Biology subjects

Gorelick, D. A.

Publications and source records attributed to Gorelick, D. A..

13 recordsLinked to original sources

bioRxiv2026

Beyond hazard identification: Discovering mechanisms of action from a ToxCast chemical screen in zebrafish

Large-scale chemical screens are important tools for hazard identification and chemical prioritization, but they less commonly progress from identifying a phenotype to identifying its mechanism. Here, we used zebrafish embryos to screen 4,657 chemicals from the U.S. EPA ToxCast Phase III library for disruption of embryonic development and advanced selected hits through sequential validation using original library stocks, independently sourced chemicals, concentration-response analysis, transcriptomics, and functional experiments. Of 61 primary hits subjected to repeat testing, 33 reproduced the original phenotype, and four of eight compounds subsequently tested using independently sourced chemicals exhibited reproducible concentration-dependent developmental toxicity. We then investigated purpurin, an understudied anthraquinone pigment that caused pericardial edema, circulation defects, and body-axis abnormalities. Transcriptomic analysis of purpurin-exposed embryos revealed coordinated suppression of pathways involved in calcium regulation, ion transport, and neuronal signaling. Increasing extracellular calcium produced a concentration-dependent rescue of purpurin-induced developmental abnormalities, whereas equivalent magnesium supplementation did not, supporting a role for calcium availability or homeostasis in purpurin developmental toxicity. These results demonstrate that large-scale in vivo toxicity screening can be integrated with independent chemical validation and functional follow-up to move beyond hazard identification toward mechanistic understanding of how environmental chemicals disrupt embryonic development.

pharmacology and toxicology↗

bioRxiv2026

Expanded implementation of Fast & Fair paid peer review reduces time to first decision without reducing review quality in a biology journal

Traditional peer review is often slowed by delays in identifying willing reviewers and waiting for completed review reports. In a 2024 pilot on the journal Biology Open, we showed that Fast & Fair peer review, which uses pre-contracted paid reviewers and a structured editorial timeline, could deliver rapid, high-quality peer. Here, we report the expanded implementation of Fast & Fair at Biology Open in 2025. From 1 April 2025 onward, all direct submissions to the journal were considered for Fast & Fair peer review unless appropriate pre-contracted reviewer expertise was unavailable. Reviewers were paid 220 GBP per manuscript only if they completed the review on time, and the review met editorial quality expectations. Among peer-reviewed manuscripts submitted in 2025, Fast & Fair reduced time to first decision with reviews from a mean of 37.7 working days under conventional peer review to 5.5 working days. Reviewer commitment also improved. Fast & Fair invitations were accepted more often than conventional invitations (67% versus 23%), had lower nonresponse (13% versus 39%), and had higher completion among accepted invitations (98% versus 87%). Faster review was not associated with reduced review quality. Handling editors scored each review for usefulness in editorial decision-making. Fast & Fair produced fewer low-scoring reports than conventional peer review. Editorial behavior was also unchanged, with similar first-decision profiles and final acceptance rates (59% versus 61%). While financial sustainability remains to be tested at scale, the Fast & Fair model addresses a major bottleneck in traditional peer review by replacing ad hoc reviewer recruitment with conditional compensation, predefined quality standards and a strict editorial timeline.

scientific communication and education↗

bioRxiv2025

Dolutegravir Developmental Toxicity is Mitigated by Magnesium and Folate in Zebrafish Embryos

Integrase-strand-transfer inhibitors have transformed HIV therapy, yet the widely prescribed drug dolutegravir (DTG) has been linked to developmental toxicity and its teratogenic mechanism remains uncertain. Here we use zebrafish to dissect DTG toxicity during early vertebrate development. DTG exposure from 2-4 h post-fertilization (hpf) to 24 hpf produced high mortality and abnormal morphology; co-treatment with folic acid or 5-methyltetrahydrofolate partially restored normal morphology, whereas calcium had no effect. Strikingly, supplementation with magnesium (Mg) rescued DTG-exposed embryos almost as effectively as folate, implicating magnesium availability in protection. In competitive binding assays, Mg increased binding of folate to purified folate receptor (FOLR1) by 30% in the presence of DTG. Maternal-zygotic zebrafish folr1 mutant embryos contained significantly less endogenous folate than wild-type embryos yet displayed marked hypersensitivity to DTG that could not be mitigated by folate supplementation. Critically, magnesium supplementation partially rescued DTG toxicity in folr1 mutants, indicating a Folr1-independent component and placing the free DTG vs Mg-bound DTG balance upstream of folate transport. These results support a model in which free DTG antagonizes FOLR1, and Mg modifies DTG developmental toxicity by both FOLR1 dependent and independent processes. Our work identifies magnesium status as a modifiable determinant of DTG teratogenicity and provides a proof-of-concept zebrafish model that could be adapted for rapid in vivo screening of integrase inhibitors for developmental phenotypes.

