Biology subjects

Amaral, L.

Publications and source records attributed to Amaral, L..

8 recordsLinked to original sources

bioRxiv2025

Dual effect of alpha-synuclein disease variants on condensate formation

-synuclein is a pre-synaptic protein1,2 implicated in synucleinopathies like Parkinsons disease and Dementia with Lewy Bodies, where it accumulates in intracellular aggregates termed Lewy bodies and Lewy neurites3. Recent studies have reported that -synuclein undergoes phase separation to form biomolecular condensates both in vitro and in mammalian cells4-7. -synuclein condensates are thought to contribute to disease through progressive aggregation5,8,9. Here we show that specific PD-associated -synuclein variants fail to form biomolecular condensates. We demonstrate that only two -synuclein variants associated with familial disease, E46K and E83Q, enhance condensate formation in vitro and in cells. However, variants including A30G, G51D, and A53E fail to form or have reduced levels of condensate formation in cells. The same phenotypes are reflected in the budding yeast model showing differential inclusion formation. In iPSC-derived neurons, the propensity of -synuclein variants to undergo VAMP2-mediated phase separation reflects the level of synaptic enrichment. We show that the intrinsic propensity of -synuclein to form condensates and the ability to bind lipid membranes are important to mediate condensate formation in cells. Our results emphasize that -synuclein pathology follows divergent pathways, with both increased and decreased condensate formation contributing to disease. This study establishes biomolecular condensates as a key intermediate in -synuclein dysfunction, providing a novel foundation for translational research.

neuroscience↗

bioRxiv2025

Tool-use brain representations are independent of the acting body part and motor experience

The sensorimotor system is broadly organized somatotopically. However, an action-type organization has also been found: a division based on action-type independent of acting body parts has been shown for reaching and grasping actions. Does this generalization extend to non-ethological actions? Here, we examined fMRI responses for tool-use actions that participants performed with their hands or feet. We additionally tested individuals born without hands to control for hand motor imagery when performing foot actions. We show that the primary sensorimotor cortices have hand and foot selectivity, consistent with a somatotopic organization. In contrast, higher-level motor areas within the tool-use network, such as the premotor cortex, supplementary motor area, and superior parietal cortices, showed a shared preference for tool-use independent of the executing body part and sensorimotor experience. Multivariate decoding of action-type in these areas generalized between controls hand and foot and was successful in individuals born without hands. Finally, the temporal dynamics pattern in primary and association areas carried effector-specific and action-type information, respectively. Altogether, we show that the tool-use network in motor association areas represents higher-order action information beyond concrete motor parameters associated with specific effectors, and regardless of hand motor experience. This suggests that an action-type, effector-independent organization extends beyond ethological actions, supporting a hierarchical organization in the action domain. Further, it shows that functional organization in congenital handlessness is based on the hierarchical organization of the intact cortex.

neuroscience↗

bioRxiv2024

The antifungal activity of cymoxanil is associated with proton pump inhibition and disruption of plasma membrane potential

Worldwide use of agrochemicals, particularly pesticides, is necessary to increase agricultural production to feed the ever-growing population. However, despite widespread use, the biochemical mode of action of many agrochemicals and their potential deleterious effects on the environment are poorly characterized. Cymoxanil (CYM) is a fungicide used to combat downy mildew diseases in grapevine cultures and late blight diseases in tomato and potato cultures caused by the oomycetes Plasmopara viticola and Phytophthora infestans, respectively. Previous reports indicate that CYM affects growth, DNA and RNA synthesis in Phytophthora and inhibits cell growth, biomass production and respiration rate in the well-characterized fungal model Saccharomyces cerevisiae. We therefore used this model to further dissect mechanisms underlying the toxicological effects of CYM. We found that CYM induced genome-wide alterations, particularly in membrane transporter systems. These alterations were associated with perturbations in lipid-raft organization and inhibition of Pma1p, leading to a decrease in plasma membrane potential and intracellular acidification. Altogether, these findings identify the plasma membrane as one of the targets of CYM and proposes a mode of action underlying its antifungal activity.

cell biology↗

bioRxiv2024

Unraveling the impact of congenital deafness on individual brain organization

Research on brain plasticity, particularly in the context of deafness, consistently emphasizes the reorganization of the auditory cortex. However, a critical question arises: to what extent do all individuals with deafness show the same level of reorganization? To address this question, we examined the individual differences in deafness functional connectivity (FC), specifically from the deprived auditory cortex. Our findings demonstrate a remarkable differentiation between individuals deriving from the absence of shared auditory experiences, resulting in heightened FC variability among deaf individuals, compared to more consistent FC in the hearing group. Notably, connectivity to language regions becomes more diverse across individuals in deafness. This does not stem from delayed language acquisition, as it is found in deaf native signers, who are exposed to rich natural language since birth. However, comparing FC diversity between deaf native signers and deaf delayed signers who were deprived of language in early development, we show that language experience also impacts individual differences, although to a more moderate extent. Overall, our research points out the intricate interplay between brain plasticity and individual differences, shedding light on the diverse ways reorganization manifests among individuals. It further joins findings in blindness, showing that individual differences are affected by sensory experience. Finally, these findings highlight the importance of considering individual differences in personalized rehabilitation for hearing loss.

