Biology subjects

Wallace, H.

Publications and source records attributed to Wallace, H..

4 recordsLinked to original sources

bioRxiv2025

Three-dimensional Tracking Method for Water-Hopping Mudskippers in Natural Habitats

We present a portable, non-invasive, and low-cost three-dimensional tracking method to quantify in situ water-hopping kinematics of mudskippers. By combining dual-camera video recordings with tracking fish path, Gaussian Splatting terrain reconstruction and epipolar geometric analysis, we capture detailed 3D trajectories of mudskippers in their natural tidal-flat habitats. Our proposed method resolves complex hopping motions, including both straight and curved escape paths, and reveals that horizontal distance, hopping height, and speed are strongly influenced by fish size and local terrain features. These results highlight both the biomechanical and ecological significance of water-hopping in mudskippers, demonstrating how a simple, deployable 3D approach can resolve complex amphibious movements in challenging field environments.

animal behavior and cognition↗

bioRxiv2025

Multi-omic analysis of the ciliogenic transcription factor RFX3 reveals a role in promoting activity-dependent responses via enhancing CREB binding in human neurons

Heterozygous loss-of-function (LoF) variants in RFX3, a transcription factor known to play key roles in ciliogenesis, result in autism spectrum disorder (ASD) and neurodevelopmental delay. RFX binding motifs are also enriched upstream of genes found to be commonly dysregulated in transcriptomic analyses of brain tissue from individuals with idiopathic ASD. Still, the precise functions of RFX3 in the human brain is unknown. Here, we studied the impact of RFX3 deficiency using human iPSC-derived neurons and forebrain organoids. Biallelic loss of RFX3 disrupted ciliary gene expression and delayed neuronal differentiation, while monoallelic loss of RFX3 did not. Instead, transcriptomic and DNA binding analyses demonstrated that monoallelic RFX3 loss disrupted synaptic target gene expression and diminished neuronal activity-dependent gene expression. RFX3 binding sites co-localized with CREB binding sites near activity-dependent genes, and RFX3 deficiency led to decreased CREB binding and impaired induction of CREB targets in response to neuronal depolarization. This study demonstrates a novel role of the ASD-associated gene RFX3 in shaping neuronal synaptic development and plasticity.

neuroscience↗

bioRxiv2024

Mastering the Manu - How humans create large splashes

Manu jumping, a popular water diving style amongst M[a]ori people in New Zealand, focuses on creating large splashes. Divers perform aerial maneuvers such as the "utkatasana" pose, entering the water in a V-shape, and executing underwater maneuvers to maximize the splash size. Our study explores the underlying fluid dynamics of Manu jumping and demonstrates how two key parameters, the V-angle and the timing of body opening, can maximize the Worthington jet formation. To accurately replicate human manu jumping, we studied water entry of both passive solid objects with varying V angles and an active body opening robot (Manubot). The analysis revealed that a 45-degree V angle is optimal for maximizing Worthington jet formation, consistent with human diving data. This angle balances a large cavity size and a deep pinch-off depth. The body opening within a timing window of [Formula] synchronizes the robots potential energies to be timely transferred to the cavity formation, producing the strongest and most vertical, i.e., ideal, Worthington jets. Based on our experimental findings, we propose optimal parameters for generating the largest Manu splashes. These insights offer engineering perspectives on how to modulate underwater cavity dynamics using both passive and active body formations.

biophysics↗

bioRxiv2023

De novo Design of Peptides that Bind Specific Conformers of α-Synuclein

Insoluble amyloids rich in cross-{beta} fibrils are observed in a number of neurodegenerative diseases. Depending on the clinicopathology, the amyloids can adopt distinct supramolecular assemblies, termed conformational strains. However, rapid methods to study amyloid in a conformationally specific manner are lacking. We introduce a novel computational method for de novo design of peptides that tile the surface of -synuclein fibrils in a conformationally specific manner. Our method begins by identifying surfaces that are unique to the conformational strain of interest, which becomes a "target backbone" for the design of a peptide binder. Next, we interrogate structures in the PDB database with high geometric complementarity to the target. Then, we identify secondary structural motifs that interact with this target backbone in a favorable, highly occurring geometry. This method produces monomeric helical motifs with a favorable geometry for interaction with the strands of the underlying amyloid. Each motif is then symmetrically replicated to form a monolayer that tiles the amyloid surface. Finally, amino acid sequences of the peptide binders are computed to provide a sequence with high geometric and physicochemical complementarity to the target amyloid. This method was applied to a conformational strain of -synuclein fibrils, resulting in a peptide with high specificity for the target relative to other amyloids formed by -synuclein, tau, or A{beta}40. This designed peptide also markedly slowed the formation of -synuclein amyloids. Overall, this method offers a new tool for examining conformational strains of amyloid proteins.

biophysics↗