developmental biology↗

bioRxiv2025

Fast & Fair peer review: a pilot study demonstrating feasibility of rapid, high-quality peer review in a biology journal

Traditional peer review is slow, often delayed by the time-consuming process of identifying reviewers and lengthy review turnaround times. This study tests the feasibility of the Fast & Fair peer review initiative by evaluating whether we could implement and adhere to a structured timeline for rapid peer review at Biology Open. A 6-month pilot conducted from July to December 2024 evaluated a structured workflow with pre-contracted reviewers under two payment models: a freelance model or a retainer model. All manuscripts assigned to two of the journals ten academic editors were included in the Fast & Fair peer review initiative experiment. A structured editorial time-line ensured that all manuscripts received reviews and first decisions within 7 business days. The results demonstrated that 100% of Fast & Fair peer review initiative manuscripts met the turnaround target, with a mean of 4.6 business days (n=20 manuscripts). Review quality was maintained, as indicated by assessments by academic editors. The freelancer model outperformed retainers in cost-effectiveness. These findings suggest that the Fast & Fair peer review initiative is feasible and does not compromise review quality. While scalability remains to be tested, the initiative eliminates a major bottleneck in traditional peer review by streamlining reviewer identification and enforcing a strict editorial timeline.

scientific communication and education↗

bioRxiv2023

Functional genomic analysis of non-canonical DNA regulatory elements of the aryl hydrocarbon receptor

The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor activated by environmental toxicants like halogenated and polycyclic aromatic hydrocarbons, which then binds to DNA and regulates gene expression. AHR is implicated in numerous physiological processes, including liver and immune function, cell cycle control, oncogenesis, and metabolism. Traditionally, AHR binds a consensus DNA sequence (GCGTG), the xenobiotic response element (XRE), recruits coregulators, and modulates gene expression. Yet, recent evidence suggests AHR can also regulate gene expression via a non-consensus sequence (GGGA), termed the non-consensus XRE (NC-XRE). The prevalence and functional significance of NC-XRE motifs in the genome have remained unclear. While ChIP and reporter studies hinted at AHR-NC-XRE interactions, direct evidence for transcriptional regulation in a native context was lacking. In this study, we analyzed AHR binding to NC-XRE sequences genome-wide in mouse liver, integrating ChIP-seq and RNA-seq data to identify candidate AHR target genes containing NC-XRE motifs in their regulatory regions. We found NC-XRE motifs in 82% of AHR-bound DNA, significantly enriched compared to random regions, and present in promoters and enhancers of AHR targets. Functional genomics on the Serpine1 gene revealed that deleting NC-XRE motifs reduced TCDD-induced Serpine1 upregulation, demonstrating direct regulation. These findings provide the first direct evidence for AHR-mediated regulation via NC-XRE in a natural genomic context, advancing our understanding of AHR-bound DNA and its impact on gene expression and physiological relevance.

genomics↗

bioRxiv2023

Testosterone acts through membrane protein GPRC6A to cause cardiac edema in zebrafish embryos

Androgen actions are classically thought to be mediated by intracellular androgen receptors (AR), but they can also exert non-genomic effects via binding to integral membrane proteins. Although several putative membrane androgen receptors were cloned and characterized in vitro, their function as androgen receptors in vivo remains to be further investigated. Here, we used a chemical-genetic screen in zebrafish and found that the G-protein coupled receptor GPRC6A mediates non-genomic androgen action during embryonic development. Exposure to three androgens, 5-Androstane-3,17-dione (androstanedione), dihydrotestosterone (DHT), and testosterone, caused cardiac edema or tail curvature in wild-type embryos. ar mutant embryos also exhibited cardiac edema or tail curvature following exposure to these androgens, suggesting the involvement of ar-independent pathways. To identify the causative receptor, we mutated putative membrane androgen receptors gprc6a, hcar1-4, or zip9 genes and exposed mutant embryos to the androgens. We found that hcar1-4 and zip9 mutant embryos were susceptible to the identified androgens and developed cardiac edema or tail curvature phenotype following exposure. In contrast, we observed a significant reduction in cardiac edema phenotype in the gprc6a mutants compared to the wild-type embryos following testosterone treatment. Additionally, we exposed wild-type embryos to testosterone together with GPRC6A antagonists and observed a significant suppression of the cardiac edema phenotype. These results suggest that testosterone causes cardiac edema in zebrafish embryos by acting via the integral membrane protein GPRC6A, independently of nuclear androgen receptors. Using RNA-seq and RNA rescue approaches, we find that testosterone-GPRC6A causes cardiac phenotypes by reducing Pak1 signaling. Our study provides insights into non-genomic androgen signaling during embryonic development and identifies GPRC6A as a key receptor mediating androgen action.

