable region with two distinct alleles–one with G at the SNP locus (GG) and one with a T and the 16 bp deletion (TT)–associated with differential susceptibility was found. Sensitive fish had significantly lower sox7 expression. Due to their location and the observed expression differences, we hypothesized that these sequences differentially regulate sox7. A luciferase reporter gene assay was used to test if these sequences, alone, could lead to expression differences. The TT allele showed significantly lower expression than the GG allele in MCF-7 cells. To better understand the mechanism behind these expression differences, predicted transcription factor binding differences between individuals were compared in silico, and several putative binding differences were identified. EMSA was used to test for binding differences in whole embryo protein lysate to investigate these TF binding predictions. We confirmed that the GG sequence is bound to protein in zebrafish. Through a competition EMSA using an untagged oligo titration, we confirmed that the GG oligo had a higher binding affinity than the TT oligo, explaining the observed expression differences. This study identified differential susceptibility to chemical exposure in a genetically diverse population, then identified a plausible mechanism behind those differences from a genetic to molecular level. Thus, an HTS-compatible zebrafish model is valuable and adaptable in identifying GxE mechanisms behind susceptibility differences to chemical exposure.
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Affiliation(s)
- Dylan J. Wallis
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Jane La Du
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Preethi Thunga
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Daniel Elson
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Lisa Truong
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Siva K. Kolluri
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Robyn L. Tanguay
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - David M. Reif
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
- *Correspondence: David M. Reif,
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12
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Janik AJ, Whipps CM. Differences in susceptibility to Mycobacterium chelonae in zebrafish (Danio rerio) lines commonly used in scientific research. JOURNAL OF FISH DISEASES 2022; 45:435-443. [PMID: 34905233 PMCID: PMC8828697 DOI: 10.1111/jfd.13572] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/13/2021] [Accepted: 10/17/2021] [Indexed: 06/14/2023]
Abstract
Mycobacteriosis is one of the most common diseases encountered in laboratory zebrafish. These infections can present a problem to researchers using zebrafish because they may introduce unknown experimental variables. Whilst differences in severity of infections between species of Mycobacterium infecting zebrafish have been well documented, little is known about differences in susceptibility between zebrafish lines. Previous surveys have found higher prevalence in the TU zebrafish line relative to other lines, suggesting that there may be underlying genetic differences in susceptibility. This study investigates Mycobacterium chelonae H1E2-GFP infections in four different zebrafish lines commonly used in research (AB, 5D, casper and TU). Fish were exposed to a labelled (green-fluorescent protein (GFP)) strain of M. chelonae by intraperitoneal injection, and infection status was evaluated after 10 weeks. Visualization of GFP in euthanized fish and histology were used as endpoints. In GFP images, severity was assessed by image analysis, and in histological sections, counts of granulomas containing acid-fast bacteria were used. Results indicated differences in severity of infections between lines, but no significant differences in prevalence.
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Affiliation(s)
- Andrew J Janik
- SUNY-ESF, State University of New York College of Environmental Science and Forestry, Environmental and Forest Biology, Syracuse, NY, USA
| | - Christopher M Whipps
- SUNY-ESF, State University of New York College of Environmental Science and Forestry, Environmental and Forest Biology, Syracuse, NY, USA
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13
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Bourgeois JS, Smith CM, Ko DC. These Are the Genes You're Looking For: Finding Host Resistance Genes. Trends Microbiol 2021; 29:346-362. [PMID: 33004258 PMCID: PMC7969353 DOI: 10.1016/j.tim.2020.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Humanity's ongoing struggle with new, re-emerging and endemic infectious diseases serves as a frequent reminder of the need to understand host-pathogen interactions. Recent advances in genomics have dramatically advanced our understanding of how genetics contributes to host resistance or susceptibility to bacterial infection. Here we discuss current trends in defining host-bacterial interactions at the genome-wide level, including screens that harness CRISPR/Cas9 genome editing, natural genetic variation, proteomics, and transcriptomics. We report on the merits, limitations, and findings of these innovative screens and discuss their complementary nature. Finally, we speculate on future innovation as we continue to progress through the postgenomic era and towards deeper mechanistic insight and clinical applications.
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Affiliation(s)
- Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Duke Human Vaccine Institute, School of Medicine, Duke University Durham, NC, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC, USA.
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14
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Suurväli J, Whiteley AR, Zheng Y, Gharbi K, Leptin M, Wiehe T. The Laboratory Domestication of Zebrafish: From Diverse Populations to Inbred Substrains. Mol Biol Evol 2021; 37:1056-1069. [PMID: 31808937 PMCID: PMC7086173 DOI: 10.1093/molbev/msz289] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of “personalized medicine.” Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behavior, and physiology, for modeling diseases, and for testing pharmaceutic compounds in vivo. However, all of these strains are derived from artificial bottleneck events and therefore are likely to represent only a fraction of the genetic diversity present within the species. Here, we use restriction site-associated DNA sequencing to genetically characterize wild populations of zebrafish from India, Nepal, and Bangladesh, and to compare them to previously published data on four common laboratory strains. We measured nucleotide diversity, heterozygosity, and allele frequency spectra, and find that wild zebrafish are much more diverse than laboratory strains. Further, in wild zebrafish, there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are most distinct from all other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic, physiological, pharmaceutic, and evolutionary studies in Danio rerio.
