Biology subjects

Nowotarski, S. H.

Publications and source records attributed to Nowotarski, S. H..

10 recordsLinked to original sources

bioRxiv2026

Cth1 is essential for gametogenesis and fertility in zebrafish

Infertility frequently arises from defects in germ cells and early embryonic transition. Successful fertilization depends on the developmental competence and molecular integrity of mature gametes from both parents, which are established through tightly coordinated programs of RNA regulation, metabolism, and genome maintenance. In our previous work, we identified Cth1 as a maternally regulated RNA decay factor essential for early embryonic development, acting through spatiotemporal control of maternal transcript clearance. Interestingly, Cth1 loss of function in adults also resulted in infertility, suggesting an additional and unexplored role during gametogenesis. Here, we extend these findings by defining the gametogenic function of Cth1 in zebrafish. Through detailed phenotypic, cytological and molecular characterization of Cth1 loss of function mutants, we show that Cth1 is highly enriched in germ cells and early embryos and is spatio-temporally localized across oogenesis and early development. Loss of Cth1 causes severe defects in early oogenesis and spermatogenesis, resulting in complete infertility in males and females. Mutant germ cells display transcriptomic changes consistent with metabolic and translational dysregulation, increased DNA damage, and striking abnormalities in gamete morphology. Together, these findings identify Cth1 as essential for gamete quality and fertility. Our study suggests a link between RNA decay mediated regulation of metabolism and genome integrity during germ cell development and reveals disruption of post-transcriptional control as a potential mechanism underlying infertility.

developmental biology↗

bioRxiv2026

Spatio-temporally regulated maternal RNA decay factor essential for zebrafish development

Maternal mRNA decay is essential for the Maternal-to-Zygotic Transition (MZT), yet its impact on spatial regulation has remained largely unexplored. We identify Cth1 as the first maternally encoded RNA-decay factor regulated in a spatiotemporal manner outside the germline in zebrafish, driven by conserved 3'UTR cis-elements. RfxCas13-dmediated depletion of maternal cth1 revealed early developmental defects that could not be assessed with SpyCas9 mutants due to infertility from impaired gametogenesis. Mechanistically, Cth1 acts independently of zygotic genome activation, recognizing AUrich motifs in maternal 3'UTRs to promote deadenylation and decay in a spatio-temporal manner; deletion of these motifs or depletion of Cth1 stabilizes both reporter and endogenous transcripts. These findings establish Cth1 as a key component of the maternal program and provide the first direct evidence that spatio-temporally regulated mRNA decay, outside the germline, contributes to early vertebrate development.

developmental biology↗

bioRxiv2026

Comparative 3D analysis reveals species-specific patterns of coral polyp morphology and gastrovascular integration

Coral reefs are constructed by colonial cnidarians whose survival depends on the coordinated growth and physiological integration of thousands of interconnected polyps. While coral skeletons have been extensively studied, the internal three-dimensional organization of coral tissues remains poorly resolved, limiting our understanding of how reef-building corals function as integrated modular organisms. In this study, we established a contrast-enhanced X-ray tomography (XRT) workflow for decalcified coral tissues, enabling detailed visualization and quantitative comparison of internal polyp architecture across four reef-building species with distinct colony forms: Acropora cervicornis, Acropora millepora, Montipora capitata, and Pocillopora damicornis. Importantly, this methodology resolved previously inaccessible patterns of tissue organization and structural connectivity among neighboring polyps. The two Acropora species shared a conserved axial - radial organization but differed in mesenterial morphology, whereas M. capitata exhibited complex, entangled mesenterial networks that connected both neighboring and distant polyps. In contrast, P. damicornis displayed superficial connectivity restricted to the coenosarc. Together, these results suggest that internal tissue architecture is an evolutionarily flexible trait, shaped by ecological and developmental pressures rather than strictly by shared ancestry. Our XRT workflow thus provides a new comparative framework for understanding how corals function as integrated living colonies.

evolutionary biology↗

bioRxiv2026

Nucleolar Dynamics During Oogenesis

Ribosome biogenesis is a conserved and highly regulated process that starts in the nucleolus, a membrane-less multi-phase organelle. Although the architecture of the nucleolus is known to change due to perturbations, how nucleolar organization is modulated during physiological processes to meet changing translational demands remains unclear. Here, we use zebrafish oogenesis as a developmental context requiring a rapid expansion of translational capacity to investigate the regulation of nucleolar architecture. We show nucleoli undergo coordinated changes in number, size, subnuclear localization, and layering throughout oogenesis. We further demonstrate that nucleoli form around extrachromosomal DNA circles that contain the rDNA locus. Notably, mouse oocytes undergo similar developmental changes in nucleolar layering and phase organization, indicating that remodeling of nucleolar condensates is a conserved feature of oogenesis. These findings reveal previously unexplored regulation of nucleolar architecture as developmental adaptations to changing biosynthetic needs.