pharmacology and toxicology↗

bioRxiv2022

Hemato-vascular specification requires arnt1 and arnt2 genes in zebrafish embryos

During embryonic development, a subset of cells in the mesoderm germ layer are specified as hemato- vascular progenitor cells, which then differentiate into endothelial cells and hematopoietic stem and progenitor cells. In zebrafish, the transcription factor npas4l, also known as cloche, is required for the specification of hemato-vascular progenitor cells. However, it is unclear if npas4l is the sole factor at the top of the hemato-vascular specification cascade. Here we show that arnt1 and arnt2 genes are required for hemato-vascular specification. We found that arnt1;arnt2 double homozygous mutant zebrafish embryos (herein called arnt1/2 mutants), but not arnt1 or arnt2 single mutants, lack blood cells and most vascular endothelial cells. arnt1/2 mutants have reduced or absent expression of etsrp and tal1, the earliest known endothelial and hematopoietic transcription factor genes. npas4l and the arnt genes are PAS domain-containing bHLH transcription factors that function as dimers. We found that Npas4l binds both Arnt1 and Arnt2 proteins in vitro, consistent with the idea that PAS domain- containing bHLH transcription factors act in a multimeric complex to regulate gene expression. Our results demonstrate that npas4l, arnt1 and arnt2 act together to regulate endothelial and hematopoietic cell fate, where each gene is necessary, but by itself not sufficient, to drive hemato-vascular specification. Our results also demonstrate that arnt1 and arnt2 act redundantly in a transcriptional complex containing npas4l, but do not act redundantly when interacting with another PAS domain- containing bHLH transcription factor, the aryl hydrocarbon receptor. Altogether, our data enhance our understanding of hemato-vascular specification and the function of PAS domain-containing bHLH transcription factors.

developmental biology↗

bioRxiv2019

The Antagonism of Folate Receptor by the Integrase Inhibitor Dolutegravir

Human immunodeficiency virus (HIV) integrase inhibitors are increasingly being used for antiretroviral therapy (ART), and dolutegravir (DTG/Tivicay) has emerged as a leading core agent. In 2018, the Tsepamo study reported a 6- to 9-fold increase for neural tube defect (NTD) risk among the offspring of mothers receiving DTG during early gestation. Maternal folate (vitamin B9) status is the largest known modifier of NTD risk, so we evaluated folate-related mechanisms of action and the critical period for DTG developmental toxicity. Folate receptor (FOLR1) binding studies indicate DTG is a non-competitive FOLR1 antagonist at therapeutic concentrations. In vitro testing indicates calcium (2mM) increases FOLR1-folate interactions and alters DTG-FOLR1-folate interactions and cytotoxicity. DTG does not inhibit downstream folate metabolism by dihydrofolate reductase (DHFR). Early embryonic exposure to DTG is developmentally toxic in zebrafish, and supplemental folic acid can mitigate DTG developmental toxicity. The results from these studies are expected to inform and guide future animal models and clinical studies of DTG-based ART in women of childbearing age.

pharmacology and toxicology↗

bioRxiv2018

ahr2, but not ahr1a or ahr1b, is required for craniofacial and fin development and TCDD-dependent cardiotoxicity in zebrafish

The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that binds environmental toxins and regulates gene expression. AHR also regulates developmental processes, like craniofacial development and hematopoiesis, in the absence of environmental exposures. Zebrafish have three paralogues 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 while 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. AHR was shown to interact with estrogen receptor alpha, yet it is not known whether these interactions are constitutive or dependent on ahr1 genes. 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 while 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.

developmental biology↗

bioRxiv2018

G protein-coupled estrogen receptor is not required for sex determination or ovary function in zebrafish