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Affiliation(s)
- Jaanus Suurväli
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Andrew R Whiteley
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Yichen Zheng
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Maria Leptin
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Thomas Wiehe
- Institute for Genetics, University of Cologne, Cologne, Germany
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15
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Gui Z, Wu L, Cai H, Mu L, Yu JF, Fu SY, Si XY. Genetic diversity analysis of Dermacentor nuttalli within Inner Mongolia, China. Parasit Vectors 2021; 14:131. [PMID: 33648549 PMCID: PMC7923491 DOI: 10.1186/s13071-021-04625-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/03/2021] [Indexed: 11/18/2022] Open
Abstract
Background Ticks (Arthropoda, Ixodida), after mosquitoes, are the second most prevalent vector of infectious diseases. They are responsible for spreading a multitude of pathogens and threatening the health and welfare of animals and human beings. However, given the history of tick-borne pathogen infections in the Inner Mongolia Autonomous Region of China, surprisingly, neither the genetic diversity nor the spatial distribution of haplotypes within ticks has been studied. Methods We characterized the haplotype distribution of Dermacentor nuttalli in four main pastoral areas of the Inner Mongolia Autonomous Region, by sampling 109 individuals (recovered from sheep) in April–August 2019. The 16S rRNA gene, cytochrome c oxidase subunit I (COI), and the internal transcribed spacer 2 region (ITS2) were amplified and sequenced from extracted DNA. Results Twenty-six haplotypes were identified using 16S rRNA sequences, 57 haplotypes were identified with COI sequences, and 75 haplotypes were identified with ITS2 sequences. Among the three genes, total haplotype diversity was greater than 0.7, while total nucleotide diversity was greater than 0.06. Neutrality tests revealed a significantly negative Tajima’s D result, while Fu's Fs was not significantly positive. Fixation index values (FST) indicated that the degree of genetic differentiation among some sampled populations was small, while for others it was moderate. Analysis of molecular variance (AMOVA) revealed that the variation within populations was greater than that among populations. The mismatch analysis of D. nuttalli exhibited double peaks. Conclusion The genetic diversity of D. nuttalli populations in our region can likely adapt to different geographical environments, thereby leading to genetic diversity, and creating genetic differentiation among different populations. However, genetic differentiation is cryptic and does not form a pedigree geographical structure.![]()
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Affiliation(s)
- Zheng Gui
- Graduate School, Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, China
| | - Lin Wu
- Graduate School, Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, China
| | - Hao Cai
- Graduate School, Inner Mongolia Medical University, Hohhot, 010059, Inner Mongolia, China
| | - Lan Mu
- Department of Parasitology, Inner Mongolia Medical University, Hohhot, 010110, Inner Mongolia, China.
| | - Jing-Feng Yu
- Department of Parasitology, Inner Mongolia Medical University, Hohhot, 010110, Inner Mongolia, China.
| | - Shao-Yin Fu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Science, Hohhot, 010031, Inner Mongolia, China.
| | - Xiao-Yan Si
- Inner Mongolia Center for Disease Control and Prevention, Hohhot, 010000, Inner Mongolia, China.
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16
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Alyenbaawi H, Kanyo R, Locskai LF, Kamali-Jamil R, DuVal MG, Bai Q, Wille H, Burton EA, Allison WT. Seizures are a druggable mechanistic link between TBI and subsequent tauopathy. eLife 2021; 10:58744. [PMID: 33527898 PMCID: PMC7853719 DOI: 10.7554/elife.58744] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 12/07/2020] [Indexed: 12/18/2022] Open
Abstract
Traumatic brain injury (TBI) is a prominent risk factor for dementias including tauopathies like chronic traumatic encephalopathy (CTE). The mechanisms that promote prion-like spreading of Tau aggregates after TBI are not fully understood, in part due to lack of tractable animal models. Here, we test the putative role of seizures in promoting the spread of tauopathy. We introduce ‘tauopathy reporter’ zebrafish expressing a genetically encoded fluorescent Tau biosensor that reliably reports accumulation of human Tau species when seeded via intraventricular brain injections. Subjecting zebrafish larvae to a novel TBI paradigm produced various TBI features including cell death, post–traumatic seizures, and Tau inclusions. Bath application of dynamin inhibitors or anticonvulsant drugs rescued TBI-induced tauopathy and cell death. These data suggest a role for seizure activity in the prion-like seeding and spreading of tauopathy following TBI. Further work is warranted regarding anti-convulsants that dampen post-traumatic seizures as a route to moderating subsequent tauopathy. Traumatic brain injury can result from direct head concussions, rapid head movements, or a blast wave generated by an explosion. Traumatic brain injury often causes seizures in the short term and is a risk factor for certain dementias, including Alzheimer’s disease and chronic traumatic encephalopathy in the long term. A protein called Tau undergoes a series of chemical changes in these dementias that makes it accumulate, form toxic filaments and kill neurons. The toxic abnormal Tau proteins are initially found only in certain regions of the brain, but they spread as the disease progresses. Previous studies in Alzheimer’s disease and other diseases where Tau proteins are abnormal suggest that Tau can spread between neighboring neurons and this can be promoted by neuron activity. However, scientists do not know whether similar mechanisms are at work following traumatic brain injury. Given that seizures are very common following traumatic brain injury, could they be partly responsible for promoting dementia? To investigate this, researchers need animal models in which they can measure neural activity associated with traumatic brain injury and observe the spread of abnormal Tau proteins. Alyenbaawi et al. engineered zebrafish so that their Tau proteins would be fluorescent, making it possible to track the accumulation of aggregated Tau protein in the brain. Next, they invented a simple way to perform traumatic brain injury on zebrafish larvae by using a syringe to produce a pressure wave. After this procedure, many of the fish exhibited features consistent with progression towards dementia, and seizure-like behaviors. The results showed that post-traumatic seizures are linked to the spread of aggregates of abnormal Tau following traumatic brain injury. Alyenbaawi et al. also found that anticonvulsant drugs can lower the levels of abnormal Tau proteins in neurons, preventing cell death, and could potentially ameliorate dementias associated with traumatic brain injury. These drugs are already being used to prevent post-traumatic epilepsy, but more research is needed to confirm whether they reduce the risk or severity of Tau-related neurodegeneration.
