Biology subjects

Dias, J. M.

Publications and source records attributed to Dias, J. M..

5 recordsLinked to original sources

bioRxiv2026

Determinants of the Transition Zone Width of Morphogen Readouts

In tissue patterning, cell fate boundaries often form transition zones with mixed or gradual fates rather than sharp demarcations. Traditionally, such zones in morphogen-driven systems were attributed to fluctuations in morphogen concentrations, especially at low molecule numbers. Here, we present experimental data from the mouse neural tube, the precursor of the central nervous system, which challenges this view. Contrary to expectations, we find that the transition zone width (TZW) does not increase with distance from the morphogen source. By combining experiments, theory, and computational modelling, we identify key factors shaping the TZW. Our findings suggest that cellular readout noise, rather than morphogen fluctuations, determine the TZW. The inferred variability in the parameters defining morphogen dynamics and cellular readout remains within previously reported physiological ranges. This discovery adds to earlier findings that morphogen gradients maintain higher-than-expected patterning precision over long distances, offering new insights into the robustness of developmental processes.

developmental biology↗

bioRxiv2023

Biodistribution of DNA-origami nanostructures in live zebrafish embryos with single-cell resolution

DNA origami-based nanotechnology is a versatile tool for exploring fundamental biological questions and holds significant promise for future biomedical applications. However, the development of DNA origami-based therapeutic agents is hindered by the challenge of translating in vitro performance into effective applications in vivo. Here, we exploit the optical transparency of the embryonic zebrafish to track intravenously injected, fluorescently labelled wireframe DNA origami nanostructures. Our approach integrated long-term, high-resolution imaging of transgenic live embryos with single-cell RNA sequencing, to elucidate the biodistribution of DNA nanostructures over time, up to 3 days post-injection (dpi). Notably, we observed rapid accumulation of nanostructures in the caudal hematopoietic tissue (CHT), akin to the fetal liver in mammals. We tested the effects of coating the nanostructures with an oligolysine PEG copolymer (K-PEG), a widely used strategy to enhance their stability. The K-PEG coating mitigated the accumulation rate in CHT, enabling higher percentages of the nanostructures to engage with other tissues. Additionally, our findings highlighted the pivotal role of scavenger endothelial cells in DNA origami clearance, with K-PEG offering sustained protection for the nanostructures at the CHT. Furthermore, by monitoring DNA origami in a transgenic zebrafish line designed for targeted macrophage ablation, we found that macrophages contribute to nanostructure clearance at later time points. This study introduces a framework for the analyses of the biodistribution and clearance of DNA origami nanostructures in vivo with single cell resolution and establishes a foundation for the investigation of DNA origami-based nanomedicines in animal models.

bioengineering↗

bioRxiv2023

An inverse agonist of orphan receptor GPR61 reveals a novel allosteric mechanism

GPR61 is a biogenic amine receptor-related orphan GPCR associated with phenotypes relating to appetite and thus, is of interest as a druggable target to treat disorders of metabolism and body weight, such as obesity and cachexia. To date, lack of structural information or a known biological ligand or tool compound has hindered comprehensive efforts to study its structure and function. Here, we report the first ever structural characterization of GPR61, in both its active-like complex with heterotrimeric G protein and in its inactive state. Moreover, we report the discovery of a potent and selective small-molecule inverse agonist against GPR61 and structural elucidation of its unprecedented allosteric site and mode of action. These findings offer key mechanistic insights into an orphan GPCR, while providing both a new structural framework and tool compound to support further studies of GPR61 function and modulation.

biophysics↗

bioRxiv2020

A small-molecule oral agonist of the human glucagon-like peptide-1 receptor

Peptide agonists of the glucagon-like peptide-1 receptor (GLP-1R) have revolutionized diabetes therapy, but their use has been limited by the requirement for injection. Here we describe the first effective, orally bioavailable small molecule GLP-1R agonists. A sensitized high-throughput screen identified a series of small molecule GLP-1R agonists that were optimized to promote endogenous GLP-1R signaling with nM potency. These small molecule agonists increased insulin levels in primates but not rodents, which is explained by a cryo-EM structure that revealed a binding pocket requiring primate-specific tryptophan 33. Importantly, oral administration of agonist PF-06882961 to healthy humans produced dose-dependent declines in serum glucose (NCT03309241). This opens the door to a new era of oral small molecule therapies that target the well-validated GLP-1R pathway for metabolic health. One Sentence SummaryPF-06882961 is an orally administered small molecule that activates the GLP-1 receptor to lower blood glucose in humans.

pharmacology and toxicology↗

bioRxiv2019

A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells

How time is measured by neural stem cells during temporal neurogenesis has remained unresolved. By combining experiments and computational modelling, we here define a Shh/Gli-driven three-node timer underlying the sequential generation of motor neurons (MNs) and serotonergic neurons in the brainstem. The timer is founded on temporal decline of Gli-activator and Gli-repressor activities established through downregulation of Gli transcription. The circuitry conforms an incoherent feedforward loop, whereby Gli proteins promote expression of Phox2b and thereby MN-fate, but also account for a delayed activation of a self-promoting Tgf{beta}-node triggering a fate switch by repressing Phox2b. Hysteresis and spatial averaging by diffusion of Tgf{beta} counteracts noise and increases temporal accuracy at the population level. Our study defines how time is reliably encoded during the sequential specification of neurons.

developmental biology↗