Xenbase: key features and resources of the Xenopus model organism knowledgebase

Genetics, Journal Year: 2023, Volume and Issue: 224(1)

Published: Feb. 9, 2023

Abstract Xenbase (https://www.xenbase.org/), the Xenopus model organism knowledgebase, is a web-accessible resource that integrates diverse genomic and biological data from research on laboratory frogs laevis tropicalis. The goal of to accelerate discovery empower research, enhance impact data, facilitate dissemination these data. also enhances value through high-quality curation, integration, providing bioinformatics tools optimized for experiments, linking human other organisms. plays an indispensable role in making interoperable accessible broader biomedical community accordance with FAIR principles. provides annotated updates organizations such as NCBI, UniProtKB, Ensembl, Gene Ontology consortium, most recently, Alliance Genomic Resources, common clearing house humans This article brief overview key recently added features Xenbase. New include processing high-throughput sequencing NCBI Expression Omnibus; curation anatomical, physiological, expression phenotypes newly created Phenotype Ontology; annotations; new anatomical drawings Normal Table development; integration latest v10.1 genome annotations. Finally, we highlight areas future development at continue support community.

Language: Английский

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Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors

eLife, Journal Year: 2020, Volume and Issue: 9

Published: April 27, 2020

Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable growth and differentiation new tissue, a process executed over multiple days across dozens cell types. The heterogeneity tissues temporally-sensitive fate decisions involved has made it difficult articulate gene regulatory programs enabling individual To better understand how regenerative program is fulfilled by neural progenitor cells (NPCs) spinal cord, we analyzed pax6-expressing NPCs isolated from regenerating Xenopus tropicalis tails. By intersecting chromatin accessibility data with single-cell transcriptomics, find that place an early priority on neuronal differentiation. Late in regeneration, returns proliferation. Our analyses identify Pbx3 Meis1 as critical regulators tail axon organization. Overall, use dynamics present model for their during regeneration.

Language: Английский

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Micro(nano)plastics as an emerging risk factor to the health of amphibian: A scientometric and systematic review

Chemosphere, Journal Year: 2021, Volume and Issue: 283, P. 131090 - 131090

Published: June 14, 2021

Language: Английский

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Xenopus leads the way: Frogs as a pioneering model to understand the human brain

genesis, Journal Year: 2020, Volume and Issue: 59(1-2)

Published: Dec. 27, 2020

From its long history in the field of embryology to recent advances genetics, Xenopus has been an indispensable model for understanding human brain. Foundational studies that gave us our first insights into major embryonic patterning events serve as a crucial backdrop newer avenues investigation organogenesis and organ function. The vast array tools available laevis tropicalis allows interrogation developmental phenomena at all levels, from molecular behavioral, application CRISPR technology enabled disorder risk genes higher-throughput manner. As only tetrapod which stages are easily manipulated observed, frogs provide unique opportunity study development earliest stages. All these features make premier studying brain, notoriously complex process demands fertilization beyond. Importantly, core processes brain conserved between human, underlining advantages this model. This review begins by summarizing discoveries made amphibians form cornerstones vertebrate neurodevelopmental biology goes on discuss have catapulted relation disease. we engage new era patient-driven gene discovery, offers exceptional potential uncover underlying disorders move towards rational drug design.

Language: Английский

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Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: Sept. 4, 2020

Abstract CRISPR/Cas9 genome editing has revolutionized functional genomics in vertebrates. However, edited F 0 animals too often demonstrate variable phenotypic penetrance due to the mosaic nature of outcomes after double strand break (DSB) repair. Even with high efficiency levels editing, phenotypes may be obscured by proportional presence in-frame mutations that still produce protein. Recently, studies cell culture systems have shown CRISPR/Cas9-mediated can dependent on local sequence context and predicted computational methods. Here, we similar approaches used forecast gene Xenopus tropicalis , laevis, zebrafish. We show a publicly available neural network previously trained mouse embryonic stem cultures (InDelphi-mESC) is able accurately predict early vertebrate embryos. Our observations direct implications for experiment design, allowing selection guide RNAs repair outcome signatures enriched towards frameshift mutations, maximization phenotype generation.