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Affiliation(s)
- Hadeel Alyenbaawi
- Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Canada.,Majmaah University, Majmaah, Saudi Arabia
| | - Richard Kanyo
- Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Laszlo F Locskai
- Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Razieh Kamali-Jamil
- Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton, Canada.,Department of Biochemistry, University of Alberta, Edmonton, Canada
| | - Michèle G DuVal
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Qing Bai
- Department of Neurology, University of Pittsburgh, Pittsburgh, United States
| | - Holger Wille
- Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton, Canada.,Department of Biochemistry, University of Alberta, Edmonton, Canada
| | - Edward A Burton
- Department of Neurology, University of Pittsburgh, Pittsburgh, United States.,Geriatric Research, Education and Clinical Center, Pittsburgh VA Healthcare System, Pittsburgh, United States
| | - W Ted Allison
- Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Canada
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17
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Demin KA, Taranov AS, Ilyin NP, Lakstygal AM, Volgin AD, de Abreu MS, Strekalova T, Kalueff AV. Understanding neurobehavioral effects of acute and chronic stress in zebrafish. Stress 2021; 24:1-18. [PMID: 32036720 DOI: 10.1080/10253890.2020.1724948] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Stress is a common cause of neuropsychiatric disorders, evoking multiple behavioral, endocrine and neuro-immune deficits. Animal models have been extensively used to understand the mechanisms of stress-related disorders and to develop novel strategies for their treatment. Complementing rodent and clinical studies, the zebrafish (Danio rerio) is one of the most important model organisms in biomedicine. Rapidly becoming a popular model species in stress neuroscience research, zebrafish are highly sensitive to both acute and chronic stress, and show robust, well-defined behavioral and physiological stress responses. Here, we critically evaluate the utility of zebrafish-based models for studying acute and chronic stress-related CNS pathogenesis, assess the advantages and limitations of these aquatic models, and emphasize their relevance for the development of novel anti-stress therapies. Overall, the zebrafish emerges as a powerful and sensitive model organism for stress research. Although these fish generally display evolutionarily conserved behavioral and physiological responses to stress, zebrafish-specific aspects of neurogenesis, neuroprotection and neuro-immune responses may be particularly interesting to explore further, as they may offer additional insights into stress pathogenesis that complement (rather than merely replicate) rodent findings. Compared to mammals, zebrafish models are also characterized by increased availability of gene-editing tools and higher throughput of drug screening, thus being able to uniquely empower translational research of genetic determinants of stress and resilience, as well as to foster innovative CNS drug discovery and the development of novel anti-stress therapies.
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Affiliation(s)
- Konstantin A Demin
- Institute of Experimental Biomedicine, Almazov National Medical Research Center, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
- Laboratory of Biological Psychiatry, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Alexander S Taranov
- Laboratory of Biological Psychiatry, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Preclinical Bioscreening, Granov Russian Research Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia
| | - Nikita P Ilyin
- Laboratory of Biological Psychiatry, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Preclinical Bioscreening, Granov Russian Research Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia
| | - Anton M Lakstygal
- Laboratory of Biological Psychiatry, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Preclinical Bioscreening, Granov Russian Research Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia
| | - Andrey D Volgin
- Laboratory of Preclinical Bioscreening, Granov Russian Research Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia
| | - Murilo S de Abreu
- Bioscience Institute, University of Passo Fundo, Passo Fundo, Brazil
- The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA
| | - Tatyana Strekalova
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Maastricht University, Maastricht, The Netherlands
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - Allan V Kalueff
- School of Pharmacy, Southwest University, Chongqing, China
- Ural Federal University, Ekaterinburg, Russia
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18
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De Oliveira J, Chadili E, Turies C, Brion F, Cousin X, Hinfray N. A comparison of behavioral and reproductive parameters between wild-type, transgenic and mutant zebrafish: Could they all be considered the same "zebrafish" for reglementary assays on endocrine disruption? Comp Biochem Physiol C Toxicol Pharmacol 2021; 239:108879. [PMID: 32877737 DOI: 10.1016/j.cbpc.2020.108879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 12/19/2022]
Abstract
Transgenic zebrafish models are efficiently used to study the effects of endocrine disrupting chemicals (EDC); thereby informing on their mechanisms of action. However, given the reported differences between zebrafish strains at the genetical, physiological and behavioral levels; care should be taken before using these transgenic models for EDC testing. In the present study, we undertook a set of experiments in different transgenic and/or mutant zebrafish strains of interest for EDC testing: casper, cyp19a1a-eGFP, cyp19a1a-eGFP-casper, cyp11c1-eGFP, cyp11c1-eGFP-casper. Some behavioral traits, and some biochemical and reproductive physiological endpoints commonly used in EDC testing were assessed and compared to those obtained in WT AB zebrafish to ensure that transgene insertion and/or mutations do not negatively modify basal reproductive physiology or behavior of the fish. Behavioral traits considered as anxiety and sociality have been monitored. Sociality was evaluated by monitoring the time spent near congeners in a shuttle box while anxiety was evaluated using the Novel tank diving test. No critical difference was observed between strains for either sociality or anxiety level. Concerning reproduction, no significant difference in the number of eggs laid per female, in the viability of eggs or in the female circulating VTG concentrations was noted between the 5 transgenic/mutants and the WT AB zebrafish studied. In summary, the transgene insertion and the mutations had no influence on the endpoints measured in basal conditions. These results were a prerequisite to the use of these transgenic/mutant models for EDC testing. Next step will be to determine the sensitivity of these biological models to chemical exposure to accurately validate their use in existing fish assays for EDC testing.
