Biology subjects

Pulver, S. R.

Publications and source records attributed to Pulver, S. R..

16 recordsLinked to original sources

bioRxiv2026

Guardians of our Rivers: transforming river health assessment through macroinvertebrate monitoring with citizen scientists

Freshwater ecosystems in Scotland are increasingly threatened by multiple interacting stressors, including pollution, hydrological alteration, land use change, and climate-driven pressures. Scotland's rivers are amongst the most physically diverse and dynamic in the UK, contributing significantly to the country-s economy and natural heritage. Monitoring 125,000 km of waterways presents an issue, with limited funding and capacity of environmental agencies creating an environmental monitoring deficit at a time when robust data are essential for delivering national and global biodiversity targets. Citizen science offers a scalable, community driven approach to strengthening environmental evidence. This study evaluates the development, implementation, and outcomes of Guardians of our Rivers (GooR), a nationwide citizen science programme using macroinvertebrate-based river health assessments based on the Anglers' Riverfly Monitoring Initiative (RMI) established by the Riverfly Partnership. Between 2022 and 2025, GooR trained more than 850 volunteers, established 123 monitoring sites across Scotland, and generated over 860 surveys-surpassing the previous 16 years of aquatic invertebrate monitoring efforts. Standardised field training, full equipment provision, and structured support enabled high-quality data collection across diverse catchments. The establishment of nationally applied trigger and target thresholds created a consistent mechanism for detecting ecological deterioration and ensured that verified trigger breaches (n = 39 in 2025) resulted in formal investigation or follow-up. Analysis of national abundance patterns revealed ecological and biogeographic trends across the eight RMI taxa, confirming data sensitivity to habitat differences, water quality, and regional pressures. A detailed case study of the Lothian Esk catchment demonstrated the programme's capacity to detect seasonal macroinvertebrate dynamics and site level ecological trajectories over time. Overall, GooR illustrates how well-designed and well-supported citizen science can deliver high resolution spatiotemporal datasets, enhance early warning systems, empower communities, and make a meaningful contribution to promoting river health. Importantly, GooR forged a working partnership with Scottish Environmental Protection Agency (SEPA) that allowed communities to not only gather data but also transformed the way citizen science is recognized as contributing to freshwater conservation. Continued investment and long-term support will be essential to sustain these gains and realise the full potential of citizen-driven freshwater stewardship.

ecology↗

bioRxiv2026

Dynamic Bayesian networks for neural information flow:evaluation of continuous and discrete scoring metrics

Neural information flow describes the movement of activity between neurons or brain areas. Advances in experimental methods have allowed production of large amounts of observational data related to neuronal activity from the single-neuron to population level. Most current methods for analysing these data are based on pairwise comparison of activity, and fall short of reliably extracting neural information flow network structure. Dynamic Bayesian networks may overcome some of these limitations. Here we evaluate the performance of a range of Bayesian network scoring metrics against the performance of multivariate Granger causality and LASSO regression for their ability to learn the connectivity underlying simulated single-neuron and neuronal population data. We find that discrete dynamic Bayesian networks are the best performing method for single-neuron data, and perform consistently for neural-population data. Continuous dynamic Bayesian networks have a tenancy to learn overly dense structures for both data types, but may have utility in scoping studies on single-neuron data. Multivariate Granger causality is the most robust method for learning structure of neural information flow between neural-populations, but performs poorly on single-neuron data. Significance testing within multivariate Granger causality produces variable results between data types. Overall, this work highlights how the analysis of neural information flow can vary depending on they type and structure of underlying data, and promotes discrete dynamic Bayesian networks as a useful and consistent tool for neural information flow analysis.

neuroscience↗

bioRxiv2026

WillCO2st: leveraging freely available real-time carbon forecasting for research sustainability reporting

Summary (Abstract)An increasing number of research institutions and funding bodies are making sustainability a focal point. The rapid rollout of auditing processes, such as the Laboratory Efficiency Assessment Framework (LEAF), and changing institutional policies, are creating demand for sustainability accounting upon researchers. Despite the increasing expectations on researchers to actively report their sustainability and demonstrate improvement, easy-to-use, and accurate reporting tools for electricity-associated emissions (scope 2) accounting are not widely available. Here, we created WillCO2st - a free program that enables fast, publication-read sustainability reports. WillCO2st makes use of real-time, region-specific conversion factor data freely available through resources like the Carbon Intensity and Electricity Maps API to create experimental carbon footprinting estimates using metadata from saved experimental files. Data can be simply click-and-dragged into WillCO2st to create an experimental sustainability audit within minutes. Further, we exemplified the utility of WillCO2sts live-nudging feature by quantifying the retrospective theoretical reduction in electricity-driven emissions from shifting experimental timing to times of day with lower carbon intensities. Overall, WillCO2st eases time and resource burden on researchers and serves as a model for how researchers can effectively and accurately engage with research sustainability auditing. Highlights WillCO2st is a free software platform that enables fast, publication-ready carbon emissions reporting for papers, grants, and internal audits. WillCO2st leverages various energy-to-emissions database to provide real-time, region-specific estimations of carbon intensity for the upcoming 48 hours, nudging users to switch to lower carbon times for research activities. WillCO2st integrates CodeCarbon to automatically audit Python-based coding scripts for experimental and computational-wide sustainability audits. Partial conformity (21%) to switching experimental time would have disproportionately produced a large carbon saving (50%) in our most recent publications experimental carbon footprint.

