Biology subjects

Clarke, T.

Publications and source records attributed to Clarke, T..

11 recordsLinked to original sources

bioRxiv2026

Rhizobacterial Biosensors Spatially Map Natural and Engineered Sucrose Exudation

Root exudation mediates the delivery of plant primary and secondary metabolites into soil, where they regulate plant-microbe interactions and terrestrial carbon cycling. Conventional exudate analyses quantify total root-released carbon yet obscure the spatial origin and rhizosphere influence of individual compounds. Here, we develop a rhizobacterial biosensor platform, named Suc-MAPP, to map local exudate profiles along the surface of colonized root tissues. Focusing on sucrose, we engineered sfGFP-based, sucrose-responsive gene circuits in Pseudomonas putida KT2440 for live imaging of exudate concentrations in the micromolar range. These biosensors reveal spatially structured sucrose exudation patterns across eudicots and monocots and implicate photoassimilated source-sink dynamics as a major determinant. We further apply this platform to phenotype exudation modulated by synthetic gene circuitry in Arabidopsis thaliana, identifying genetic design rules for graded sucrose release and quantifying how engineered export sculpts rhizosphere assembly of a defined bacterial community. Together, these results establish programmable rhizobacterial biosensors as tools to spatially resolve plant-environment carbon exchange in situ and provide a framework for extending this approach to diverse exudate targets.

synthetic biology↗

bioRxiv2026

Phase response curve and RNA-sequencing demonstrate spiders' sensitivity to light and pinpoint candidate light-responsive genes

Spiders can maintain a wide range of free-running periods while still being entrained to a 24-hour day. To investigate the underlying mechanism of this entrainment, we constructed the phase-response curve (PRC) for the orb weaver, Metazygia wittfeldae, by subjecting the spiders to one-hour light pulses at various times throughout the circadian day. The resulting type 0 PRC showed high amplitude (> 6 hour) phase advance and delays when the light pulse was applied during circadian time (CT) 16-18, with a break point of advances to delays at CT 17. We then investigated the genetic mechanism of the phase response to light by splitting M. wittfeldae adult females entrained to 12 hours light:12 hours dark (LD 12:12) into two groups. One group received a 1-hour light pulse 5 hours after lights off (CT17), and one group did not. We then sacrificed spiders for RNA isolations 1 and 10 hours after the light pulse. We identified numerous genes that were downregulated by the light pulse 1 hour after the pulse relative to no pulse group. Intriguingly, many of these genes had a flipped pattern of expression 9 hours later - the pulse group had higher expression than the no pulse group. This pattern is consistent with the shifted phase of locomotor activity expected after the light pulse application. We also identified clock gene homologs in M. wittfeldae that had distinct expression patterns from other arthropods.

animal behavior and cognition↗

bioRxiv2025

The cause-effect conundrum of local-scale site and soil factors in acute oak decline (AOD)

Background and aimsAcute oak decline (AOD), a decline syndrome affecting mature oaks, involves bacterial pathogens which likely act as opportunists under host stress. Trees displaying symptoms (bleeding cankers) appear in localized clusters, not whole stands. This study investigates the potential involvement of local-scale factors, in interaction with large-scale environmental drivers, in influencing onset and progression of AOD. MethodsAOD-symptomatic (n=30) and asymptomatic trees (n=30) across three UK oak woodlands were assessed for tree characteristics, their surrounding context, and soil properties. ResultsTree health status was linked to significant differences in soil and tree properties across sites. Symptomatic trees exhibited greater loss of crown density, lower local stand (0-20 m) basal area and shallower depth to gleying. Significant differences in soil properties included lower concentrations of Olsen P, total N, and exchangeable Mg in symptomatic trees, alongside higher exchangeable Fe, especially at 40-50 cm depth. Depth to gleying and exchangeable Fe were identified as the most influential predictors of AOD. ConclusionsAOD symptomatic trees may experience seasonal soil water saturation closer to the surface compared to asymptomatic trees, resulting in a higher proportion of their roots being exposed to an anoxic, iron-reducing environment. This study is the first to report such an association between gleying depth, likely seasonal water saturation, and symptom status for AOD. It is unclear whether water balance and associated soil nutrient variations are predisposing factors or consequences of declining tree health, though the identified local-scale factors likely contribute to AOD. A feedback loop is conceptualised where declining tree health worsens soil conditions, creating a negative cycle that accelerates tree decline.

ecology↗

bioRxiv2024

Maize genetic diversity identifies moisture-dependent root-branch signaling pathways

