Biology subjects

Gallagher, R.

Publications and source records attributed to Gallagher, R..

14 recordsLinked to original sources

bioRxiv2026

Trait - climate relations in Themeda triandra: a widely distributed C4 grass and crop wild relative

O_LIQuantifying relationships between traits and climate using plants collected from diverse climatic origins, grown under common conditions, potentially provides valuable insights into climate adaptation. C_LIO_LIWe report on fifteen accessions of kangaroo grass (Themeda triandra), a C4 species distributed across Australia, Asia, the Middle East and Africa from the Andropogoneae clade of grasses that is vital to global agriculture. Plants were grown to maturity in glasshouses under two thermal regimes, with ample water supplied. Numerous physiological, "economic" and developmental traits were characterised. C_LIO_LIAs expected, plants grown at 20{degrees}C maxima had lower photosynthetic rates (Asat) and dark respiration rates, reduced leaf expansion, and delayed flowering compared with plants grown at 30{degrees}C. However, surprisingly few traits varied with climate-of-origin: accessions from colder climates had higher Asat alongside lower leaf mass per area, but only when grown at 20{degrees}C; flowering time showed the strongest correlation with site climate, with plants from wetter, warmer or less variable climates taking longer to flower. C_LIO_LIOur findings highlight remarkable phenotypic flexibility in key traits of T. triandra; this flexibility is likely key to its wide distribution. The strong relationship between flowering time and climate-of-origin underscores the importance of reproductive phenology as an adaptive trait. C_LI

ecology↗

bioRxiv2025

Conserved strategies underpin the replicated evoluton of aridity tolerance in trees

Predicting forest responses to climate change requires a detailed understanding of trait-environment coordination. Adaptation to environment comprises both conserved and labile components of trait variation. However, few studies explore the decomposition of trait-environment relationships in a rigorous phylogenetic framework. Combining a revised phylogeny with trait, climate and soil data to achieve unprecedented species coverage ([~]85%), we identified patterns of replicated evolution that allowed the evergreen tree genus, Eucalyptus, to rapidly radiate across Australia in response to aridification. Eucalypts from arid regions are short, produce dense wood, and have small, physically robust leaves with high nitrogen content, promoting hydraulic safety and economies in photosynthetic water use. Phylogenetic modelling reveals strong niche conservatism, with adaptation to aridity occurring primarily via clade-level divergences, followed by phylogenetically independent adjustments to local conditions. Ancestral state reconstructions accounting for trends in the paleoclimate record indicate that transitions in aridity tolerance are associated with distinct signals of environmental filtering and directional selection on functional trait variation. However, astonishing repeatability of trait changes in different clades reveals a narrow optimal solution to water availability, opening a path to predict future species distributions from phylogenetically structured trait data and signalling major implications for functional and species diversity under progressive climate change.

evolutionary biology↗

bioRxiv2024

Seed banking alters native seed microbiome composition and function relative to natural populations

O_LISeed banks are a vital resource for preserving plant species diversity globally. However, seedling establishment and survival rates from banked seeds can be poor. Despite a growing appreciation for the role of seed microbiota in supporting seed quality and plant health, our understanding of the effects of conventional seed banking processes on seed microbiomes remains limited. C_LIO_LIWe investigated the composition and functional potential of the epiphytic seed microbiome of a native plant species using both 16S rRNA gene sequencing and culture-based approaches. C_LIO_LIComparing the bacterial community composition of freshly collected seeds and those sourced from seed banking organisations, we found stored seeds hosted significantly less diverse bacterial populations, with substantial reductions in both low-abundance taxa and some core community members identified in unstored seeds. Bacteria with key plant growth promoting traits including IAA production, ACC deaminase activity, phosphate solubilisation, siderophore activity, and nitrogen fixation were identified in seed epiphytic communities, but these beneficial traits were less prevalent in stored seed compared to fresh seeds. C_LIO_LIOverall, these results suggest that epiphytic seed microbiomes may undergo significant changes during the storage process, selecting for bacteria tolerant to storage conditions, and potentially reducing the population of plant-growth promoting bacteria on seeds. C_LI

microbiology↗

bioRxiv2023

Gene expression response to temperature acclimation in a model photoheterotrophic marine flavobacterium (Dokdonia sp. MED134)