neuroscience↗

bioRxiv2025

Dopamine promotes motor programs underlying substrate tunneling in larval Drosophila

Dopamine is a conserved biogenic amine with diverse neuromodulatory roles. Here we examine the role of dopamine in modulating larval Drosophila melanogaster motor programs underlying movement over and through substrates. First, we performed dual-color calcium imaging in tyrosine hydroxylase (TH)-expressing dopaminergic neurons and motor neurons to reveal cell-type specific recruitment patterns during fictive motor programs. Activity of select TH-neurons correlated strongly with fictive headsweeps as well as forward and backward locomotion. Next, bath applications of dopamine biased the isolated central nervous system towards fictive forward locomotion and inhibited fictive headsweeps. To probe whether these effects are recapitulated in intact animals, we optogenetically manipulated TH-neuron activity during surface crawling and tunneling. Optogenetic activation of TH-neurons with CsChrimson during crawling had no effect on headsweeps and slowed locomotor rhythms by increasing wave duration and decreasing wave frequency. Furthermore, posterior asymmetries, motor sequences characteristic of tunneling, were triggered. On the other hand, optogenetically inhibiting TH-neurons with GtACR1 had little effect on surface crawling. Underground, TH-neuron activation enhanced tunneling activity by increasing wave frequency, instead of duration, which increased overall time spent tunnelling, whereas inhibition decreased time spent tunneling. These results suggest that dopaminergic modulation of larval forward locomotion is dependent on sensorimotor context. We propose dopamine mediates a coordinated network effort to shift central pattern generators to promote tunneling-specific motor programs. New & NoteworthyHere, we find Drosophila larval dopaminergic neurons exhibit cell-type-specific activity in relation to fictive motor patterns. Furthermore, pharmacological and optogenetic manipulations of dopaminergic signaling acutely modifies locomotor output. Specifically, dopamine application promotes forward locomotion and inhibits headsweeps in isolated preparations, while optogenetically activating TH-neurons in freely behaving larvae mediates a shift from crawling to tunneling motor programs. This provides new insights into context-dependent dopaminergic modulation of locomotion in a genetically tractable invertebrate.

neuroscience↗

bioRxiv2025

Octopamine and Tyramine Modulate Motor Program Competition in Drosophila larvae

Dynamic interactions amongst competing motor programs shape behavioural output. Here, we use bath application of biogenic amines octopamine (OA) and tyramine (TA) to explore operating principles of competition amongst central pattern generating (CPG) networks controlling locomotion in 3 rd instar Drosophila larvae. OA and TA share the same synthesis pathway and are contained in overlapping sets of neurons. Bath application of OA promoted fictive forwards locomotion, suppressed backwards locomotion, and induced bouts of fictive head sweeps during wash periods that were proportional to the promotion of forward waves. In contrast, TA, the conceptualised inhibitory antagonist to OA, promoted collisions and overlap of motor programmes, activity-dependent inhibition, and bouts of silence during wash periods. Co-application of OA and TA revealed bimodal state-dependent modulation with forward bias promotion exclusively if the pre-application network was not already forward dominant. Overall, our work provides insights into how adrenergic-like systems can modulate dynamics of motor competition among interacting CPGs within locomotor networks.

neuroscience↗

bioRxiv2025

Cis-regulatory divergence and mate recognition in behaviourally isolated cricket species.

Cis-regulatory evolution has been implicated in morphological and physiological reproductive isolation, but its role in divergence of mate recognition behaviours is unknown. The latter are often the first, most powerful mating barriers to evolve during speciation, but understanding their genetics is hampered by the context-dependence of mate choice. We circumvented this challenge by using allele-specific expression analyses in F1 hybrids of sexually isolated cricket species, Teleogryllus oceanicus and T. commodus. Female crickets choose mating partners based on species-specific male advertisement songs, and we found extensive cis-regulatory divergence in neural tissues exposed to conspecific, heterospecific, or mixed-species songs. Genes with divergent expression were implicated in learning, memory and transcriptional regulation, and they showed elevated population genetic differentiation in allopatry but not sympatry. This implies that genes recruited during evolutionary divergence of mate recognition systems may be homogenised by gene flow. Regulatory divergence was asymmetrical between the two species; divergent selection on genes associated with female perception of male song was more prominent in T. oceanicus than in T. commodus. Evolved differences in gene regulation are strongly associated with sexual signal perception in closely related species, supporting the idea that rapid cis-regulatory evolution of mate recognition can accelerate speciation.

