Biology subjects

Webb, R.

Publications and source records attributed to Webb, R..

4 recordsLinked to original sources

bioRxiv2025

Is the whole the sum of its parts? Neural computation of consumer bundle valuation in humans

Humans are often tasked with making decisions about bundles of multiple items and very little is known about how the human brain aggregates, computes and represents value in such cases. We investigated how the human brain evaluates consumer items, both individually and in bundles, and how this activity relates to choice behavior. Participants underwent a deep-fMRI scanning protocol while we elicited behavioral valuations for single and bundled items. Behaviorally, we find that bundle values are sub-additively discounted compared to the sum of individual item values. Neurally, we find that the same distributed network in pre-frontal cortex computes the value of a bundle and its constituent individual items, but the value representation undergoes a normalization that actively re-scales across bundle and single item contexts. These findings suggest that generalized value regions contextually adapt within a valuation hierarchy, as opposed to utilizing an absolute value code.

neuroscience↗

bioRxiv2025

MotorBench: A Cryo-Electron Tomography Dataset of Bacterial Flagellar Motors for Testing Detection Algorithms

Understanding bacterial nanomachines like flagellar motors, which are crucial for pathogenic bacteria motility, is vital for microbiological and therapeutic research. Cryogenic electron tomography (cryo-ET) enables visualization of these structures within cells at near-native conditions. But manual identification remains challenging due to low contrast, limited resolution, and crowded in vivo environments. To address this, we introduce MotorBench, an expert-annotated dataset of bacterial flagellar motors that has been curated as part of a Kaggle competition BYU - Locating Bacterial Flagellar Motors 2025, engaging data scientists globally to create automated detection algorithms. MotorBench and its accompanying tools are intended to serve as a benchmark for evaluating and comparing future algorithms in automated cryo-ET analysis.

molecular biology↗

bioRxiv2020

APEX-Gold: A genetically-encoded particulate marker for robust 3D electron microscopy

Genetic tags allow rapid localization of tagged proteins in cells and tissues. APEX, an ascorbate peroxidase, has proven to be one of the most versatile and robust genetic tags for ultrastructural localization by electron microscopy. Here we describe a simple method, APEX-Gold, which converts the diffuse oxidized diaminobenzidine reaction product of APEX into a silver/gold particle akin to that used for immunogold labelling. The method increases the signal to noise ratio for EM detection, providing unambiguous detection of the tagged protein, and creates a readily quantifiable particulate signal. We demonstrate the wide applicability of this method for detection of membrane proteins, cytoplasmic proteins and cytoskeletal proteins. The method can be combined with different electron microscopic techniques including fast freezing and freeze substitution, focussed ion beam scanning electron microscopy, and electron tomography. The method allows detection of endogenously expressed proteins in genome-edited cells. We make use of a cell-free expression system to generate membrane particles with a defined quantum of an APEX-fusion protein. These particles can be added to cells to provide an internal standard for estimating absolute density of expressed APEX-fusion proteins.

cell biology↗

bioRxiv2017

Effects Of Curcumin Nanoformulations On Cellular Function In Niemann-Pick Disease Type C Astrocytes

Niemann-Pick disease type C1 (NPC disease) is a neurodegenerative multi-lipid lysosomal storage disease caused by mutations in the NPC1 gene presenting with reduced lysosomal Ca2+ signalling and inhibited late endosome-lysosome transport. Elevating cytosolic Ca2+ levels in NPC cells has been shown to reduce lysosomal lipid storage. Treating Npc1-/- mice with the Ca2+ modulator curcumin led to reduced lipid storage, improved life expectancy and function. These studies led to reported utilisation of curcumin supplements by NPC disease families despite there being no clinical evidence of benefit and a report indicating no benefit of nanoformulated curcumin in Npc1-/- mice. The aim of this study was to determine whether various commercially available curcumin nanoformulations were capable of reproducing the findings obtained with unformulated pharmaceutical grade curcumin. We compared seven curcumin nanoformulations in Npc1-/- mouse astrocytes. All the nanoformulations elevate cytosolic Ca2+ levels but only two lowered lysosomal lipid storage. Importantly, some caused elevations in NPC lysosomal storage and/or decreased cellular viability. Although this is an in vitro study, our findings suggest that care should be taken when contemplating the use of curcumin supplements for NPC disease.

pharmacology and toxicology↗