Temperature stands as one of the key factors influencing the community structure and distribution of marine microorganisms. Yet, the physiological adaptations of marine bacteria to rising temperatures remain underexplored. This study examines the transcriptional response of Dokdonia sp. MED134, a proteorhodopsin-based phototrophic organism within the class Flavobacteriia, to a gradient of temperature acclimation conditions from 10 to 34{degrees}C. Light availability during day/night cycles exerted minimal influence on the transcriptional patterns of this strain, with only a few genes mostly related to light sensing, light protecting mechanisms and phototrophy being upregulated during daytime. By contrast, temperature significantly impacted the expression of a large fraction of MED134 genes (>60%), including components of the stress response, cellular translation, DNA replication, and some metabolic pathways such as the anaplerotic carbon fixation and the glyoxylate shunt, suggesting intracellular carbon flow adjustments to temperature. Notably, the expression of some highly expressed TonB transporters, prominent in flavobacteria, was also temperature-sensitive. Our findings provide insights into the transcriptional adjustments of Dokdonia sp. MED134 in response to temperature variations, suggesting potential implications for carbon cycling and organic matter processing in marine environments.

microbiology↗

bioRxiv2023

A near-complete dataset of plant growth form, life history, and woodiness for all Australian plants

Tabular records of plant trait data are essential for diverse research purposes. Here we present scorings for a trio of core plant traits, plant growth form, woodiness, and life history, for nearly all accepted taxon concepts included in the Australian Plant Census (APC). This dataset is predominately derived from Australias state and national floras, supplemented by the taxonomic literature and diverse web resources. In total, 29,993 species and infraspecific taxa were scored for plant growth form, 30,279 for woodiness, and 30,056 for life history, with taxa scored as displaying a single or multiple trait values, as appropriate. This resource will enable rapid assessment of plant responses to disturbance events and new biogeographic analyses of trait distributions.

ecology↗

bioRxiv2023

Insects pollinated flowering plants for most of angiosperm evolutionary history

O_LIPollination is a fundamental process driving the speciation of angiosperms (flowering plants). Most contemporary angiosperms are insect pollinated, but abiotic pollination by wind or water and vertebrate pollination by birds or mammals occurs in many lineages. We model the evolution of pollination across angiosperms and quantify the timing and environmental associations of pollination shifts. C_LIO_LIWe use a robust dated phylogeny and trait-independent species-level sampling across all families of angiosperms to model the evolution of pollination modes. Data on the pollination system or syndrome of 1160 species were collated from primary literature. C_LIO_LIAngiosperms were ancestrally insect pollinated, and insects have pollinated angiosperms for approximately 86% of angiosperm evolutionary history. Wind pollination evolved at least 42 times, with few reversals back to animal pollination. Transitions between insect and vertebrate pollination were more frequent: vertebrate pollination evolved at least 39 times from an insect pollinated ancestor with at least 26 reversals. The probability of wind pollination increases with habitat openness (measured by Leaf Area Index) and with distance from the equator. C_LIO_LIOur reconstruction of pollination across angiosperms sheds light on a key question in angiosperm macroevolution, highlighting the long history of interactions between insect pollinators and angiosperms still vital to global biodiversity today. C_LI

evolutionary biology↗

bioRxiv2022

Socioeconomics and biogeography jointly drive geographic biases in our knowledge of plant traits: a global assessment of the Raunkiaerian shortfall in plants