developmental biology↗

bioRxiv2026

The Nematostella synaptonemal complex mediates divergent and sex-specific meiotic programs

Throughout eukaryotes, the synaptonemal complex (SC) is a supramolecular structure essential for meiotic chromosome dynamics and sexual reproduction. While metazoan SC proteins display significant sequence divergence, the lack of functional analyses beyond bilaterian models has obscured a mechanistic understanding of SC evolution. Here we report that the sea anemone Nematostella vectensis exhibits synapsis of homologous chromosomes in a classic zipper-like manner and expresses eight orthologs of ten known vertebrate SC proteins. Surprisingly, mutagenesis of the core SC components sycp1, syce2, and sycp3 resulted in divergent and sexually dimorphic phenotypes, indicating the functional diversification of these conserved factors. Combined, these findings challenge the assumption that the conservation of protein sequence or ultrastructure implies mechanistic homology.

evolutionary biology↗

bioRxiv2025

Impacts of stress and aging on spore health in Schizosaccharomyces pombe

Most fungi can produce dormant, long-lived cells known as spores. Spores play a critical role in fungal biology and human health, but much about spores is unknown. Here, we investigate factors affecting spore fitness using the fission yeast Schizosaccharomyces pombe as a model. We found that storage conditions affect spore longevity, and that spore health declines over time. We identified a delay in dormancy breaking (germination), decreased asymmetry during cell division, and reduced stress tolerance as aging phenotypes. These results support that S. pombe spores are affected by both time and experiences during dormancy, highlighting critical features of spore biology and revealing parallels between aging in spores and aging in animal cells. ImportanceFungi are integral to human health and well-being. Fungi also offer scientists easy experimental systems to study facets of life shared with other eukaryotes, including humans. Most studies of fungal cell biology focus on actively growing cells, but fungi can also produce dormant cells known as spores. Spores promote fungal survival and dispersal and are often the agents of infection in pathogenic fungi. In this work, we characterize the spores produced by an easy to study model fungus, Schizosaccharomyces pombe. We find that the longevity and the health of S. pombe spores declines over time and in response to heat stress. We characterize several traits associated with stressed and aged spores and identify parallels to aging cells in animals. This study expands the foundation for using S. pombe spores as a model system for fungal spore biology and as a model for aging of non-dividing cells.

cell biology↗

bioRxiv2025

Reproductive Adaptation of Astyanax mexicanus Under Nutrient Limitation

Reproduction is a fundamental biological process for the survival and continuity of species. Examining changes in reproductive strategies offers valuable insights into how animals have adapted their life histories to different environments. Since reproduction is one of the most energy-intensive processes in female animals, nutrient scarcity is expected to interfere with the ability to invest in gametes. Lately, a new model to study adaptation to nutrient limitation has emerged; the Mexican tetra Astyanax mexicanus. This fish species exists as two different morphs, a surface river morph and a cave-dwelling morph. The cave-dwelling morph has adapted to the dark, biodiversity, and nutrient-limited cave environment and consequently evolved an impressive starvation resistance. However, how reproductive strategies have adapted to nutrient limitations in this species remains poorly understood. Here, we compared breeding activities and maternal contributions between laboratory-raised surface fish and cavefish. We found that cavefish produce different clutch sizes of eggs with larger yolk compared to surface fish, indicating a greater maternal nutrient deposition in cavefish embryos. To systematically characterize yolk compositions, we used untargeted proteomics and lipidomics approaches to analyze protein and lipid profiles in 2-cell stage embryos and found an increased proportion of sphingolipids in cavefish compared to surface fish. Additionally, we generated transcriptomic profiles of surface fish and cavefish ovaries using a combination of single cell and bulk RNA sequencing to examine differences in maternal contribution. We found that genes essential for hormone regulation were upregulated in cavefish follicular somatic cells compared to surface fish. To evaluate whether these differences contribute to their reproductive abilities under natural-occurring stress, we induced breeding in starved female fish. Remarkably, cavefish maintained their ability to breed under starvation, whereas surface fish largely lost this ability. We identified insulin-like growth factor 1a receptor (igf1ra) as a potential candidate gene mediating the downregulation of ovarian development genes, potentially contributing to the starvation-resistant fertility of cavefish. Taken together, we investigated the female reproductive strategies in Astyanax mexicanus, which will provide fundamental insights into the adaptations of animals to environments with extreme nutrient deficit.