evolutionary biology↗

bioRxiv2025

Doctoral Students as Carbon Accountants: Calculating Carbon Costs of a PhD in Neuroscience

Research is an energy and resource-demanding activity. However, despite increasing awareness and emerging sustainability initiatives, a paucity of data and methodological inconsistency continue to hamper effective and accountable emissions mitigation. With > 250,000 doctoral students graduating annually across all academic disciplines, empowering PhD students to engage in carbon accounting could provide a sizable and robust source of carbon data alongside a powerful generational force for decarbonisation. Here, we demonstrate how doctoral students and other researchers can consistently measure the carbon footprint of their work, using one PhD students research in a neuroscience Drosophila lab as our case study. We present a comprehensive life-cycle assessment of the equivalent carbon dioxide emissions (CO2e) generated by the students research activities, including measurement of scope 1 emissions associated with Drosophila husbandry; calculation of time- and region-specific scope 2 emissions produced by widely used techniques including calcium imaging, electrophysiology, and optogenetics; and estimation of scope 3 emissions associated with procurement and research-related travel. We found that research-related travel and procurement of laboratory supplies were responsible for the majority of annual emissions, up to 1942 kg CO2e and 543 kg CO2e respectively after accounting for aircraft radiative forcing. Using NESOs open-source Carbon Intensity API to account for temporal and geographical variation in the carbon intensity of UK National Grid energy, we found that persistent laboratory energy consumption released 10.99 kg CO2e, with an additional 3.56 kg CO2e scope 2 and 3.6 kg CO2e scope 1 emissions underpinning direct research activities. Finally, we discuss the challenges of accurately carbon foot printing research across disciplines in the UK and beyond, highlighting the value of regionally precise open-source energy mix data and the need for data openness within research supply chains. Overall, we present a common framework for including carbon footprint analyses as Carbon Appendices to PhD theses to generate carbon footprint data across disciplines. Beyond the benefits of such data for informed emissions mitigation, we envision doctoral students carrying insights from carbon appendices forward into academia and industry to catalyse a community-driven decarbonisation of the research sector.

neuroscience↗

bioRxiv2024

Generation of motor program diversity and variability through inhibitory circuit motifs in the Drosophila larval locomotor system

How do neural networks generate and regulate diversity and variability in motor outputs with finite cellular components? Here we examine this problem by exploring the role that inhibitory neuron motifs play in generating mixtures of motor programs in the segmentally organised Drosophila larval locomotor system. We developed a computational model that is constrained by experimental calcium imaging data. The model comprises single-compartment cells with a single voltage-gated calcium current, which are interconnected by graded excitatory and inhibitory synapses. Local excitatory and inhibitory neurons form conditional oscillators in each hemisegment. Surrounding architecture reflects key aspects of inter- and intrasegmental connectivity motifs identified in the literature. The model generates metachronal waves of activity that recapitulate key features of fictive forwards and backwards locomotion, as well as bilaterally asymmetric activity in anterior regions that represents fictive head sweeps. The statistics of inputs to competing command-like motifs, coupled with inhibitory motifs that detect activity across multiple segments generate network states that promote diversity in motor outputs, while at the same time preventing maladaptive overlap in motor programs. Overall, the model generates testable predictions for connectomics and physiological studies while providing a platform for uncovering how inhibitory circuit motifs underpin generation of diversity and variability in motor systems.

neuroscience↗

bioRxiv2024

Steering From the Rear: Coordination of Central Pattern Generators Underlying Navigation by Ascending Interneurons

Understanding how animals coordinate movements to achieve goals is a fundamental pursuit in neuroscience. Here we explore how neurons that reside in posterior lower-order regions of a locomotor system project to anterior higher-order regions to influence steering and navigation. We characterized the anatomy and functional role of a population of ascending interneurons in the ventral nerve cord of Drosophila larvae. Through electron microscopy reconstructions and light microscopy, we determined that the cholinergic 19f cells receive input primarily from premotor interneurons and synapse upon a diverse array of postsynaptic targets within the anterior segments including other 19f cells. Calcium imaging of 19f activity in isolated central nervous system (CNS) preparations in relation to motor neurons revealed that 19f neurons are recruited into most larval motor programmes. 19f activity lags behind motor neuron activity and as a population, the cells encode spatio-temporal patterns of locomotor activity in the larval CNS. Optogenetic manipulations of 19f cell activity in isolated CNS preparations revealed that they coordinate the activity of central pattern generators underlying exploratory headsweeps and forward locomotion in a context and location specific manner. In behaving animals, activating 19f cells suppressed exploratory headsweeps and slowed forward locomotion, while inhibition of 19f activity potentiated headsweeps, slowing forward movement. Inhibiting activity in 19f cells ultimately affected the ability of larvae to remain in the vicinity of an odor source during an olfactory navigation task. Overall, our findings provide insights into how ascending interneurons monitor motor activity and shape interactions amongst rhythm generators underlying complex navigational tasks.