Estrogens regulate vertebrate development and function through binding to nuclear estrogen receptors alpha and beta (ER, ER{beta}) and the G protein-coupled estrogen receptor (GPER). Studies in mutant animal models demonstrated that ER and ER{beta} are required for normal ovary development and function. However, the degree to which GPER signaling contributes to ovary development and function is less well understood. Previous studies using cultured fish oocytes found that estradiol inhibits oocyte maturation in a GPER-dependent manner, but whether GPER regulates oocyte maturation in vivo is not known. To test the hypothesis that GPER regulates oocyte maturation in vivo, we assayed ovary development and function in gper mutant zebrafish. We found that homozygous mutant gper embryos developed into male and female adults with normal sex ratios and fertility. Adult mutant fish exhibited normal secondary sex characteristics and fertility. Additionally, mutant ovaries were histologically normal. We observed no differences in the number of immature versus mature oocytes in mutant versus wild-type ovaries from both young and aged adults. Furthermore, expression of genes associated with sex determination and ovary function were normal in gper mutant ovaries compared to wild type. Our findings suggest that GPER is not required for sex determination, ovary development or fertility in zebrafish.

developmental biology↗

bioRxiv2017

Assaying uptake of endocrine disruptor compounds in zebrafish embryos and larvae

To study the effects of environmental endocrine disruptors (EEDs) on aquatic animals, embryos and larvae are typically incubated in water containing defined concentrations of EEDs. However, the amount of EED uptake into the animal is often difficult to determine. Using radiolabeled estradiol ([3H]E2), we previously developed a rapid, straightforward assay to measure estradiol uptake from water into zebrafish embryos and larvae. Here, we extend this approach to measure the uptake of two additional EEDs, bisphenol A (BPA) and ethinyl estradiol (EE2). As with E2, the uptake of each compound by individual larvae was low (< 6%), and increased with increasing concentration, duration, and developmental stage. We found that E2 and EE2 had similar uptake under equivalent exposure conditions, while BPA had comparatively lower uptake. One application of this assay is to test factors that influence EED uptake or efflux. It has been suggested that persistent organic pollutants (POPs) inhibit ABC transporters that may normally efflux EEDs and their metabolites, inducing toxicity in aquatic organisms. We measured [3H]E2 levels in zebrafish in the presence or absence of the POP PDBE-100, and cyclosporine A, a known inhibitor of ABC transporters. Neither chemical significantly affected [3H]E2 levels in zebrafish, suggesting that zebrafish maintain estradiol efflux in the presence of PDBE-100, independently of cyclosporine A-responsive transporters. These uptake results will be a valuable reference for EED exposure studies in developing zebrafish, and provide a rapid assay to screen for chemicals that influence estrogen-like EED levels in vivo.

pharmacology and toxicology↗

bioRxiv2017

Nuclear androgen receptor regulates testes organization and oocyte maturation in zebrafish

Androgens act through the nuclear androgen receptor (AR) to regulate gonad differentiation and development. In mice, AR is required for spermatogenesis, testis development and formation of external genitalia in males and oocyte maturation in females. However, the extent to which these phenotypes are conserved in nonmammalian vertebrates is not well understood, because mutations in AR have not been generated in any other species. Here, we generate zebrafish with a mutation in the ar gene and examine the role of AR on sexual differentiation and gonad development. We find that zebrafish AR is not required for male sexual differentiation, since a portion of ar mutants develop a testis. However, we show that in zebrafish, as in mice, AR is required for the development of secondary sexual characteristics and for proper organization of the testis in males and for oocyte maturation in females. Additionally, we find that zebrafish ar mutant males have functional, mature sperm present in their testis, but are infertile due to an inability to release sperm. These findings suggest that AR is required for male sexual development and fertility, but not essential for sexual differentiation in zebrafish. The ar mutant we developed will be useful for modeling human endocrine function in zebrafish.

developmental biology↗

bioRxiv2016

G protein-coupled estrogen receptor regulates heart rate in zebrafish embryos

Estrogens act by binding to estrogen receptors alpha and beta (ER, ER{beta}), ligand-dependent transcription factors that play crucial roles in sex differentiation, tumor growth and cardiovascular physiology. Estrogens also activate the G protein-coupled estrogen receptor (GPER), however the function of GPER in vivo is less well understood. Here we find that GPER is required to maintain normal heart rate in zebrafish embryos. Acute exposure to estrogens increased heart rate in wildtype and in ER and ER{beta} mutant embryos but not in GPER mutants. Nuclear estrogen receptor signaling remained normal in GPER mutant embryos, however GPER mutant embryos exhibited reduced basal heart rate while heart rate was normal in ER and ER{beta} mutants. We detected GPER transcript in discrete regions of the brain but not in the heart. In the brain, we observed gper expression in cells lacking nuclear estrogen receptor activity, suggesting that GPER acts in the brain to regulate heart rate independently of nuclear estrogen receptor signaling. Our results demonstrate that estradiol plays a previously unappreciated role in the acute modulation of heart rate during zebrafish embryonic development and that GPER functions as an autonomous estrogen receptor in vivo to regulate basal heart rate.

pharmacology and toxicology↗