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Affiliation(s)
- Julie De Oliveira
- INERIS, Unité d'écotoxicologie in vitro et in vivo, UMR I-02 SEBIO, Verneuil-en-Halatte, France
| | - Edith Chadili
- INERIS, Unité d'écotoxicologie in vitro et in vivo, UMR I-02 SEBIO, Verneuil-en-Halatte, France
| | - Cyril Turies
- INERIS, Unité d'écotoxicologie in vitro et in vivo, UMR I-02 SEBIO, Verneuil-en-Halatte, France
| | - François Brion
- INERIS, Unité d'écotoxicologie in vitro et in vivo, UMR I-02 SEBIO, Verneuil-en-Halatte, France
| | - Xavier Cousin
- MARBEC Univ. Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France; Univ. Paris-Saclay, AgroParisTech, INRAE, GABI, France
| | - Nathalie Hinfray
- INERIS, Unité d'écotoxicologie in vitro et in vivo, UMR I-02 SEBIO, Verneuil-en-Halatte, France.
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19
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A fish is not a mouse: understanding differences in background genetics is critical for reproducibility. Lab Anim (NY) 2020; 50:19-25. [PMID: 33268901 DOI: 10.1038/s41684-020-00683-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023]
Abstract
Poorly controlled background genetics in animal models contributes to the lack of reproducibility that is increasingly recognized in biomedical research. The laboratory zebrafish, Danio rerio, has been an important model organism for decades in many research areas, yet inbred strains and traditionally managed outbred stocks are not available for this species. Sometimes incorrectly referred to as 'inbred strains' or 'strains', zebrafish wild-type lines possess background genetics that are often not well characterized, and breeding practices for these lines have not been consistent over time or among institutions. In this Perspective, we trace key milestones in the history of one of the most widely used genetic backgrounds, the AB line, to illustrate the dynamic complexity within an example background that is largely invisible when reading the scientific literature. Failure to adequately control for genetic background compromises the validity of experimental outcomes. We therefore propose that authors provide as much specific detail about the origin and genetic makeup of zebrafish lines as is reasonable and possible, and that the terms used to describe background genetics be applied in a way that is consistent with other fish and mammalian model organisms. We strongly encourage the adoption of genetic monitoring for the characterization of existing zebrafish lines, to help detect genetic contamination in breeding colonies and to verify the level of genetic heterogeneity in breeding colonies over time. Careful attention to background genetics will improve transparency and reproducibility, therefore improving the utility of the zebrafish as a model organism.
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20
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Saralahti AK, Uusi-Mäkelä MIE, Niskanen MT, Rämet M. Integrating fish models in tuberculosis vaccine development. Dis Model Mech 2020; 13:13/8/dmm045716. [PMID: 32859577 PMCID: PMC7473647 DOI: 10.1242/dmm.045716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis is a chronic infection by Mycobacterium tuberculosis that results in over 1.5 million deaths worldwide each year. Currently, there is only one vaccine against tuberculosis, the Bacillus Calmette–Guérin (BCG) vaccine. Despite widespread vaccination programmes, over 10 million new M. tuberculosis infections are diagnosed yearly, with almost half a million cases caused by antibiotic-resistant strains. Novel vaccination strategies concentrate mainly on replacing BCG or boosting its efficacy and depend on animal models that accurately recapitulate the human disease. However, efforts to produce new vaccines against an M. tuberculosis infection have encountered several challenges, including the complexity of M. tuberculosis pathogenesis and limited knowledge of the protective immune responses. The preclinical evaluation of novel tuberculosis vaccine candidates is also hampered by the lack of an appropriate animal model that could accurately predict the protective effect of vaccines in humans. Here, we review the role of zebrafish (Danio rerio) and other fish models in the development of novel vaccines against tuberculosis and discuss how these models complement the more traditional mammalian models of tuberculosis. Summary: In this Review, we discuss how zebrafish (Danio rerio) and other fish models can complement the more traditional mammalian models in the development of novel vaccines against tuberculosis.