evolutionary biology↗

bioRxiv2024

Critical role of Spatio-Temporally Regulated Maternal RNAs in Zebrafish Embryogenesis

The maternal-to-zygotic transition shifts regulatory control from maternal to zygotic messenger RNAs (mRNA) through maternal mRNA degradation. While temporal aspects of maternal mRNA decay are known, spatial mechanisms remain underexplored. Using CRISPR-Cas9 and CRISPR-Cas13d systems, we functionally dissected the contribution of maternal versus zygotic fractions and overcame challenges of studying embryonic lethal genes. We identified differentially distributed maternal mRNAs in specific cells and evidenced the critical role of five maternal mRNAs, cth1, arl4d, abi1b, foxa and lhx1a, in embryogenesis. Further, we focused on the functionally uncharacterized cth1 gene, revealing its essential role in gametogenesis and embryogenesis. Cth1 acts as a spatio-temporal RNA decay factor regulating mRNA stability and accumulation of its targets in a spatio-temporal manner through 3UTR recognition during early development. Furthermore, Cth1 3UTR drives its spatio-temporal RNA localization. Our findings provide new insights into spatio-temporal RNA decay mechanisms and highlight dual CRISPR-Cas strategies in studying embryonic development. HighlightsO_LIDifferentially distributed marginal maternal RNAs have a critical role in early embryogenesis. C_LIO_LICas13d complements the Cas9 limitation to study the functions of embryonic lethal genes. C_LIO_LICth1 is essential for gametogenesis and early embryonic development. C_LIO_LICth1 is a maternal RNA decay factor required for spatio-temporal RNA regulation. C_LIO_LI3UTR of Cth1 drives its spatio-temporal RNA dynamics. C_LI

developmental biology↗

bioRxiv2022

Stem cells partner with matrix remodeling cells during regeneration

Stem cells enable regeneration by self-renewing and differentiating as instructed by a local microenvironment called a niche1-3. In most cases, the repair or replacement of tissues is fueled by tissue-specific or lineage-restricted stem cells that proliferate in response to local injury and apoptosis4-11. However, in organisms that regenerate using abundant adult pluripotent stem cells, the stem cell niches that support tissue repair have not been identified or characterized. Since these adult pluripotent stem cells are often more widely distributed and plentiful than lineage-restricted stem cells of other organisms, defining their microenvironments may uncover alternative forms of stem cell regulation12-14. Here we used unbiased spatial transcriptomics to define the cellular and molecular environments that support pluripotency in the highly regenerative freshwater planarian Schmidtea mediterranea. We determined that stem cells associate with a diverse collection of differentiated cell types, and these associations are highly dynamic during regeneration. We explored associations with two distinct cell types: secretory cells we term hecatonoblasts, and intestinal cells. While both cell types regulate stem cell proliferation, their spatial relationships to stem cells defy the concept of a single regenerative niche. Thus, the planarian stem cell pool is likely maintained by a dynamic collection of distinct microenvironments that cooperatively power whole-body regeneration.

developmental biology↗

bioRxiv2020

A new species of planarian flatworm from Mexico: Girardia guanajuatiensis

Planarian flatworms are best known for their impressive regenerative capacity, yet this trait varies across species. In addition, planarians have other features that share morphology and function with the tissues of many other animals, including an outer mucociliary epithelium that drives planarian locomotion and is very similar to the epithelial linings of the human lung and oviduct. Planarians occupy a broad range of ecological habitats and are known to be sensitive to changes in their environment. Yet, despite their potential to provide valuable insight to many different fields, very few planarian species have been developed as laboratory models for mechanism-based research. Here we describe a previously undocumented planarian isolate, Girardia sp. (Guanajuato). After collecting this isolate from a freshwater habitat in central Mexico, we characterized it at the morphological, cellular, and molecular level. We show that Girardia sp. (Guanajuato) shares features with animals in the Girardia genus but also possesses traits that appear unique to this isolate. By thoroughly characterizing this new planarian isolate, our work facilitates future comparisons to other flatworms and further molecular dissection of the unique and physiologically-relevant traits observed in this Girardia sp. (Guanajuato) isolate.

developmental biology↗