Zebrafish最新文献

{"title":"AquaMaze: A Computer Vision-Based Framework for Automated Behavioral Analysis of Zebrafish in Controlled Environments.","authors":"Ali Samet Ayık, Ceren Aydoğan, Bora Deniz Yılmaz, Ayça Arslan","doi":"10.1177/15458547251408038","DOIUrl":"10.1177/15458547251408038","url":null,"abstract":"<p><p>Zebrafish (Danio rerio) have become a prominent model organism in behavioral neuroscience and pharmacological studies due to their genetic homology with humans and transparent physiology. Despite their increasing use, many laboratories still rely on manual or semi-automated tracking systems to assess behavior. There are programs commercially available, which are expensive and may not be possible to purchase for those researchers with a limited budget. Here, we introduce AquaMaze, a standalone, open-source desktop application built with PyQt5 and OpenCV, designed for real-time and post-hoc video-based behavioral tracking of zebrafish. AquaMaze computes locomotion metrics, including swim distance, speed, quadrant occupancy, and rest/activity patterns, from user-defined video inputs. The software provides intuitive visualization with heatmaps and exports detailed CSV reports, offering a scalable solution for high-throughput behavioral assays. We demonstrate the capabilities of AquaMaze using standard zebrafish locomotor activity paradigms such as the novel tank test, swim behavior test, novel object recognition, and Y-maze paradigms. In all of these tests, it is shown that AquaMaze gives reliable and consistent results. Hereby we provide a fast and cheap tool for the zebrafish behavioral experiments.</p>","PeriodicalId":94273,"journal":{"name":"Zebrafish","volume":"23 2-3","pages":"33-40"},"PeriodicalIF":1.2,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148019736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotyping at 48 hpf for Early Identification of Mutant Zebrafish Embryos.","authors":"Salome Brodd, Friedrich G Kapp","doi":"10.1177/15458547261448182","DOIUrl":"10.1177/15458547261448182","url":null,"abstract":"<p><p>The zebrafish (<i>Danio rerio</i>) is a commonly used model organism for human diseases due to its genetic similarities with humans since over 80% of genes associated with human diseases are also found in the zebrafish. For most genetic experiments, it is essential to gather tissue for genotyping in a nonlethal procedure. A common method is removing a part of the tail fin from individual adult zebrafish with a scalpel. The fin usually regenerates within 14 days, leaving the fish without permanent damage. However, larval genotyping might offer significant advantages, such as saving resources and reducing the number of research animals and enabling experiments on zebrafish embryos with a specific genotype. Here, we show a cost-efficient method for fin-clipping zebrafish embryos as early as 48 h postfertilization (hpf). When done correctly, the fin will regrow quickly, being nearly completely restored at 120 hpf. While the amount of extracted DNA is low, it is still sufficient for commonly used methods of genotyping. Embryos with the desired genotype can then be used for phenotypic or functional analyses or be raised to adulthood.</p>","PeriodicalId":94273,"journal":{"name":"Zebrafish","volume":" ","pages":"71-76"},"PeriodicalIF":1.2,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global Landscape of Zebrafish Research (2000-2025): A Bibliometric Analysis of Publication Trends, Collaboration, and Thematic Evolution.","authors":"Nebojsa Andric, Robert N Kelsh, Svetlana Fa Nedeljkovic, Kristina Pogrmic-Majkic, Daniëlle Copmans, Annelii Ny, Lyudmila Nikolova, Máté Varga, Breandán Kennedy, Matthias Carl, Melissa Marie Formosa, Katerina Goracinova, Justyna Zmorzynska, Alin Stelian Ciobica, Aleksandra Divac Rankov, Bojana Žegura, Marta Sendra, Matjaž Novak, Antonio Figueras, Beatriz Novoa García, Laia Ribas, Stefan H Fuss, Diane Fatkin, Kirsten C Sadler Edepli, Hacer Akgül Ceyhun, Robyn L Tanguay, Murilo Sander de Abreu, Allan V Kalueff, Saltuk Buğrahan Ceyhun","doi":"10.1177/15458547261448804","DOIUrl":"10.1177/15458547261448804","url":null,"abstract":"<p><p>This study presents a comprehensive bibliometric analysis of zebrafish (<i>Danio rerio</i>) research published between 2000 and 2025, based on data retrieved from the Web of Science Core Collection and analyzed using Clarivate's InCites platform. A total of 74,675 records were examined to uncover trends in publication volume, geographical and institutional distribution, international collaborations, disciplinary coverage, and thematic evolution over time. The results indicate a steady growth in zebrafish-related publications, particularly between 2000 and 2021, followed by a relative