Language: Английский

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Advances in the Xenopus immunome: Diversification, expansion, and contraction

Developmental & Comparative Immunology, Journal Year: 2023, Volume and Issue: 145, P. 104734 - 104734

Published: May 10, 2023

Language: Английский

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Adeno-Associated Viral Tools to Trace Neural Development and Connectivity Across Amphibians

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 16, 2024

Summary The development, evolution, and function of the vertebrate central nervous system (CNS) can be best studied using diverse model organisms. Amphibians, with their unique phylogenetic position at transition between aquatic terrestrial lifestyles, are valuable for understanding origin evolution tetrapod brain spinal cord. Their metamorphic developmental transitions regenerative abilities also facilitate discovery mechanisms neural circuit remodeling replacement. genetic toolkit amphibians, however, remains limited, only a few species having sequenced genomes small number transgenic lines available. In mammals, recombinant adeno-associated viral vectors (AAVs) have become powerful alternative to genome modification visualizing perturbing system. AAVs DNA viruses that enable neuronal transduction in both developing adult animals low toxicity spatial, temporal, cell-type specificity. However, never been shown transduce amphibian cells efficiently. To bridge this gap, we established simple, scalable, robust strategy screen AAV serotypes three distantly-related species: frogs Xenopus laevis Pelophylax bedriagae, salamander Pleurodeles waltl, larval tadpoles post-metamorphic animals. For each species, successfully identified least two capable infecting CNS; no pan-amphibian serotype was identified, indicating rapid tropism. addition, developed an AAV-based targets isochronic cohorts neurons – critical tool parsing assembly. Finally, visualization manipulation circuits, variants retrograde tracing projections Our findings expand amphibians include AAVs, establish generalizable workflow screening non-canonical research organisms, generate testable hypotheses tropism, lay foundation modern cross-species comparisons CNS function, evolution.

Language: Английский

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The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 1, 2024

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding features this animal class that other terrestrial vertebrates. The need for genomic resources is more urgent than ever due to increasing threats group. are one most imperiled taxonomic groups, with approximately 41% species threatened extinction habitat loss, changes in land use patterns, disease, climate change, synergistic effects. Amphibian have provided better ontogenetic diversity, tissue regeneration, life history reproductive modes, antipredator strategies, resilience adaptive responses. They also serve as essential models studying broad traits, such evolutionary genome expansions contractions, they exhibit widest range sizes among all taxa possess multiple mechanisms genetic sex determination. Despite these features, sequencing amphibians has significantly lagged behind vertebrates, primarily challenges assembling large, repeat-rich genomes relative lack societal support. emergence long-read technologies, combined advanced molecular computational techniques improve scaffolding reduce workloads, now making it possible address some challenges. To promote accelerate production research international coordination collaboration, we launched Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) early 2023. This burgeoning community already 282 members from 41 countries. AGC aims leverage capabilities its advance bridge implementation gap biologists, bioinformaticians, conservation practitioners. Here evaluate state field genomics, highlight previous studies, present overcome, call on communities unite part enable "leap" next level.

Language: Английский

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Global analysis of cell behavior and protein dynamics reveals region-specific roles for Shroom3 and N-cadherin during neural tube closure

eLife, Journal Year: 2022, Volume and Issue: 11

Published: March 3, 2022

Failures of neural tube closure are common and serious birth defects, yet we have a poor understanding the interaction genetics cell biology during closure. Additionally, mutations that cause defects (NTDs) tend to affect anterior or posterior regions but rarely both, indicating regional specificity NTD genetics. To better understand behaviors closure, analyzed dynamic localization actin N-cadherin via high-resolution tissue-level time-lapse microscopy Xenopus investigate regionality gene function, generated mosaic in shroom3 , key regulator This new analytical approach elucidates several differences between cranial/anterior spinal/posterior provides mechanistic insight into function shroom3, demonstrates ability imaging analysis generate biological insights

Language: Английский

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Characterisation and automated quantification of induced seizure‐related behaviours in Xenopus laevis tadpoles

Journal of Neurochemistry, Journal Year: 2023, Volume and Issue: 168(12), P. 4014 - 4024

Published: May 2, 2023

Abstract Epilepsy, a clinical diagnosis characterised by paroxysmal episodes known as seizures, affects 1% of people worldwide. Safe and patient‐specific treatment is vital can be achieved the development rapid pre‐clinical models for identified epilepsy genes. Epilepsy result from either brain injury or gene mutations, also induced chemically. Xenopus laevis tadpoles could useful model confirmation variants unknown significance found in patients, drug re‐purposing screens that eventually lead to benefits patients. Here, we characterise quantify seizure‐related behaviours X. arrayed 24‐well plates. To provoke acute seizure behaviours, were chemically with pentylenetetrazole (PTZ) 4‐aminopyridine (4‐AP). test capacity adapt this method testing, exposed anti‐seizure valproate (VPA). Four seizure‐like described manually quantified, two these (darting, circling) accurately detected automatically, using video analysis software TopScan. Additionally, recorded swimming trajectories mean velocity. Automatic detection showed PTZ 4‐AP darting behaviour increased velocity compared untreated controls. Both parameters significantly reduced presence VPA. In particular, was shown sensitive measure epileptic activity. While not automatically detect full range shows promise future studies since well‐characterised genetically tractable organism. image

Language: Английский

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