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Affiliation(s)
- Anni K Saralahti
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere FI-33014, Finland
| | - Meri I E Uusi-Mäkelä
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere FI-33014, Finland
| | - Mirja T Niskanen
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere FI-33014, Finland
| | - Mika Rämet
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere FI-33014, Finland .,Vaccine Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere FI-33014, Finland.,PEDEGO Research Unit, Medical Research Center, University of Oulu, Oulu FI-90014, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu FI-90029, Finland
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21
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Souder JP, Gorelick DA. ahr2, But Not ahr1a or ahr1b, Is Required for Craniofacial and Fin Development and TCDD-dependent Cardiotoxicity in Zebrafish. Toxicol Sci 2020; 170:25-44. [PMID: 30907958 DOI: 10.1093/toxsci/kfz075] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that binds environmental toxicants and regulates gene expression. AHR also regulates developmental processes, like craniofacial development and hematopoiesis, in the absence of environmental exposures. Zebrafish have 3 paralogs of AHR: ahr1a, ahr1b, and ahr2. Adult zebrafish with mutations in ahr2 exhibited craniofacial and fin defects. However, the degree to which ahr1a and ahr1b influence ahr2 signaling and contribute to fin and craniofacial development are not known. We compared morphology of adult ahr2 mutants and ahr1a;ahr1b single and double mutant zebrafish. We found that ahr1a;ahr1b single and double mutants were morphologically normal whereas ahr2 mutant zebrafish demonstrated fin and craniofacial malformations. At 5 days post fertilization, both ahr1a;ahr1b and ahr2 mutant larvae were normal, suggesting that adult phenotypes are due to defects in maturation or maintenance. Next, we analyzed the function of zebrafish AHRs activated by environmental ligands. The prototypical AHR ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), induces toxicity in humans and rodents via AHR and causes cardiotoxicity in zebrafish embryos. It has been shown that embryos with mutations in ahr2 are resistant to TCDD toxicity, yet it is unclear whether ahr1 receptors are required. Furthermore, though AHR was shown to interact with estrogen receptor alpha following TCDD treatment, it is not known whether this interaction is constitutive or context-dependent. To determine whether estrogen receptors are constitutive cofactors for AHR signaling, we used genetic and pharmacologic techniques to analyze TCDD-dependent toxicity in estrogen receptor and ahr mutant embryos. We found that embryos with mutations in ahr1a;ahr1b or estrogen receptor genes are susceptible to TCDD toxicity whereas ahr2 mutant embryos are TCDD-resistant. Moreover, pharmacologic blockade of nuclear estrogen receptors failed to prevent TCDD toxicity. These findings suggest that ahr1 genes do not have overlapping functions with ahr2 in fin and craniofacial development or TCDD-dependent toxicity, and that estrogen receptors are not constitutive partners of ahr2.
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Affiliation(s)
- Jaclyn P Souder
- Medical Scientist Training Program & Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, 35294.,Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, 77030
| | - Daniel A Gorelick
- Medical Scientist Training Program & Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, 35294.,Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, 77030
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22
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Bandara SB, Carty DR, Singh V, Harvey DJ, Vasylieva N, Pressly B, Wulff H, Lein PJ. Susceptibility of larval zebrafish to the seizurogenic activity of GABA type A receptor antagonists. Neurotoxicology 2019; 76:220-234. [PMID: 31811871 DOI: 10.1016/j.neuro.2019.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 01/18/2023]
Abstract
Previous studies demonstrated that pentylenetetrazole (PTZ), a GABA type A receptor (GABAAR) antagonist, elicits seizure-like phenotypes in larval zebrafish (Danio rerio). Here, we determined whether the GABAAR antagonists, tetramethylenedisulfotetramine (TETS) and picrotoxin (PTX), both listed as credible chemical threat agents, similarly trigger seizures in zebrafish larvae. Larvae of three, routinely used laboratory zebrafish lines, Tropical 5D, NHGRI and Tupfel long fin, were exposed to varying concentrations of PTZ (used as a positive control), PTX or TETS for 20 min at 5 days post fertilization (dpf). Acute exposure to PTZ, PTX or TETS triggered seizure behavior in the absence of morbidity or mortality. While the concentration-effect relationship for seizure behavior was similar across zebrafish lines for each GABAAR antagonist, significantly less TETS was required to trigger seizures relative to PTX or PTZ. Recordings of extracellular field potentials in the optic tectum of 5 dpf Tropical 5D zebrafish confirmed that all three GABAAR antagonists elicited extracellular spiking patterns consistent with seizure activity, although the pattern varied between chemicals. Post-exposure treatment with the GABAAR positive allosteric modulators (PAMs), diazepam, midazolam or allopregnanolone, attenuated seizure behavior and activity but did not completely normalize electrical field recordings in the optic tectum. These data are consistent with observations of seizure responses in mammalian models exposed to these same GABAAR antagonists and PAMs, further validating larval zebrafish as a higher throughput-screening platform for antiseizure therapeutics, and demonstrating its appropriateness for identifying improved countermeasures for TETS and other convulsant chemical threat agents that trigger seizures via GABAAR antagonism.
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Affiliation(s)
- Suren B Bandara
- Department of Molecular Biosciences, University of California, Davis, School of Veterinary Medicine, Davis, CA 95616, United States.
| | - Dennis R Carty
- Department of Molecular Biosciences, University of California, Davis, School of Veterinary Medicine, Davis, CA 95616, United States.
| | - Vikrant Singh
- Department of Pharmacology, University of California, Davis, School of Medicine, Davis, CA 95616, United States.
| | - Danielle J Harvey
- Department of Public Health Sciences, University of California, Davis, School of Medicine, Davis, CA 95616, United States.
| | - Natalia Vasylieva
- Department of Entomology, University of California, Davis, College of Agricultural and Environmental Sciences, Davis, CA 95616, United States.
| | - Brandon Pressly
- Department of Pharmacology, University of California, Davis, School of Medicine, Davis, CA 95616, United States.
| | - Heike Wulff
- Department of Pharmacology, University of California, Davis, School of Medicine, Davis, CA 95616, United States.
| | - Pamela J Lein
- Department of Molecular Biosciences, University of California, Davis, School of Veterinary Medicine, Davis, CA 95616, United States.