neuroscience↗

bioRxiv2023

Longitudinal stability of individual brain plasticity patterns in blindness

The primary visual cortex (V1) in individuals born blind is engaged in a wide spectrum of tasks and sensory modalities, including audition, touch, language, and memory. This widespread involvement raises questions regarding the constancy of its role and whether it might exhibit flexibility in its function over time, connecting to diverse network functions in response to task-specific demands. This would suggest that reorganized V1 takes on a role similar to cognitive multiple-demand system regions. Alternatively, it is possible that the varying patterns of plasticity observed in the blind V1 can be attributed to individual factors, whereby different blind individuals recruit V1 for different functions, highlighting the immense idiosyncrasy of plasticity. In support of this second account, we have recently shown that V1 functional connectivity varies greatly across blind individuals. But do these represent stable individual patterns of plasticity or merely instantaneous changes, for a multiple-demand system now inhabiting V1? Here we tested if individual connectivity patterns from the visual cortex of blind individuals are stable over time. We show that over two years, fMRI functional connectivity from the primary visual cortex is unique and highly stable in a small sample of repeatedly sampled congenitally blind individuals. Further, using multivoxel pattern analysis, we demonstrate that the unique reorganization patterns of these individuals allow decoding of participant identity. Together with recent evidence for substantial individual differences in visual cortex connectivity, this indicates there may be a consistent role for the visual cortex in blindness, which may differ for each individual. Further, it suggests that the variability in visual reorganization in blindness across individuals could be used to seek stable neuromarkers for sight rehabilitation and assistive approaches.

neuroscience↗

bioRxiv2021

Disentangling hand and tool processing: distal effects of neuromodulation

The neural processing within a brain region that responds to more than one object category can be separated by looking at the horizontal modulations established by that region, which suggests that local representations can be affected by connections to distal areas, in a category-specific way. Here we first wanted to test whether by applying transcranial direct current stimulation (tDCS) to a region thatre sponds both to hands and tools (posterior middle temporal gyrus; pMTG), while participants performed either a hand- or tool-related training task, we would be able to specifically target the trained category, and thereby dissociate the overlapping neural processing. Second, we wanted to see if these effects were limited to the target area or extended to distal but functionally connected brain areas. After each combined tDCS and training session, participants therefore viewed images of tools, hands, and animals, in an fMRI scanner. Using multivoxel pattern analysis, we found that tDCS stimulation to pMTG indeed improved the classification accuracy between tools vs. animals, but only when combined with a tool training task (not a hand training task). However, surprisingly, tDCS stimulation to pMTG also improved the classification accuracy between hands vs. animals when combined with a tool training task (not a hand training task). Our findings suggest that overlapping but functionally-specific networks can be separated by using a category-specific training task together with tDCS - a strategy that can be applied more broadly to other cognitive domains using tDCS - and demonstrates the importance of horizontal modulations in objectcategory representations.

neuroscience↗

bioRxiv2020

Subcutaneous nanotherapy repurposes the immunosuppressive mechanism of rapamycin to enhance allogeneic islet graft viability

Oral rapamycin administration rapamycin is plagued by poor bioavailability and wide biodistribution. Thus, this pleotropic mTOR inhibitor has a narrow therapeutic window, numerous side effects and provides inadequate transplantation protection. Parental formulation was not possible due to rapamycins hydrophobicity (log P 4.3). Here, we demonstrate that subcutaneous rapamycin delivery via poly(ethylene glycol)-b-poly(propylene sulfide)(PEG-b-PPS) polymersome (PS) nanocarriers modulates cellular biodistribution of rapamycin to change its immunosuppressive mechanism for enhanced efficacy while minimizing side effects. While oral rapamycin inhibits naive T cell proliferation directly, subcutaneously administered rapamycin-loaded polymersomes (rPS) instead modulated Ly-6Clow monocytes and tolerogenic semi-mature dendritic cells, with immunosuppression mediated by CD8+ Tregs and rare CD4+ CD8+ double-positive T cells. As PEG-b-PPS PS are uniquely non-inflammatory, background immunostimulation from the vehicle was avoided, allowing immunomodulation to be primarily attributed to rapamycins cellular biodistribution. Repurposing mTOR inhibition significantly improved maintenance of normoglycemia in a clinically relevant, MHC-mismatched, allogeneic, intraportal (liver) islet transplantation model. These results demonstrate the ability of engineered nanocarriers to repurpose drugs for alternate routes of administration by rationally controlling cellular biodistribution.

bioengineering↗

bioRxiv2019

Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila

Mosaic analysis provides a means to probe developmental processes in situ by generating loss-of-function mutants within otherwise wildtype tissues. Combining these techniques with quantitative microscopy enables researchers to rigorously compare RNA or protein expression across the resultant clones. However, visual inspection of mosaic tissues remains common in the literature because quantification demands considerable labor and computational expertise. Practitioners must segment cell membranes or cell nuclei from a tissue and annotate the clones before their data are suitable for analysis. Here, we introduce Fly-QMA, a computational framework that automates each of these tasks for confocal microscopy images of Drosophila imaginal discs. The framework includes an unsupervised annotation algorithm that incorporates spatial context to inform the genetic identity of each cell. We use a combination of real and synthetic validation data to survey the performance of the annotation algorithm across a broad range of conditions. By contributing our framework to the open-source software ecosystem, we aim to contribute to the current move toward automated quantitative analysis among developmental biologists.\n\nAuthor summaryBiologists use mosaic tissues to compare the behavior of genetically distinct cells within an otherwise equivalent context. The ensuing analysis is often limited to qualitative insight. However, it is becoming clear that quantitative models are needed to unravel the complexities of many biological systems. In this manuscript we introduce Fly-QMA, an open-source software framework that automates the quantification of mosaic analysis for Drosophila imaginal discs, a common setting for studies of developmental processes. The software automatically extracts quantitative measurements from confocal images of mosaic tissues, rectifies any cross-talk between fluorescent reporters, and identifies clonally-related subpopulations of cells. Together, these functions allow users to rigorously ascribe changes in gene expression to the presence or absence of particular genes. We validate the performance of our framework using both real and synthetic data. Through its publication, we aim to contribute to the current move toward automated quantitative analysis among biologists.

systems biology↗