Biology subjects

Ortega, J. A.

Publications and source records attributed to Ortega, J. A..

6 recordsLinked to original sources

bioRxiv2025

Eyes wide open: Frogs with reduction of auditory communication ability show lower eye, but higher corneal, investment

Vocal communication is the primary mechanism of mate attraction in frogs, but some species have lost the auditory structures needed to hear airborne sounds, raising the question of how they communicate in their absence. We hypothesized that frog species with auditory system reductions have compensated through enhanced visual ability, including through enlarged eyes. To test this trade-off hypothesis, we estimated relative eye and corneal investment across 264 species and tested for correlations with auditory reduction. Contrary to our expectations, we found that species with auditory reductions had smaller eye size and lower eye investment. Instead, we found that non-fossorial species with auditory reductions had significantly greater corneal investment, after controlling for habitat-based variation. Enlarged corneas enhance light sensitivity but are expected to have a lower metabolic cost than larger eyes. Relatively larger corneas may, in combination with other changes, allow frogs with auditory reductions to rely more on vision for communication, while at the same time minimizing energetic costs in small animals that are already metabolically constrained. Our findings suggest that the visual system plays an adaptive role in response to the reduction of auditory communication and highlights the condition of sensory systems as an important factor shaping frog evolution.

evolutionary biology↗

bioRxiv2025

CONSERVED NUCLEAR MORPHOLOGY IDENTIFIES FUNCTIONAL RADIAL GLIA NEURAL PROGENITORS

Mechanical cues influence neural development, yet how tissue architecture is integrated into progenitor cell states remains poorly understood. Here, we show that defined microtopographies induce an early nuclear remodeling program associated with radial glia (RG)-like competence. Aligned microgrooves promote nuclear elongation, reduced Lamin A/C to B1 ratio, sustained {beta}-catenin activity, and distinct patterns of nuclear calcium dynamics, all of which merge before peak Pax6 expression. Pharmacological inhibition of mechanosensitive calcium signaling abolishes RG-associated marker induction while preserving nuclear remodeling, indicating that calcium-dependent pathways are required for Pax6 induction but are dispensable for the establishment of the underlying morphometric state. To quantitatively describe these transitions, we developed an interpretable model based on nuclear geometry and local cell density that identifies morphometric states associated with RG-like competence across experimental conditions. Application of this framework to embryonic mouse and human cortex revealed analogous signatures in native RG populations. Together, these findings indicate that tissue architecture influences RG-like competence through conserved nuclear morphometric states across developmental contexts.

developmental biology↗

bioRxiv2022

CLIP-Seq Analysis Enables the Design of Ribosomal RNA Bait Oligonucleotides That Protect Against C9orf72 ALS/FTD-Associated Poly-GR Pathophysiology

Amyotrophic lateral sclerosis and frontotemporal dementia patients with a hexanucleotide repeat expansion in C9ORF72 (C9-HRE) accumulate poly-GR and poly-PR aggregates. The pathogenicity of these arginine-rich dipeptide repeats (R-DPRs) is thought to be driven by their propensity to bind to low complexity domains of multivalent proteins. However, the ability of R-DPRs to bind native RNA and the significance of this interaction remains unclear. We used computational and experimental approaches to characterize the physicochemical properties of R-DPRs and their interaction with RNA. We find that poly-GR predominantly binds ribosomal RNA (rRNA) in cells and exhibits an interaction that is predicted to be energetically stronger than that for associated ribosomal proteins. Critically, modified rRNA "bait" oligonucleotides restore poly-GR-associated ribosomal deficits in cells and ameliorate poly-GR toxicity in patient neurons and Drosophila models. Our work strengthens the hypothesis that ribosomal function is impaired by R-DPRs, highlights a role for direct rRNA binding in mediating ribosomal disfunction, and presents a strategy for protecting against C9-HRE pathophysiological mechanisms.

neuroscience↗

bioRxiv2021

Structure-based Design of CDC42 Effector Interaction Inhibitors For the Treatment of Cancer

CDC42 family GTPases (RHOJ, RHOQ, CDC42) are upregulated but rarely mutated in cancer and control both the ability of tumor cells to invade surrounding tissues and the ability of endothelial cells to vascularize tumors. Here we use computer-aided drug design to discover a new chemical entity (ARN22089) that targets CDC42 GTPases and blocks CDC42 effector interactions without affecting the binding between closely related GTPases (RAC1, RAS, RAL) and their downstream effectors. Our lead compound has broad activity against a panel of cancer cell lines, inhibits S6 phosphorylation and MAPK activation, activates pro-inflammatory and apoptotic signaling, and blocks tumor growth and angiogenesis in three-dimensional vascularized microtumor models (VMT) in vitro. In addition, ARN22089 has a favorable pharmacokinetic profile and can inhibit the growth of BRAF mutant mouse melanomas and patient-derived xenografts in vivo. Taken together, this work identifies a promising new class of therapeutic agents that influence tumor growth by modulating CDC42 signaling in both the tumor cell and its microenvironment.

molecular biology↗

bioRxiv2019

Nucleocytoplasmic Proteomic Analysis Uncovers ETF1 and Nonsense Mediated Decay as Modifiers of ALS C9orf72 Toxicity

The most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is a hexanucleotide repeat expansion in C9orf72 (C9-HRE). While RNA and dipeptide repeats produced by the C9-HRE disrupt nucleocytoplasmic transport, the proteins that become redistributed remain unknown. Here, we utilized subcellular fractionation coupled with tandem mass spectrometry and identified 126 proteins, enriched for protein translation and RNA metabolism pathways, which collectively drive a shift towards a more cytosolic proteome in C9-HRE cells. Amongst these was eRF1, which regulates translation termination and nonsense-mediated decay (NMD). eRF1 accumulates within elaborate nuclear envelope invaginations in patient iPSC-neurons and postmortem tissue and mediates a protective shift from protein translation to NMD-dependent mRNA degradation. Overexpression of eRF1 and the NMD-driver UPF1 ameliorate C9-HRE toxicity in vivo. Our findings provide a resource for proteome-wide nucleocytoplasmic alterations across neurodegeneration-associated repeat expansion mutations and highlight eRF1 and NMD as therapeutic targets in C9orf72-associated ALS/FTD.

neuroscience↗

bioRxiv2018

All-optical electrophysiology for high-throughput functional characterization of human iPSC-derived motor neuron model of ALS

Human induced pluripotent stem cell (iPSC)-derived neurons are an attractive substrate for modeling disease, yet the heterogeneity of these cultures presents a challenge for functional characterization by manual patch clamp electrophysiology. Here we describe an optimized all-optical electrophysiology, \"Optopatch\", pipeline for high-throughput functional characterization of human iPSC-derived neuronal cultures. We demonstrate the method in a human iPSC-derived motor neuron model of ALS. In a comparison of neurons with an ALS-causing mutation (SOD1 A4V) with their genome-corrected controls, the mutants showed elevated spike rates under weak or no stimulus, and greater likelihood of entering depolarization block under strong optogenetic stimulus. We compared these results to numerical simulations of simple conductance-based neuronal models and to literature results in this and other iPSC-based models of ALS. Our data and simulations suggest that deficits in slowly activating potassium channels may underlie the changes in electrophysiology in the SOD1 A4V mutation.

neuroscience↗