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23
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Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins. Sci Data 2019; 6:190011. [PMID: 30747917 PMCID: PMC6371892 DOI: 10.1038/sdata.2019.11] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022] Open
Abstract
Sequential window acquisition of all theoretical mass spectra (SWATH-MS) requires a spectral library to extract quantitative measurements from the mass spectrometry data acquired in data-independent acquisition mode (DIA). Large combined spectral libraries containing SWATH assays have been generated for humans and several other organisms, but so far no publicly available library exists for measuring the proteome of zebrafish, a rapidly emerging model system in biomedical research. Here, we present a large zebrafish SWATH spectral library to measure the abundance of 104,185 proteotypic peptides from 10,405 proteins. The library includes proteins expressed in 9 different zebrafish tissues (brain, eye, heart, intestine, liver, muscle, ovary, spleen, and testis) and provides an important new resource to quantify 40% of the protein-coding zebrafish genes. We employ this resource to quantify the proteome across brain, muscle, and liver and characterize divergent expression levels of paralogous proteins in different tissues. Data are available via ProteomeXchange (PXD010876, PXD010869) and SWATHAtlas (PASS01237).
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24
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Bao W, Volgin AD, Alpyshov ET, Friend AJ, Strekalova TV, de Abreu MS, Collins C, Amstislavskaya TG, Demin KA, Kalueff AV. Opioid Neurobiology, Neurogenetics and Neuropharmacology in Zebrafish. Neuroscience 2019; 404:218-232. [PMID: 30710667 DOI: 10.1016/j.neuroscience.2019.01.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 01/28/2023]
Abstract
Despite the high prevalence of medicinal use and abuse of opioids, their neurobiology and mechanisms of action are not fully understood. Experimental (animal) models are critical for improving our understanding of opioid effects in vivo. As zebrafish (Danio rerio) are increasingly utilized as a powerful model organism in neuroscience research, mounting evidence suggests these fish as a useful tool to study opioid neurobiology. Here, we discuss the zebrafish opioid system with specific focus on opioid gene expression, existing genetic models, as well as its pharmacological and developmental regulation. As many human brain diseases involve pain and aberrant reward, we also summarize zebrafish models relevant to opioid regulation of pain and addiction, including evidence of functional interplay between the opioid system and central dopaminergic and other neurotransmitter mechanisms. Additionally, we critically evaluate the limitations of zebrafish models for translational opioid research and emphasize their developing utility for improving our understanding of evolutionarily conserved mechanisms of pain-related, addictive, affective and other behaviors, as well as for fostering opioid-related drug discovery.
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Affiliation(s)
- Wandong Bao
- School of Pharmacy and School of Life Sciences, Southwest University, Chongqing, China
| | - Andrey D Volgin
- Military Medical Academy, St. Petersburg, Russia; Institute of Experimental Medicine, Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia; Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia
| | - Erik T Alpyshov
- School of Pharmacy and School of Life Sciences, Southwest University, Chongqing, China
| | - Ashton J Friend
- Tulane University School of Science and Engineering, New Orleans, LA, USA; The International Zebrafish Neuroscience Research Consortium, New Orleans, LA, USA
| | - Tatyana V Strekalova
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Laboratory of Psychiatric Neurobiology and Department of Normal Physiology, Moscow, Russia; Department of Neuroscience, Maastricht University, Maastricht, Netherlands; Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - Murilo S de Abreu
- The International Zebrafish Neuroscience Research Consortium, New Orleans, LA, USA; Bioscience Institute, University of Passo Fundo (UPF), Passo Fundo, RS, Brazil
| | - Christopher Collins
- ZENEREI Research Center, Slidell, LA, USA; The International Zebrafish Neuroscience Research Consortium, New Orleans, LA, USA
| | - Tamara G Amstislavskaya
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia; The International Zebrafish Neuroscience Research Consortium, New Orleans, LA, USA
| | - Konstantin A Demin
- Institute of Experimental Medicine, Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia; Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Allan V Kalueff
- School of Pharmacy and School of Life Sciences, Southwest University, Chongqing, China; Institute of Experimental Medicine, Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia; Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Ural Federal University, Ekaterinburg, Russia; Granov Russian Research Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia; Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia; ZENEREI Research Center, Slidell, LA, USA; The International Zebrafish Neuroscience Research Consortium, New Orleans, LA, USA.
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25
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Hamm JT, Ceger P, Allen D, Stout M, Maull EA, Baker G, Zmarowski A, Padilla S, Perkins E, Planchart A, Stedman D, Tal T, Tanguay RL, Volz DC, Wilbanks MS, Walker NJ. Characterizing sources of variability in zebrafish embryo screening protocols. ALTEX 2018; 36:103-120. [PMID: 30415271 PMCID: PMC10424490 DOI: 10.14573/altex.1804162] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/30/2018] [Indexed: 11/23/2022]
Abstract
There is a need for fast, efficient, and cost-effective hazard identification and characterization of chemical hazards. This need is generating increased interest in the use of zebrafish embryos as both a screening tool and an alternative to mammalian test methods. A Collaborative Workshop on Aquatic Models and 21st Century Toxicology identified the lack of appropriate and consistent testing protocols as a challenge to the broader application of the zebrafish embryo model. The National Toxicology Program established the Systematic Evaluation of the Application of Zebrafish in Toxicology (SEAZIT) initiative to address the lack of consistent testing guidelines and identify sources of variability for zebrafish-based assays. This report summarizes initial SEAZIT information-gathering efforts. Investigators in academic, government, and industry laboratories that routinely use zebrafish embryos for chemical toxicity testing were asked about their husbandry practices and standard protocols. Information was collected about protocol components including zebrafish strains, feed, system water, disease surveillance, embryo exposure conditions, and endpoints. Literature was reviewed to assess issues raised by the investigators. Interviews revealed substantial variability across design parameters, data collected, and analysis procedures. The presence of the chorion and renewal of exposure media (static versus static-renewal) were identified as design parameters that could potentially influence study outcomes and should be investigated further with studies to determine chemical uptake from treatment solution into embryos. The information gathered in this effort provides a basis for future SEAZIT activities to promote more consistent practices among researchers using zebrafish embryos for toxicity evaluation.