plateau. The United States and China lead in research output, with China showing rapid growth over the last decade. Collaboration networks remain dominated by a limited number of high-capacity countries, while many others, particularly those with limited infrastructure, remain underrepresented. The Cooperation in Science and Technology Member Countries also showed a noticeable decline in publication numbers following a 2021 peak. Thematic keyword analysis revealed a clear shift from early developmental biology themes-such as hindbrain and retinal development-toward emerging topics such as regeneration, oxidative stress, and toxicology. However, the findings suggest that this thematic diversification has not yet translated into widespread interdisciplinary integration. Zebrafish research remains largely anchored within classical biological disciplines, despite its increasing relevance to fields such as neuroscience, environmental health, pharmacology, and biomedical engineering. This mismatch between thematic scope and interdisciplinary adoption represents a potentially missed opportunity-especially in addressing complex global challenges. Strengthening cross-disciplinary collaborations and promoting the adoption of zebrafish in innovative, technology-driven research contexts may help unlock the full strategic potential of this versatile model organism.</p>","PeriodicalId":94273,"journal":{"name":"Zebrafish","volume":"23 2-3","pages":"77-87"},"PeriodicalIF":1.2,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148019709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Micro- and Nanoplastics Exposure and Effects on Embryonic Development and Larval Behavior of Zebrafish.","authors":"Kaila Savage, Tiara Harris, Luke Itomura, Corina Liang, Keala Mak, Zachary Oglesby, Vincent Ooi, Gemma Quiroz, Kelley M Withy, Chris Pierret, Soaleha Shams","doi":"10.1177/15458547261441746","DOIUrl":"10.1177/15458547261441746","url":null,"abstract":"<p><p>Hawai'i and other island communities around the globe are experiencing high exposures to micro- and nanoplastics (MNPs). Widespread use of various types of plastics and the action of wave physics coupled with abundant silica creates a constant production of MNPs. The community health effects of exposure to MNPs are not yet fully understood. The aquatic vertebrate model zebrafish, <i>Danio rerio</i>, was utilized to evaluate the developmental and behavioral effects of nanoplastic (NP) exposure as well as visual confirmation of plastic accumulation after embryonic and larval exposure. Eye and yolk size, heart rate, angle of development, and early larval locomotion behavior were quantified after early NP exposure lasting 3 or 5 days. In this work, a digital laboratory environment is used as the context for research trainees spanning high school to graduate and medical school in Hawai'i to explore health outcomes of developmental NP exposures. Presence of MNPs in the early developmental environment led to changes in growth and behavior of exposed fish. Data analysis showed significant effects of exposures on changes in the rate of development and yolk consumption on day 2 and reduced body length and increased locomotion on day 6. Nanoplastic exposure also affected overall body length, but this effect was not significant. These data support the potential dangers of MNP exposure and demonstrate their persistent detrimental effects on development and behavior in young zebrafish. Accordingly, our work contributes toward shifting focus toward understanding longer impacts on health, growth, and behaviors and potentially the reduction of harm in developing vertebrates.</p>","PeriodicalId":94273,"journal":{"name":"Zebrafish","volume":" ","pages":"53-63"},"PeriodicalIF":1.2,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147641133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Corrigendum to:</i> A Zebrafish Heart Failure Model for Assessing Therapeutic Agents.","authors":"","doi":"10.1177/15458547261446043","DOIUrl":"https://doi.org/10.1177/15458547261446043","url":null,"abstract":"","PeriodicalId":94273,"journal":{"name":"Zebrafish","volume":"23 2-3","pages":"99"},"PeriodicalIF":1.2,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148019767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ewsr1a Regulates the Development of the Axial Skeleton in Zebrafish.","authors":"Chris Merkes, Hyewon Park, Mizuki Azuma","doi":"10.1177/15458547261438422","DOIUrl":"10.1177/15458547261438422","url":null,"abstract":"<p><p>The <i>EWSR1</i> (<i>EWS RNA binding protein 1</i>) was originally discovered in Ewing sarcoma, a pediatric bone cancer. In a previous study, we identified zebrafish <i>ewsr1a,</i> the homologue of human <i>EWSR1</i>. Using