Biology subjects

Carey, S.

Publications and source records attributed to Carey, S..

7 recordsLinked to original sources

bioRxiv2026

Proteomic Analysis Reveals Widespread Regulation of Substrate Protein Abundance by O-fucosylation and O-GlcNAcylation

O-glycosylation of nucleocytosolic proteins by the Arabidopsis enzymes SPINDLY (SPY; O-fucosyltransferase) and SECRET AGENT (SEC; O-GlcNAc transferase) is essential for plant growth and development, yet the scope of their substrates and regulatory impact remains poorly defined. Here, we combined TurboID-based proximity labeling with quantitative proteomics to systematically map the SPY interactome and determine how SPY- and SEC-dependent modifications influence protein abundance. A functional SPY-TD enriched 221 proxiome proteins, including 80 known O-fucosylated substrates and 141 new interactors. The SPY-TD proxiome is enriched in nuclear pore components, chromatin regulators, transcription factors, and RNA-processing proteins. Integration with O-fucose and O-GlcNAc datasets yielded a comprehensive Arabidopsis SPY/SEC (At-S/S) protein list of 886 candidates. We quantified proteome-wide changes in spy single mutants and inducible spy sec double mutants. Loss of SPY alone caused selective stabilization or destabilization of targets, whereas combined SPY/SEC depletion triggered widespread, synergistic protein abundance changes, particularly affecting nucleoporins, transcriptional regulators, and RNA-binding proteins. Integration with ubiquitination datasets revealed extensive overlap, supporting potential crosstalk between O-fucosylation, O-GlcNAcylation, and ubiquitin-mediated protein turnover. Together, our study establishes proximity labeling as a powerful strategy to define plant O-glycosylation networks and reveals dual, context-dependent roles of SPY and SEC in controlling protein homeostasis and stress-responsive pathways.

systems biology↗

bioRxiv2025

Next-Generation Mapping of the ACINUS-Mediated Alternative Splicing Machinery and Its Regulation by O-glycosylation in Arabidopsis

Alternative splicing (AS) is a key mechanism of gene regulation, but the full repertoire of proteins involved and the regulatory mechanisms governing this process remain poorly understood. Using TurboID-based proximity labeling coupled with mass spectrometry (PL-MS), we comprehensively mapped the Arabidopsis AS machinery, focusing on the evolutionarily conserved splicing factor ACINUS, its paralog PININ, and the stable interactor SR45. We identified 298 high-confidence components, including both established and novel interactors, providing strong evidence that alternative splicing is coupled to transcription and that multiple RNA processing steps occur simultaneously in plants. Bioinformatic analysis reveals high redundancy, conserved mechanisms, and unique plant-specific features. Selected known and novel interactors were validated by AS readouts and phenotypic analysis, which also revealed a coordinated influence on splicing. Furthermore, a systematic evaluation of O-glycosylation double mutants revealed that SECRET AGENT (O-GlcNAc transferase) and SPINDLY (O-fucose transferase) modulate AS through both ACINUS-dependent and -independent pathways. Our results reveal the conserved as well as plant-specific AS regulatory network and highlight the global role of sugar modification in RNA processing.

plant biology↗

bioRxiv2024

Reasoning by exclusion in food-caching Eurasian jays (Garrulus glandarius)

Two related methods have been widely used to test animals capacity to reason by exclusion: Calls (2004) 2-cups task, where subjects choose between two cups in which one reward was hidden and the empty cup is revealed; and Premack & Premacks task (1994) where one reward goes in each of the two cups and one reward is removed. In both cases, success is identifying the cup with the reward. It has been suggested that among corvids, the demands associated with caching may foster exclusion abilities by reinforcing the experience of relevant contraries (e.g., empty vs. full), or by supporting domain general capacities that support caching and exclusion inferences. However, Shaw et al. (2013) found that Eurasian jays, proficient cachers, failed a version of Calls 2-cups task. To further test the caching hypothesis, we amended the procedure using invisible displacement to hide rewards, removing aspects of Shaw et al.s procedure that may have masked competence of Eurasian jays. We tested seven Eurasian jays, who showed spontaneous success on both Calls 1-reward/show-empty (80% correct) and Premack and Premacks 2-reward/remove-1 (85% correct). These results align with the hypothesis that corvids exclusion reasoning is related to caching behaviour.

animal behavior and cognition↗

bioRxiv2024

Influence of Cognitive Demand and Auditory Noise on Postural Dynamics

The control of human balance involves an interaction between the human motor, cognitive, and sensory systems. The dynamics of this interaction are yet to be fully understood, however, work has shown the performance of cognitive tasks to have a hampering effect on motor performance, while additive sensory noise to have a beneficial effect. The current study aims to examine whether postural control will be impacted by a concurrent working memory task, and similarly, if additive noise can counteract the expected negative influence of the added cognitive demand. Postural sway of healthy young adults was collected during the performance of a modified N-back task with varying difficulty, in the presence and absence of auditory noise. Our results show a reduction in postural stability scaled to the difficulty of the cognitive task, but this effect is less prominent in the presence of additive noise. Additionally, by separating postural sway into different frequency bands, typically used to assess the exploratory vs feedback-driven stabilizing dynamics of sway, we found a differential effect between the cognitive task and additive noise, thus demonstrating that both frequency regimes of postural sway are sensitive to high cognitive load and increased sensory information.