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Affiliation(s)
- Jon T Hamm
- Integrated Laboratory Systems, Research Triangle Park, NC, USA
| | - Patricia Ceger
- Integrated Laboratory Systems, Research Triangle Park, NC, USA
| | - David Allen
- Integrated Laboratory Systems, Research Triangle Park, NC, USA
| | - Matt Stout
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Elizabeth A Maull
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Greg Baker
- Battelle, Life Sciences Research, Columbus, OH, USA
| | | | - Stephanie Padilla
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Edward Perkins
- United States Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Antonio Planchart
- Department of Biological Sciences and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | | | - Tamara Tal
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Robert L Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - David C Volz
- Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Mitch S Wilbanks
- United States Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Nigel J Walker
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
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26
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Holden LA, Wilson C, Heineman Z, Dobrinski KP, Brown KH. An Interrogation of Shared and Unique Copy Number Variants Across Genetically Distinct Zebrafish Strains. Zebrafish 2018; 16:29-36. [PMID: 30418105 DOI: 10.1089/zeb.2018.1644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Zebrafish (Danio rerio) are a widely utilized model system for human disorders, but common laboratory strains have distinct behavioral and physiological differences. Accompanying these known strain differences, commonly used "wildtype" zebrafish strains have both shared and unique suites of single nucleotide polymorphisms and copy number variants (CNVs). Despite this, genomic variation is often ignored in study design, and the actual strain used is often not adequately reported. The goal of this study was to assess CNVs across three common laboratory strains of zebrafish-AB, Tubingen (TU), and WIK-and provide these data as a tool for the zebrafish community. Herein we identified 1351 CNV regions within the most recent genome assembly (GRCz11) covering 1.9% of the zebrafish genome (31.7 Mb). CNVs were found across all chromosomes, and 2200 genes (5121 transcripts) lie within ±5 kb of identified CNVs, pointing to likely cis regulatory actions of CNVs on nearby gene neighbors. We have created a Public Session accessible on the UCSC Genome Browser to view CNVs from this study titled "danRer11 zebrafish CNV across strains" as a tool for the zebrafish community.
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Affiliation(s)
- Lindsay A Holden
- 1 Department of Biology, Portland State University, Portland, Oregon
| | - Charles Wilson
- 1 Department of Biology, Portland State University, Portland, Oregon
| | - Zachary Heineman
- 1 Department of Biology, Portland State University, Portland, Oregon
| | | | - Kim H Brown
- 1 Department of Biology, Portland State University, Portland, Oregon
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27
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Kent ML, Gaulke CA, Watral V, Sharpton TJ. Pseudocapillaria tomentosa in laboratory zebrafish Danio rerio: patterns of infection and dose response. DISEASES OF AQUATIC ORGANISMS 2018; 131:121-131. [PMID: 30460918 PMCID: PMC6474349 DOI: 10.3354/dao03286] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Parasites in wild populations almost always exhibit aggregation (overdispersion), in which relatively few hosts are infected with high numbers of the parasites. This pattern of infection has also been observed in laboratory studies, where many of the sources of natural variation are removed. Pseudocapillaria tomentosa (Nematoda) is common in zebrafish (Danio rerio) facilities. We describe here patterns of infections in zebrafish experimentally infected with larvated P. tomentosa eggs in various trials with defined numbers of eggs. One trial with eggs delivered in a gelatin diet is also included. Fish were exposed at 25, 75, and 200 eggs fish-1, and the minimal infectious dose was estimated to be 1.5 eggs fish-1. The ID50 (50% infective dose) was calculated to be 17.5 eggs fish-1. We also included data from a trial and 2 previously published experiments with undefined doses in which zebrafish were exposed to infectious water and detritus from a tank that previously contained infected fish. All doses resulted in a high prevalence of infection (>70%), except at the 25 eggs fish-1 dose, where the prevalence was 43-46%. Mean abundance of worms corresponded to dose, from 0.57 worms fish-1 at 25 eggs fish-1 to 7 worms fish-1 at 200 eggs fish-1. Variance to mean ratios (V/M) and the k parameters showed aggregation across the 8 separate trials, including the gelatin diet. Aggregation increased with increased parasite abundance. Given the consistent observation of aggregation across our experiments, the zebrafish/P. tomentosa system provides a potentially robust, high-throughput model to investigate factors that influence differences in host susceptibility within defined populations.
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Affiliation(s)
- Michael L. Kent
- Department of Microbiology, Oregon State University, Corvallis, OR 97331
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331
| | | | - Virginia Watral
- Department of Microbiology, Oregon State University, Corvallis, OR 97331
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR 97331
- Department of Statistics, Oregon State University, Corvallis, OR 97331
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28
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Rusyn I, Kleeberger SR, McAllister KA, French JE, Svenson KL. Introduction to mammalian genome special issue: the combined role of genetics and environment relevant to human disease outcomes. Mamm Genome 2018; 29:1-4. [PMID: 29460122 DOI: 10.1007/s00335-018-9740-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
| | | | | | - John E French
- UNC Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA
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29
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Li Z, Tyrpak DR, Lien CL, MacKay JA. Tunable assembly of protein-microdomains in living vertebrate embryos. ACTA ACUST UNITED AC 2018; 2. [PMID: 31840042 DOI: 10.1002/adbi.201800112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Subcellular events such as trafficking and signaling are regulated by self-assembled protein complexes inside the cell. The ability to rapidly and reversibly manipulate these protein complexes would likely enhance studies of their mechanisms and their roles in biological function and disease manifestation.[1, 2] This manuscript reports that thermally-responsive elastin-like polypeptides (ELPs) linked to fluorescent proteins can regulate the self-assembly and disassembly of protein microdomains within the individual cells of zebrafish embryos. By exploring a library of fluorescent ELP proteins, this reports demonstrates that ELPs can co-assemble different fluorescent proteins inside of embryos. By tuning ELP length and sequence, fluorescent protein microdomains can be assembled at different temperatures, in varying sizes, or for desired periods of time. For the first time in a multicellular living embryo, these studies demonstrate that temperature-mediated ELP assembly can reversibly manipulate assembly of subcellular protein complexes, which may have applications in the study and manipulation of in vivo biological functions.