a zebrafish mutant for <i>ewsr1a</i>, we demonstrated that Ewsr1a promotes differentiation of chondrogenesis in Meckel's cartilage, a component of the facial skeletal elements. Furthermore, we demonstrated that Ewsr1a interacts with the transcription factor SRY-BOX transcription factor 9 (SOX9) and modulates the transcription of its target genes. In this study, the role of Ewsr1a was further investigated in axial skeletogenesis. The maternal zygotic (MZ) <i>ewsr1a/ewsr1a</i> zebrafish display curved spines derived from irregularly spaced intervertebral discs (IVDs) and aberrant differentiation of nucleus pulposus cells. Using an <i>in vitro</i> cell culture system, we further show that the N-terminus of Ewsr1a is required for the interaction with Sox9. In zebrafish, the Ewsr1a also interacts with a Sox9 target gene, specifically the first intron of <i>col2a1a</i>. Zebrafish with the MZ <i>ewsr1a/ewsr1a</i> genotype display an increased level of collagen type II protein in the notochord starting at 36 h post fertilization. We propose that Ewsr1a contributes to IVD formation by regulating the expression of <i>col2a1a</i>.</p>","PeriodicalId":94273,"journal":{"name":"Zebrafish","volume":" ","pages":"46-52"},"PeriodicalIF":1.2,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147625153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lactic-Acid-Induced Zebrafish Skin Apoptosis as a Model for Evaluating Skin Barrier Function.","authors":"Qinqian Tao, Mingjie He, Jiaqi Zeng, Yaxin Wang, Xingmei Chen, Yingxin Li, Erping Yan, Haishan Zhao","doi":"10.1177/15458547261449928","DOIUrl":"10.1177/15458547261449928","url":null,"abstract":"<p><strong>Objective: </strong>The skin barrier function is essential for maintaining skin health. Consequently, it is crucial to evaluate the protective and restorative effects of topical medications and cosmetics on the skin barrier. However, methods that can directly assess the skin barrier function in zebrafish beyond their regenerative capabilities are limited. Therefore, we aimed to develop an <i>in vivo</i>, <i>in situ</i>, high-throughput screening model for assessing skin barrier function in zebrafish embryos.</p><p><strong>Methods: </strong>Lactic acid was used to induce skin barrier damage and crystal violet was used for staining to observe skin barrier damage. Histopathology was assessed using H&E, Masson, and Victoria blue staining. Cellular apoptosis was evaluated using <i>in situ</i> acridine orange (AO) staining and flow cytometry with propidium iodide (PI) staining.</p><p><strong>Results: </strong>A significant increase was noted in fluorescence in the trunk and tail regions of zebrafish embryos following lactic acid stimulation compared with those in the control group, whereas exposure to the positive control for 4 h significantly reduced the fluorescence area, showing 35%-45% inhibition. Histological sections revealed that lactic acid caused noticeable damage to the epidermis of zebrafish embryos, characterized by thinning of the epidermal layer and the presence of inflammatory cell infiltrates. An increase in apoptotic cells was observed through <i>in situ</i> AO and PI staining using flow cytometry, and RT-qPCR revealed elevated expression levels of apoptosis-related genes, including <i>fas</i>, <i>bax</i>, and <i>caspase 3</i>. Furthermore, six additional samples from various sources were screened using this model, which yielded reasonable outcomes for both positive and negative samples, indicating its potential application value in evaluating the skin barrier protective efficacy of drugs or compounds.</p><p><strong>Conclusion: </strong>Our study supports the use of the lactic-acid-induced zebrafish skin injury model as a reliable <i>in vivo</i> and <i>in situ</i> method for evaluating skin barrier function.</p>","PeriodicalId":94273,"journal":{"name":"Zebrafish","volume":"23 2-3","pages":"88-98"},"PeriodicalIF":1.2,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148019715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing Equilibration Time to Enhance Post-Thaw Viability of Cryopreserved Zebrafish (<i>Danio rerio</i>) Ovarian Fragments.","authors":"Maya L Wade, Matthew K Litvak","doi":"10.1177/15458547261441744","DOIUrl":"10.1177/15458547261441744","url":null,"abstract":"<p><p>Cryopreservation enables the long-term storage of viable biological material at ultra-low temperatures and forms the foundation for germplasm cryobanks that maintain valuable genetic lines of model organisms such as zebrafish (<i>Danio rerio</i>). However, reliable and reproducible cryopreservation protocols for fish germline stem cells remain difficult to develop, partly because key steps such as equilibration are often overlooked or