Plants grow complex root systems to extract unevenly distributed resources from soils. Spatial differences in soil moisture are perceived by root tips leading to the patterning of new root branches towards available water, a process called hydropatterning. Little is known about hydropatterning behavior and its genetic basis in crops plants. Here, we develop an assay to measure hydropatterning in maize and reveal substantial differences between tropical/subtropical and temperate maize breeding germplasm that likely resulted from divergent selection. Genetic dissection of hydropatterning confirmed the regulatory role of auxin and revealed that the gaseous hormone ethylene acts to locally inhibit root branching from air-exposed tissues. These findings demonstrate the crop relevance of hydropatterning and establish its genetic basis.

plant biology↗

bioRxiv2022

Visiomode: an open-source platform for building rodent touchscreen-based behavioral assays

BackgroundTouchscreen-based behavioral assays provide a robust method for assessing cognitive behavior in rodents, offering great flexibility and translational potential. The development of touchscreen assays presents a significant programming and mechanical engineering challenge, where commercial solutions can be prohibitively expensive and open-source solutions are underdeveloped, with limited adaptability. New methodHere, we present Visiomode (www.visiomode.org), an open-source platform for building rodent touchscreen-based behavioral tasks. Visiomode leverages the inherent flexibility of touchscreens to offer a simple yet adaptable software and hardware platform. The platform is built on the Raspberry Pi computer combining a web-based interface and powerful plug-in system with an operant chamber that can be adapted to generate a wide range of behavioral tasks. ResultsAs a proof of concept, we use Visiomode to build both simple stimulus-response and more complex visual discrimination tasks, showing that mice display rapid sensorimotor learning including switching between different motor responses (i.e., nose poke versus reaching). Comparison with existing methodsCommercial solutions are the go to for rodent touchscreen behaviors, but the associated costs can be prohibitive, limiting their uptake by the wider neuroscience community. While several open-source solutions have been developed, efforts so far have focused on reducing the cost, rather than promoting ease of use and adaptability. Visiomode addresses these unmet needs providing a low-cost, extensible platform for creating touchscreen tasks. ConclusionsDeveloping an open-source, rapidly scalable and low-cost platform for building touchscreen-based behavioral assays should increase uptake across the science community and accelerate the investigation of cognition, decision-making and sensorimotor behaviors both in health and disease.

neuroscience↗

bioRxiv2022

A report card methodology to showcase progress towards threatened species recovery

Among the conservation community, it is well known that Earths mass species extinction crisis is getting worse. Yet, an often neglected problem is the need for effectively communicating the species extinction crisis to diverse audiences in ways that catalyse immediate action. Here we generated a streamlined threatened species recovery report card methodology, which combined two input indicators including planning and funding, one output indicator capturing habitat protection, and one outcome indicator which highlights threatened species trajectories, to provide simple scores for all Australian threatened species. We show that just 41 (2.3%) of species achieved an A grade for the input indicator (i.e., recovery plans and federal funding), 240 (13.3%) achieved a C grade, and 1,521 (84.4%) achieved an F. Five hundred and twenty nine (29.3%) species achieved an A for the output indicator (i.e, habitat protection), 130 (7.2%) achieved a B, 158 (8.8%) achieved a C, 189 (10.5%) achieved a D, 212 (11.8%) achieved an E, and 584 (32.4%) achieved a F. While five (0.3%) species achieved an A for the output indicator (i.e., threat status improvement), every other species (99.7%) achieved an F. We provide a method to combine scores to test how individual jurisdictions are tracking and show that Australia is achieving an F for the input and outcome indicators, and a D for the output indicator. While the threatened species recovery report card highlighted a clear failure in many federal environmental legislation responsibilities, it provides a baseline from which different governments can track policy progress and outlines clear direction for immediate improvement including developing adequate recovery plans, funding the actions in the recovery plans, protecting habitat from further destruction, verifying recovery through monitoring and evaluation of species trajectories, and supporting transparency and collaboration on the execution on the plans through an improved data infrastructure. Without an immediate step change in how Australia communicates and faces its species crisis, we will leave a tragic legacy of extinction and fail our obligations to future generations of Australians, and the international community.

scientific communication and education↗

bioRxiv2020

Nanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels.