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Affiliation(s)
- Zhe Li
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, Los Angeles, CA 90089, USA
| | - David R Tyrpak
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, Los Angeles, CA 90089, USA
| | - Ching-Ling Lien
- The Saban Research Institute,Children's Hospital Los Angeles, Department of Surgery, Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA Los Angeles, CA 90027, USA
| | - J Andrew MacKay
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, Los Angeles, CA 90089, USA
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30
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Balik-Meisner M, Truong L, Scholl EH, La Du JK, Tanguay RL, Reif DM. Elucidating Gene-by-Environment Interactions Associated with Differential Susceptibility to Chemical Exposure. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:067010. [PMID: 29968567 PMCID: PMC6084885 DOI: 10.1289/ehp2662] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Modern societies are exposed to vast numbers of potentially hazardous chemicals. Despite demonstrated linkages between chemical exposure and severe health effects, there are limited, often conflicting, data on how adverse health effects of exposure differ across individuals. OBJECTIVES We tested the hypothesis that population variability in response to certain chemicals could elucidate a role for gene-environment interactions (GxE) in differential susceptibility. METHODS High-throughput screening (HTS) data on thousands of chemicals in genetically heterogeneous zebrafish were leveraged to identify a candidate chemical (Abamectin) with response patterns indicative of population susceptibility differences. We tested the prediction by generating genome-wide sequence data for 276 individual zebrafish displaying susceptible (Affected) vs. resistant (Unaffected) phenotypes following identical chemical exposure. RESULTS We found GxE associated with differential susceptibility in the sox7 promoter region and then confirmed gene expression differences between phenotypic response classes. CONCLUSIONS The results for Abamectin in zebrafish demonstrate that GxE associated with naturally occurring, population genetic variation play a significant role in mediating individual response to chemical exposure. https://doi.org/10.1289/EHP2662.
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Affiliation(s)
- Michele Balik-Meisner
- Bioinformatics Research Center, Center for Human Health and the Environment, Dept. of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Lisa Truong
- Sinnhuber Aquatic Research Laboratory, Dept. of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, USA
| | - Elizabeth H Scholl
- Bioinformatics Research Center, Center for Human Health and the Environment, Dept. of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Jane K La Du
- Sinnhuber Aquatic Research Laboratory, Dept. of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, USA
| | - Robert L Tanguay
- Sinnhuber Aquatic Research Laboratory, Dept. of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, USA
| | - David M Reif
- Bioinformatics Research Center, Center for Human Health and the Environment, Dept. of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
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31
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Bugel SM, Tanguay RL. Multidimensional chemobehavior analysis of flavonoids and neuroactive compounds in zebrafish. Toxicol Appl Pharmacol 2018; 344:23-34. [PMID: 29499247 DOI: 10.1016/j.taap.2018.02.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/22/2018] [Accepted: 02/25/2018] [Indexed: 12/23/2022]
Abstract
The comparative analysis of complex behavioral phenotypes is valuable as a reductionist tool for both drug discovery and defining chemical bioactivity. Flavonoids are a diverse class of chemicals that elicit robust neuroactive and hormonal actions, though bioactivity information is limited for many, particularly for neurobehavioral endpoints. Here, we used a zebrafish larval chemomotor response (LCR) bioassay to comparatively evaluate a suite of 24 flavonoids, and in addition a panel of 30 model neuroactive compounds representing diverse modes of action (e.g. caffeine, chlorpyrifos, methamphetamine, nicotine, picrotoxin). Naïve larval zebrafish were exposed to concentration ranges of each compound at 120 hour post-fertilization (hpf) and locomotor activity measured for 5 h. The model neuroactive compounds were largely behaviorally bioactive (20 of 30) with most effects phenotypic of their known modes of action. Flavonoids rapidly and broadly elicited hyperactive locomotor effects (22 of 24). Multidimensional analyses compared responses over time and identified three distinct bioactive groups of flavonoids based on efficacy and potency. Using GABAergics to modulate hyperactive responses, two flavonoids, (S)-equol and kaempferol were tested for GABAA receptor antagonism, as well as a known GABAA receptor antagonist, picrotoxin. Pharmacological intervention with positive allosteric modulators of the GABAA receptor, alfaxalone and chlormethiazole, ameliorated the hyperactive response to picrotoxin, but not for (S)-equol or kaempferol. Taken together, these studies demonstrate that flavonoids are differentially bioactive and that the chemobehavioral effects likely do not involve a GABAA receptor mediated mode of action. Overall, the integrative zebrafish platform provides a useful framework for comparatively evaluating high-content chemobehavioral data for sets of structurally- and mechanistically-related flavonoids and neuroactive compounds.
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Affiliation(s)
- Sean M Bugel
- Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR 97333, United States.
| | - Robert L Tanguay
- Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR 97333, United States.
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