The traits of plants determine how they interact with each other and their environment, constituting key knowledge for diverse fields. The lack of comprehensive knowledge of plant traits (the "Raunkiaerian shortfall") poses a major, cross-disciplinary, barrier to scientific advancement. Spatial biases in trait coverage may also lead to erroneous conclusions affecting ecosystem management and conservation planning. Thus, there is an urgent need to assess the spatial completeness of plant trait data, understand drivers of geographic biases, and to identify solutions for filling regional gaps. Here, we leverage a comprehensive set of regional species checklists for vascular plants and trait data for 2,027 traits and 128,929 plant species from the TRY database to assess trait data completeness across the globe. We show that trait data availability in TRY is associated with socioeconomic and biological factors influencing sampling likelihood: trait completeness was positively associated with mean species range size, research expenditure, and human population density and negatively associated with endemism and vascular plant species richness. Integration of a second, regional trait database (AusTraits) more than doubled trait completeness for the continent covered, indicating that the creation and integration of regional databases can rapidly expand trait completeness. Plain Language SummaryThe traits of plants determine how they interact with each other and their environment. Our knowledge of plant traits is incomplete, limiting scientific advancement as well as our ability to manage ecosystems and plan conservation actions. We show that there are large biases in trait data availability which are associated with both biological factors (range size, endemism, species richness) and socioeconomic factors (research expenditure, human population density). We also show how regionally-focused efforts can help rapidly expand trait data availability.

ecology↗

bioRxiv2021

Predicting multimodal MRI outcomes in children with neurodevelopmental conditions following MRI simulator training

Pediatric brain imaging holds significant promise for understanding neurodevelopment. However, the requirement to remain still inside a noisy, enclosed scanner remains a challenge. Verbal or visual descriptions of the process, and/or practice in MRI simulators are the norm in preparing children. Yet, the factors predictive of successfully obtaining neuroimaging data remain unclear. We examined data from 250 children (6-12 years, 197 males) with autism and/or attention-deficit/hyperactivity disorder. Children completed systematic MRI simulator training aimed to habituate to the scanner environment and minimize head motion. An MRI session comprised multiple structural, resting-state, task and diffusion scans. Of the 201 children passing simulator training and attempting scanning, nearly all (94%) successfully completed the first structural scan in the sequence, and 88% also completed the following resting state fMRI scan. The number of successful scans decreased as the sequence progressed. Multivariate analyses revealed that age was the strongest predictor of successful scans in the session, with younger children having lower success rates. After age, sensorimotor atypicalities contributed most to prediction. Results provide insights on factors to consider in designing pediatric brain imaging protocols.

neuroscience↗

bioRxiv2021

AusTraits: a curated plant trait database for the Australian flora

We introduce the AusTraits database - a compilation of measurements of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 375 traits across 29230 taxa from field campaigns, published literature, taxonomic monographs, and individual taxa descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological parameters (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual-, species- and genus-level observations coupled to, where available, contextual information on site properties. This data descriptor provides information on version 2.1.0 of AusTraits which contains data for 937243 trait-by-taxa combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data to increase our collective understanding of the Australian flora.

ecology↗

bioRxiv2020

A Single-Cell Tumor Immune Atlas for Precision Oncology

The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell tumor immune atlas, jointly analyzing >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system for a harmonized interpretation. To enable in situ mapping of immune populations for digital pathology, we applied SPOTlight, combining single-cell and spatial transcriptomics data and identifying striking spatial immune cell patterns in tumor sections. We expect the tumor immune cell atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification approaches for prognosis and immuno-therapy.

cancer biology↗

bioRxiv2020

Targeting CXCR1 and CXCR2 to overcome radiotherapy resistance in PTEN-deficient prostate carcinoma