Nanopore sequencers enable selective sequencing of single molecules in real time by individually reversing the voltage across specific nanopores. Thus DNA molecules can be rejected and replaced with new molecules enabling targeted sequencing to enrich, deplete or achieve specific coverage in a set of reads to address a biological question. We previously demonstrated this method worked using dynamic time warping mapping signal to reference, but required significant compute and did not scale to gigabase references. Using direct base calling with GPU we can now scale to gigabase references. We enrich for specific chromosomes mapping against the human genome and we develop pipelines enriching low abundance organisms from mixed populations without prior knowledge of sample composition. Finally, we enrich panels including 25,600 exon targets from 10,000 human genes and 717 genes implicated in cancer. Using this approach we identify PML-RARA fusions in the NB4 cell line in under 15 hours sequencing. These methods can be used to efficiently screen any target panel of genes without specialised sample preparation using a single computer and suitably powerful GPU.

genomics↗

bioRxiv2019

Cerebellar-recipient motor thalamus drives behavioral context-specific movement initiation

To initiate goal-directed behavior, animals must transform sensory cues into motor commands that generate appropriately timed actions. Sensorimotor transformations along the cerebellar-thalamocortical pathway are thought to shape motor cortical output and movement timing, but whether this pathway initiates goal-directed movement remains poorly understood. Here, we recorded and perturbed activity in cerebellar-recipient regions of motor thalamus (dentate / interpositus nucleus-recipient regions, MThDN/IPN) and primary motor cortex (M1) in mice trained to execute a cued forelimb lever push task for reward. MThDN/IPN population responses were dominated by a time-locked increase in activity immediately prior to movement that was temporally uncoupled from cue presentation, providing a fixed latency feedforward motor timing signal to M1FL. Blocking MThDN/IPN output suppressed cued movement initiation. Stimulating the MThDN/IPN thalamocortical pathway in the absence of the cue recapitulated cue-evoked M1 membrane potential dynamics and forelimb behavior in the learned behavioral context, but generated semi-random movements in an altered behavioral context. Thus, cerebellar-recipient motor thalamocortical input to M1 is indispensable for the generation of motor commands that initiate goal-directed movement, refining our understanding of how the cerebellar-thalamocortical pathway contributes to movement timing.

neuroscience↗

bioRxiv2018

Association of whole-genome and NETRIN1 signaling pathway-derived polygenic risk scores for Major Depressive Disorder and thalamic radiation white matter microstructure in UK Biobank

BackgroundMajor Depressive Disorder (MDD) is a clinically heterogeneous psychiatric disorder with a polygenic architecture. Genome-wide association studies have identified a number of risk-associated variants across the genome, and growing evidence of NETRIN1 pathway involvement. Stratifying disease risk by genetic variation within the NETRIN1 pathway may provide an important route for identification of disease mechanisms by focusing on a specific process excluding heterogeneous risk-associated variation in other pathways. Here, we sought to investigate whether MDD polygenic risk scores derived from the NETRIN1 signaling pathway (NETRIN1-PRS) and the whole genome excluding NETRIN1 pathway genes (genomic-PRS) were associated with white matter integrity.\n\nMethodsWe used two diffusion tensor imaging measures, fractional anisotropy (FA) and mean diffusivity (MD), in the most up-to-date UK Biobank neuroimaging data release (FA: N = 6,401; MD: N = 6,390).\n\nResultsWe found significantly lower FA in the superior longitudinal fasciculus ({beta} = -0.035, pcorrected = 0.029) and significantly higher MD in a global measure of thalamic radiations ({beta} = 0.029, pcorrected = 0.021), as well as higher MD in the superior ({beta} = 0.034, pcorrected = 0.039) and inferior ({beta} = 0.029, pcorrected = 0.043) longitudinal fasciculus and in the anterior ({beta} = 0.025, pcorrected = 0.046) and superior ({beta} = 0.027, pcorrected = 0.043) thalamic radiation associated with NETRIN1-PRS. Genomic-PRS was also associated with lower FA and higher MD in several tracts.\n\nConclusionsOur findings indicate that variation in the NETRIN1 signaling pathway may confer risk for MDD through effects on thalamic radiation white matter microstructure.

genetics↗

bioRxiv2017

Multiuse patient monitoring equipment as a risk factor for acquisition of Candida auris

Introduction Introduction Methods Results Discussion References Candida auris is an emerging and multi-drug resistant pathogen recently associated with outbreaks worldwide, often in intensive care settings (1). Following the alerts issued by the CDC and PHE in June 2016 (2,3), a look back exercise in the neurological intensive care unit (NITU) in the Oxford University Hospitals NHS Foundation Trust identified five clinical cases of C. auris infection. After the identification of an additional isolate in a urine sample, a patient and environmental screening programme was introduced in the last week of October 2016. We report here a summary of our initial findings which other affected units may wish to consider as part of their infection prevention and control measures. ...

microbiology↗

bioRxiv2017

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neofunctionalization and/or subfunctionalization since their duplication, and therefore may have contributed to the diversification of spiders and other pulmonate arachnids.

genomics↗