Biology subjects

Hamdoun, A.

Publications and source records attributed to Hamdoun, A..

4 recordsLinked to original sources

bioRxiv2025

Automated, high-throughput in-situ hybridization of Lytechinus pictus embryos

Despite the reach of in situ hybridization (ISH) in developmental biology, it has rarely been used at scale. The major limitation has been the throughput of the assay, which typically relies upon labor intensive manual steps. The goal of this study was to develop a fully automated hybridization chain reaction (HCR) pipeline capable of large-scale gene expression pattern profiling, with dramatically reduced cost and effort, in the sea urchin Lytechinus pictus. Our resulting pipeline, which we term high throughput (HT)-HCR, can process 192 gene probe sets on whole-mount embryos within 32 hours. The unique qualities of the sea urchin embryo enabled us to automate the entire HCR assay in a 96-well plate format, and utilize highly miniaturized reaction volumes, a general purpose robotic liquid handler, and automated confocal microscopy. From this approach we produced high quality localization data for 101 target genes across three developmental stages of L. pictus. The results reveal the localization of previously undescribed physiological genes, as well as canonical developmental transcription factors. HT-HCR represents a log order increase in the rate at which spatial transcriptomic data can be resolved in the sea urchin. This study paves the way for localization of understudied genes and for sophisticated perturbation analysis. Summary StatementWe developed an automated high-throughput HCR pipeline to rapidly map expression of 101 genes in sea urchin embryos, enabling large-scale discovery of novel developmental gene expression patterns.

developmental biology↗

bioRxiv2024

Stable germline transgenesis using the Minos Tc1/mariner element in the sea urchin, Lytechinus pictus.

Stable transgenesis is a transformative tool in model organism biology. While the sea urchin is one of the oldest animal models in cell and developmental biology, it has relied on transient manipulations of wild animals, and has lacked a strategy for stable transgenesis. Here we build on recent progress to develop a more genetically tractable sea urchin species, Lytechinus pictus, to establish a robust transgene integration method. Three commonly used transposons (Minos, Tol2, piggyBac) were tested for non-autonomous transposition, using plasmids containing a polyubiquitin promoter upstream of a H2B-mCerulean nuclear marker. Minos was the only transposable element that resulted in significant expression past metamorphosis. F0 animals were raised to sexual maturity and spawned to determine germline integration, transgene inheritance frequency, and to characterize expression patterns of the transgene in F1 progeny. The results demonstrated transgene transmission through the germline, the first example of a germline transgenic sea urchin, and indeed of any echinoderm. This milestone paves the way for the generation of diverse transgenic resources that will dramatically enhance the utility, reproducibility, and efficiency of sea urchin research. Significance StatementTransgenic tools are essential for effective utilization of animal models. Despite being an established model for cell and developmental biology, the sea urchin has not previously benefited from transgenic technology. This study reports the generation of the first germline transgenic sea urchin and opens new avenues for this organism.

developmental biology↗

bioRxiv2024

Local and global changes in cell density induce reorganisation of 3D packing in a proliferating epithelium.

Tissue morphogenesis is intimately linked to the changes in shape and organisation of individual cells. In curved epithelia, cells can intercalate along their own apicobasal axes adopting a shape named "scutoid" that allows energy minimization in the tissue. Although several geometric and biophysical factors have been associated with this 3D reorganisation, the dynamic changes underlying scutoid formation in 3D epithelial packing remain poorly understood. Here we use live-imaging of the sea star embryo coupled with deep learning-based segmentation, to dissect the relative contributions of cell density, tissue compaction, and cell proliferation on epithelial architecture. We find that tissue compaction, which naturally occurs in the embryo, is necessary for the appearance of scutoids. Physical compression experiments identify cell density as the factor promoting scutoid formation at a global level. Finally, the comparison of the developing embryo with computational models indicates that the increase in the proportion of scutoids is directly associated with cell divisions. Our results suggest that apico-basal intercalations appearing just after mitosis may help accommodate the new cells within the tissue. We propose that proliferation in a compact epithelium induces 3D cell rearrangements during development. Summary statementThe study uses sea star embryogenesis as a model of a proliferating epithelium to highlight how cell division induces 3D cell rearrangements during development.

developmental biology↗

bioRxiv2023

Cold Storage and Cryopreservation Methods for Spermatozoa of the Sea Urchin, Lytechinus pictus .

Sea urchins have contributed greatly to knowledge of fertilization, embryogenesis and cell biology. However, until now, they have not been a genetic model organism because of the long generation times of commonly used species, and lack of tools for husbandry and genetic manipulation. We recently established Lytechinus pictus, as a multigenerational sea urchin model, because of its relatively short generation time of 4-6 months and ease of laboratory culture. To take full advantage of this new multigenerational species, methods are needed to biobank and share mutant L. pictus sperm. Here, we describe a new extender based on sperm ion physiology before spawning of sperm into seawater. This extender maintains sperm capable of fertilization for at least 5-10 weeks when stored at 0 {degrees}C. We use the extender, and the cryoprotectant dimethyl sulfoxide (DMSO), to cryopreserve sperm of both L. pictus, and the widely used sea urchin, Strongylocentrotus purpuratus. The simple methods we describe work well for both species, achieving > 90% development and producing larvae that successfully undergo metamorphosis to juvenile sea urchins. Sperm of these two species can be frozen and thawed at least twice and still give rise to larvae that undergo metamorphosis. Main PointsO_LISperm can maintain fertilizing capacity ex vivo for 5-10 weeks when stored at 0{degrees}C. C_LIO_LIWhen freezing in liquid nitrogen no stepwise addition of cryoprotectant, or stepwise drop in temperature are required. C_LIO_LIA standard fertilization assay is presented to score cleavage stage sea urchin embryos produced by cryopreserved sperm. C_LIO_LISperm frozen and thawed more than once can produce larvae. C_LI

developmental biology↗