Biology subjects

Paton, A.

Publications and source records attributed to Paton, A..

4 recordsLinked to original sources

bioRxiv2026

Memory-based and surround-based pattern completion show distinct laminar profiles in human V1

Visual input is often incomplete, requiring the brain to infer missing information from prior experience or contextual cues. Establishing whether memory-derived and context-derived information shape pattern completion through shared or distinct top-down pathways is central to understanding how perception emerges from the integration of sensory input and prior knowledge. Across two experiments, we used 7T layer fMRI to measure activity in an occluded region of human V1 while participants viewed natural scenes. Memory-based completion was enabled by varying the level of exposure to full scene images before scanning, while surround-based completion was implemented via two scenes that were repeatedly presented in partially occluded form but never seen intact. In both fMRI experiments, category decoding in the occluded V1 region only emerged after multiple prior exposures, whereas novel scenes did not show reliable decoding. Repeated partially occluded scenes also supported decoding, despite the hidden region never being shown, consistent with surround-based pattern completion. Critically, mnemonic and surround-based pattern completion showed opposite laminar decoding profiles across V1 depths, with mnemonic feedback dominating deep layers, and surround-based feedback dominating superficial layers. Together, these findings suggest that completion in the early visual cortex depends on the sources of inferred information, revealing dissociable feedback pathways for memory- and context-driven inference.

neuroscience↗

bioRxiv2025

A facile and reproducible method for the purification of peptide- and protein-functionalized DNA nanostructures

DNA nanotechnology has emerged as a promising field for biomedical applications, both in the therapeutic and diagnostic domains. The ability of DNA nanostructures to carry cargos in precise numbers and orientations, makes them competitive candidates for drug delivery, biosensors or imaging agents. Two of the main challenges for translating DNA nanostructures from the laboratory to the clinic are achieving cost-effective largescale production and establishing comprehensive safety profiles. Having the ability to reliably and efficiently purify functionalized DNA nanostructures is key to both challenges, and an open question in the field of DNA nanotechnology. Here, we present a scalable method for the fast and efficient purification of high concentration of peptide- or protein-functionalized DNA nanostructures. We use a gravity-driven size exclusion chromatography approach, that has the potential to purify DNA nanostructures within 10 minutes, with yield up to 93% and purity up to 99% and is appropriate for both protein and peptide conjugates. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/658483v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@4e3ea5org.highwire.dtl.DTLVardef@f2f615org.highwire.dtl.DTLVardef@fa042aorg.highwire.dtl.DTLVardef@27942a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Identifying the gene responsible for NPQ reversal in Phaeodactylum tricornutum

Algae such as diatoms and haptophytes have distinct photosynthetic pigments from plants, including a novel set of carotenoids. This includes a primary xanthophyll cycle comprised of diadinoxanthin and its de-epoxidation product diatoxanthin that enables the switch between light harvesting and non-photochemical quenching (NPQ)-mediated dissipation of light energy. The enzyme responsible for the reversal of this cycle was previously unknown. Here, we identified zeaxanthin epoxidase 3 (ZEP3) from Phaeodactylum tricornutum as the candidate diatoxanthin epoxidase. Knocking out the ZEP3 gene caused a loss of rapidly reversible NPQ following saturating light exposure. This correlated with the maintenance of high concentrations of diatoxanthin during recovery in low light. Xanthophyll cycling and NPQ relaxation were restored via complementation of the wild type ZEP3 gene. The zep3 knockout strains showed reduced photosynthetic rates at higher light fluxes and reduced specific growth rate in variable light regimes, likely due to the mutant strains becoming locked in a light energy dissipation state. We were able to toggle the level of NPQ capacity in a time and dose dependent manner by placing the ZEP3 gene under the control of an inducible promoter. Identification of this gene provides deeper understanding of the diversification of photosynthetic control in algae compared to plants and suggests a potential target to improve the productivity of industrial-scale cultures.

plant biology↗

bioRxiv2021

The colonial legacy of herbaria

Herbarium collections shape our understanding of the worlds flora and are crucial for addressing global change and biodiversity conservation. The formation of such natural history collections, however, are not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the global North, the extent of this disparity has not been rigorously quantified to date. Here, by analyzing over 85 million specimen records and surveying herbaria across the globe, we assess the colonial legacy of botanical collections and how we may move towards a more inclusive future. We demonstrate that colonial exploitation has contributed to an inverse relationship between where plant biodiversity exists in nature and where it is housed in herbaria. Such disparities persist in herbaria across physical and digital realms despite overt colonialism having ended over half a century ago, suggesting ongoing digitization and decolonization efforts have yet to alleviate colonial-era discrepancies. We emphasize the need for acknowledging the inconvenient history of herbarium collections and the implementation of a more equitable, global paradigm for their collection, curation, and use.

ecology↗