assigned arbitrarily. Here, we optimized equilibration time for cryopreservation of zebrafish ovarian tissue. Ovarian fragments were equilibrated in 2 M methanol + 0.1 M glucose + 10% egg yolk for varying durations (15-120 min) before controlled slow cooling and storage in liquid nitrogen. Post-thaw viability was assessed using a Trypan Blue exclusion assay. A 60-min equilibration yielded the highest viability of ovarian cells in Experiment 1 (55.7 ± 1.7%), whereas a 30-min equilibration yielded the highest viability in Experiment 2 (75.9 ± 2.4%), but was not significantly different from the 60-min equilibration in Experiment 2 (75.6 ± 2.0%) (<i>p</i> = 0.998). Equilibration alone accounted for a 48.7% increase in post-thaw viability relative to controls. The framework presented here provides a reproducible method for determining species-specific equilibration optima and supports the development of effective germplasm cryobanks for both model and endangered fish species.</p>","PeriodicalId":94273,"journal":{"name":"Zebrafish","volume":" ","pages":"64-70"},"PeriodicalIF":1.2,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147694696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Baby Catchers: A Novel Tank Design to Dramatically Improve Fry Recovery of Live-bearing Fishes.","authors":"Abi M Zuber, Helen Stec, Maximiliano Zuluaga-Forero, Ehren J Bentz, Meridia Jane Bryant, Matthew D Taves, Joli Vega, Lei Cao, Lynn Capani-Czebiniak, Brian Brown, Benjamin A Sandkam","doi":"10.1177/15458547261424193","DOIUrl":"10.1177/15458547261424193","url":null,"abstract":"<p><p>Live-bearing fishes (Poeciliidae) are increasingly used as laboratory models, but their utility is hampered by high rates of filial cannibalism, which reduces fry recovery and increases husbandry demands. Traditional strategies, such as mesh tank inserts (TIs), rely on fry actively seeking refuge and are often ineffective. Here, we present a novel tank design called Baby Catchers (BCs) that use water flow to passively and automatically separate newborn fry from their mothers, fitting seamlessly into standard recirculating rack systems. We tested the efficacy of BC tanks compared to open tanks (OT) and traditional mesh TIs using <i>Poecilia parae</i>, a live-bearing species that is notorious for intense filial cannibalism. In short-term trials, BC tanks yielded significantly higher initial fry counts on day 0 and day 2, while mesh inserts performed no better than OT. Over 10 days, negative binomial generalized linear models predicted substantial progressive fry loss in OT (∼60% decline) and inserts (∼68% decline), but no significant change in BC, consistent with high fry survival. These results provide the first quantitative evidence that automated water-flow separation of fry dramatically reduces filial cannibalism in live-bearing fishes. The BC design offers a scalable, low-cost, and humane method for fry recovery, reducing technician effort, minimizing animal stress, and lowering barriers for research and breeding programs involving live-bearing fishes (e.g., swordtails, mollies, <i>Poeciliopsis</i>, mosquitofish, halfbeaks, etc.).</p>","PeriodicalId":94273,"journal":{"name":"Zebrafish","volume":" ","pages":"21-26"},"PeriodicalIF":1.2,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13051513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146159820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Precision Dosing in Zebrafish: An Anesthesia-Free Oral Gavage for Reproductive Toxicity Assessment in Zebrafish.","authors":"Helena Sarret-Casellas, Laia Mejías, Samuel Jiménez, Sofía Barreiro, Lucía Lozano-White, Vincenzo Di Donato, Christian Cortés-Campos","doi":"10.1177/15458547251401445","DOIUrl":"10.1177/15458547251401445","url":null,"abstract":"<p><p>Oral gavage is ideal for studies requiring controlled dose delivery and timing, such as repeated dosing and longitudinal analysis, as shown in this study. An anesthesia-free gavage technique was used to administer daily estradiol doses to adult zebrafish for 40 days to evaluate reproductive toxicity (developmental and reproductive toxicity one stage). Results showed that neither estradiol administration nor the gavage method caused stress or injury, but both impacted reproductive capacity in a dose-dependent manner. Females exposed to the drug exhibited a reduction in gonadosomatic index (GSI) and changes in follicle maturation, while in males, only the number of cells in the testis was reduced. The authors have no interests to disclose.</p>","PeriodicalId":94273,"journal":{"name":"Zebrafish","volume":" ","pages":"5-9"},"PeriodicalIF":1.2,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145673332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}