ABSTRACTFunctional impairment of the tumour-suppressor PTEN is common in primary-prostate cancer and has been linked to relapse post-radiotherapy (RT). Pre-clinical modelling supports elevated CXC-chemokine signaling as a critical mediator of PTEN-depleted disease progression and therapeutic resistance. We assessed the correlation of PTEN-deficiency with CXC-chemokine signaling and its association with clinical outcomes. Gene expression analysis characterized a PTENLOW/CXCR1HIGH/CXCR2HIGH cluster of tumors that associates with earlier time-to-biochemical recurrence (HR 5.87 and HR 2.65 respectively) and development of systemic metastasis (HR 3.51). In vitro, CXCL-signaling was further amplified following exposure of PTEN-deficient prostate cancer cell lines to ionizing radiation (IR). Inhibition of CXCR1/2-signaling in PTEN-depleted cell-based models increased IR-sensitivity. In vivo, administration of a CXCR1/2-targeted pepducin (x1/2pal-i3), or CXCR2-specific antagonist (AZD5069), in combination with IR to PTEN-deficient xenografts attenuated tumor growth and progression compared to control or IR alone. Post-mortem analysis confirmed that x1/2pal-i3 administration attenuated IR-induced CXCL-signaling and anti-apoptotic protein expression. Interventions targeting CXC-chemokine signaling may provide an effective strategy to combine with radiotherapy, in both locally-advanced and oligometastatic-prostate cancers, with known presence of PTEN-deficient foci.

cancer biology↗

bioRxiv2018

Comparing the aftereffects of motion and causality across visual co-ordinates

Albert Michotte (1946/1963) introduced causality into the realm of experimental phenomenology. He disputed Humes (1739/1978) claim that the impression of causality comes only from conscious inference. Since then, causality adaptation studies have suggested that the visual perception of causality undergoes sensory adaptation, akin to the retinally-specific aftereffects of motion or orientation adaptation. Here we present 5 Experiments that, together, dispute a view of retinotopically-mapped neural populations dedicated to causality detection. We first point to key issues in previous studies of causality adaptation. Then we extend the basic causality adaptation paradigm to show that causality aftereffects occur in spatially global visual space. We directly compare causality aftereffects to the motion aftereffect to show important differences in their co-ordinate mapping. Our data point to a role for cognitive inferences as being an important aspect of causality aftereffects, despite causal impressions being tightly constrained by sensory perception.

neuroscience↗

bioRxiv2018

The implied motion aftereffect changes decisions, but not confidence

Viewing static images depicting movement can result in a motion aftereffect: people tend to categorise direction signals as moving in the opposite direction to the implied motion of still photographs. This finding could indicate that inferred motion direction can penetrate sensory processing and impact perception. Equally possible, however, is that inferred motion impacts decision processes, but not perception. Here we test these two possibilities. Since both categorical decisions and subjective confidence are informed by sensory information, confidence can be informative about whether an aftereffect likely results from changes to perceptual or decision processes. We therefore leveraged subjective confidence as an additional measure of the implied motion aftereffect. In Experiment 1 (implied motion), we find support for decision-level changes only, with no change in subjective confidence. In Experiment 2 (real motion), we find equal changes to decisions and confidence. Our results suggest the implied motion aftereffect produces a bias in decision-making, but leaves perceptual processing unchanged.

neuroscience↗

bioRxiv2018

Confidence as a diagnostic tool for perceptual aftereffects

Perceptual judgements are, by nature, a product of both sensation and the cognitive processes responsible for interpreting and reporting subjective experiences. Changed perceptual judgements may thus result from changes in how the world appears (perception), or subsequent interpretation (cognition). This ambiguity has led to persistent debates about how to interpret changes in decision-making, and if cognition can change how the world looks, or sounds, or feels. Here we introduce an approach that can help resolve these ambiguities. In three motion-direction experiments, we measured perceptual judgements and subjective confidence. Sensory encoding changes (i.e. the motion-direction aftereffect) impacted each measure equally, as the perceptual evidence informing both responses had changed. However, decision changes dissociated from reports of subjective uncertainty when non-perceptual effects changed decision-making. Our findings show that subjective confidence can provide important information about the cause of aftereffects, and can help inform us about the organisation of the mind.

neuroscience↗