neuroscience↗

bioRxiv2022

JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom

Gene functional descriptions, which are typically derived from sequence similarity to experimentally validated genes in a handful of model species, offer a crucial line of evidence when searching for candidate genes that underlie trait variation. Plant responses to environmental cues, including gene expression regulatory variation, represent important resources for understanding gene function and crucial targets for plant improvement through gene editing and other biotechnologies. However, even after years of effort and numerous large-scale functional characterization studies, biological roles of large proportions of protein coding genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, a public and updateable data resource consisting of transcript abundance assays from 2,090 samples derived from 604 tissues or conditions across 18 diverse species. We integrated across these diverse conditions and genotypes by analyzing expression profiles, building gene clusters that exhibited tissue/condition specific expression, and testing for transcriptional modulation in response to environmental queues. For example, we discovered extensive phylogenetically constrained and condition-specific expression profiles across many gene families and genes without any functional annotation. Such conserved expression patterns and other tightly co-expressed gene clusters let us assign expression derived functional descriptions to 64,620 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome-next.jgi.doe.gov), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

plant biology↗

bioRxiv2020

Motor variability prior to learning is a poor predictor of the ability to adopt new movement solutions

Many contexts in motor learning require a learner to change from an existing movement solution to a novel movement solution to perform the same task. Recent evidence has pointed to motor variability prior to learning as a potential marker for predicting individual differences in motor learning. However, it is not known if this variability is predictive of the ability to adopt a new movement solution for the same task. Here, we examined this question in the context of a redundant precision task requiring control of motor variability. Fifty young adults learned a precision task that involved throwing a virtual puck toward a target using both hands. Because the speed of the puck depended on the sum of speeds of both hands, this task could be achieved using multiple solutions. Participants initially performed a baseline task where there was no constraint on the movement solution, and then performed a novel task where they were constrained to adopt a specific movement solution requiring asymmetric left and right hand speeds. Results showed that participants were able to learn the new solution, and this change was associated with changes in both the amount and structure of variability. However, individual differences in baseline motor variability were only weakly correlated with initial and final task performance when using the new solution, with greater variability being associated with higher errors. We also found a strong specificity component - initial variability when using the new solution was highly correlated with final task performance with the new solution, but once again, higher variability was associated with greater errors. These results suggest that motor variability is not necessarily indicative of flexibility and highlight the need to consider the task context in determining the relation between motor variability and learning.

neuroscience↗

bioRxiv2018

How to Build a Fruit: Transcriptomics of a Novel Fruit Type in the Brassiceae

Comparative gene expression studies are invaluable for predicting how existing genetic pathways may be modified or redeployed to produce novel and variable phenotypes. Fruits are ecologically important organs because of their impact on plant fitness and seed dispersal, modifications in which results in morphological variation across species. A novel fruit type in the Brassicaceae known as heteroarthrocarpy enables distinct dispersal methods in a single fruit through segmentation via a lateral joint and variable dehiscence at maturity. Given the close relationship to Arabidopsis, species that exhibit heteroarthrocarpy are powerful models to elucidate how differences in gene expression of a fruit patterning pathway may result in novel fruit types. Transcriptomes of distal, joint, and proximal regions from Erucaria erucarioides and Cakile lanceolata were analyzed to elucidate within and between species differences in whole transcriptome, gene ontology, and fruit patterning expression profiles. Whole transcriptome expression profiles vary between fruit regions in patterns that are consistent with fruit anatomy. These transcriptomic variances do not correlate with changes in gene ontology, as they remain generally stable within and between both species. Upstream regulators in the fruit patterning pathway, FILAMENTOUS FLOWER and YABBY3, are expressed in the distal and proximal regions of E. erucarioides, but not in the joint, implicating alterations in the pathway in heteroarthrocarpic fruits. Downstream gene, INDEHISCENT, is significantly upregulated in the abscissing joint region of C. lanceolata, which suggests repurposing of valve margin genes for novel joint disarticulation in an otherwise indehiscent fruit. In summary, these data are consistent with modifications in fruit patterning genes producing heteroarthrocarpic fruits through different components of the pathway relative to other indehiscent, non-heteroarthrocarpic, species within the family. Our understanding of fruit development in Arabidopsis is now extended to atypical siliques within the Brassicaceae, facilitating future studies on seed shattering in important Brassicaceous crops and pernicious weeds.

plant biology↗