Biology subjects

Affatato, P.

Publications and source records attributed to Affatato, P..

3 recordsLinked to original sources

bioRxiv2025

Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy

Modern biology increasingly depends on data-driven discovery, requiring scalable and affordable high-content 3D imaging across molecular to organ scales. Although tissue clearing, expansion microscopy, and light-sheet microscopy (LSM) enable subcellular-resolution imaging of intact specimens, their scalability remains fundamentally limited by detection optics: immersion objectives deliver high-resolution, aberration-free imaging but with short working distances, high cost, and multi-immersion incompatibility, while air objectives offer long working distances and portability at lower cost but suffer from severe aberrations and reduced photon collection when imaging immersed samples. We introduce the Hybrid Solid-Liquid Immersion Lens (HySIL) framework, which pairs an off-the-shelf solid optical component with a refractive index-matched liquid to precompensate aberrations and enhance resolution. Building on HySIL, we developed SCOPE and Super-SCOPE, objective-agnostic imaging devices achieving submicron lateral resolution (<0.75 {micro}m) across centimeter-scale samples using inexpensive air objectives with >30 mm working distances. Integration with a low-cost LSM platform yielded a compact, scalable system demonstrated for multi-immersion, multi-color, subcellular-resolution mapping of cleared or expanded mouse, salamander, and cavefish brains, human iPSC-derived organoids, and 3D histopathology of breast tissue. HySIL and SCOPE establish an accessible foundation for scalable, high-resolution volumetric imaging, advancing data-driven biological discovery.

bioengineering↗

bioRxiv2025

A conserved logic for the development of cortical layering in tetrapods

The cerebral cortex is part of the pallium, a brain region conserved across vertebrates yet remarkably diverse in structure and cellular composition. A defining feature of the cerebral cortex is its organization into neuronal layers with distinct gene expression profiles, input-output connectivity, and function. According to prevailing models, the cerebral cortex emerged in ancestral amniotes (mammals and reptiles) following innovations in pallial development that enabled the generation of diverse neuron types and their laminar organization.1-11 However, little is known about pallial development and architecture in amphibians, the sister group of amniotes. Here we show that in the salamander Pleurodeles waltl, the dorsal pallium is organized in distinct superficial and deep layers with neurons that develop following cellular and molecular principles of mammalian corticogenesis. Using birthdating analysis, barcode-based lineage tracing, and single-cell RNA sequencing, we find that radial glia temporal states and intermediate progenitor cells are conserved across species, while neuronal differentiation trajectories are highly evolvable. Neurons generated at different developmental time points occupy different layers and exhibit distinct molecular and projection identities. Thus, temporally-patterned neurogenesis represents an ancient organizing principle of layered pallia, although mammals display an inverted layer order along the radial axis. Together, these findings demonstrate that the core developmental principles underlying cortical layering - including temporal patterning, intermediate progenitors, and laminar organization - predate the origin of amniotes. Our results suggest that the evolutionary expansion of the mammalian neocortex built upon a deeply conserved developmental framework already present in early tetrapods.

developmental biology↗

bioRxiv2023

Convergent evolution of ventral adaptations for enrollment in trilobites and extant euarthropods

The ability to enroll for protection is an effective defensive strategy that has convergently evolved multiple times in disparate animal groups ranging from euarthropods to mammals. Enrollment is an evolutionary staple of trilobites, and their biomineralized dorsal exoskeleton offers a versatile substrate for the evolution of interlocking devices. However, it is unknown whether trilobites also featured ventral adaptations for enrolment. Here, we report ventral exoskeletal adaptations that facilitate enrollment in exceptionally preserved trilobites from the Upper Ordovician Walcott-Rust Quarry in New York State, USA. Walcott-Rust trilobites reveal the intricate three-dimensional organization of the non-biomineralized ventral anatomy preserved as calcite casts, including the spatial relationship between the articulated sternites (i.e., ventral exoskeletal plates) and the wedge-shaped protopodites. Enrollment in trilobites is achieved by ventrally dipping the anterior margin of the sternites during trunk flexure, facilitated by the presence of flexible membranes, and the close coupling of the wedge-shaped protopodites. Comparisons with the ventral morphology of extant glomerid millipedes and terrestrial isopods reveal similar mechanisms used for enrollment. The wedge-shaped protopodites of trilobites closely resemble the gnathobasic coxa/protopodite of extant horseshoe crabs. We propose that the trilobites wedge-shaped protopodite simultaneously facilitates tight enrollment and gnathobasic feeding with the trunk appendages.

paleontology↗