neuroscience↗

bioRxiv2024

Context-dependent coordination of movement in Tribolium castaneum larvae

Insect pests, like the red flour beetle Tribolium castaneum, destroy up to 20% of stored grain products worldwide, making them a significant threat to food security. Their success hinges upon adapting their movements to unpredictable, heterogeneous environments like flour. Tribolium is well developed as a genetic model system; however, little is known about their natural locomotion and how their nervous systems coordinate adaptive movement. Here, we employed videographic whole-animal and leg tracking to assess how Tribolium larvae locomote over different substrates and analyze their gait kinematics across speeds. Unlike many hexapods, larvae employed a bilaterally symmetric, posterior-to-anterior wave gait during fast locomotion. At slower speeds, coordination within thoracic segments was disrupted, although intersegmental coordination remained intact. Moreover, larvae used terminal abdominal structures (pygopods) to support challenging movements, such as climbing overhangs. Pygopod placement coincided with leg swing initiation, suggesting a stabilizing role as adaptive anchoring devices. Surgically lesioning the connective between thoracic and abdominal ganglia impaired pygopod engagement and led to escalating impairments in flat-terrain locomotion, climbing and tunnelling. These results suggest that effective movement in Tribolium larvae requires thoracic-abdominal coordination, and that larval gait and limb recruitment is context-dependent. Our work provides the first kinematic analysis of Tribolium larval locomotion and gives insights into its neural control, creating a foundation for future motor control research in a genetically tractable beetle that jeopardizes global food security. Summary statementRed flour beetle larvae walk with a legged wave gait and use their tails as anchors to climb inclines and tunnel into flour.

neuroscience↗

bioRxiv2023

Temporal dynamics of Na/K pump mediated memory traces: insights from conductance-based models of Drosophila neurons

Sodium potassium ATPases (Na/K pumps) mediate long-lasting, dynamic cellular memories that can last tens of seconds. The mechanisms controlling the dynamics of this type of cellular memory are not well understood and can be counterintuitive. Here, we use computational modeling to examine how Na/K pumps and the ion concentration dynamics they influence shape cellular excitability. In a Drosophila larval motor neuron model, we incorporate a Na/K pump, a dynamic intracellular Na+ concentration, and a dynamic Na+ reversal potential. We probe neuronal excitability with a variety of stimuli, including step currents, ramp currents, and zap currents, then monitor the sub- and suprathreshold voltage responses on a range of time scales. We find that the interactions of a Na+-dependent pump current with a dynamic Na+ concentration and reversal potential endow the neuron with rich response properties that are absent when the role of the pump is reduced to the maintenance of constant ion concentration gradients. In particular, these dynamic pump-Na+ interactions contribute to spike rate adaptation and result in long-lasting excitability changes after spiking and even after sub-threshold voltage fluctuations on multiple time scales. We further show that modulation of pump properties can profoundly alter a neurons spontaneous activity and response to stimuli by providing a mechanism for bursting oscillations. Our work has implications for experimental studies and computational modeling of the role of Na/K pumps in neuronal activity, information processing in neural circuits and the neural control of animal behavior.

neuroscience↗

bioRxiv2022

Optical mapping of Ground Reaction Force Dynamics in Freely Behaving Drosophila melanogaster larvae

During locomotion, soft-bodied terrestrial animals solve complex control problems at substrate interfaces, but our understanding of how they achieve this without rigid components remains incomplete. Here, we develop new all-optical methods based on optical interference in a deformable substrate to measure ground reaction forces (GRFs) with micrometre and nanonewton precision in behaving Drosophila larvae. Combining this with a kinematic analysis of substrate interfacing features, we shed new light onto the biomechanical control of larval locomotion. Crawling in larvae measuring [~]1 mm in length involves an intricate pattern of cuticle sequestration and planting, producing GRFs of 1-7 {micro}N. We show that larvae insert and expand denticulated, feet-like structures into substrates as they move, a process not previously observed in soft bodied animals. These protopodia form dynamic anchors to compensate counteracting forces. Our work provides a framework for future biomechanics research in soft-bodied animals and promises to inspire improved soft-robot design.

biophysics↗

bioRxiv2021

Localization of muscarinic acetylcholine receptor dependent rhythm generating modules in the Drosophila larval locomotor network

Mechanisms of rhythm generation have been extensively studied in motor systems that control locomotion over terrain in limbed animals; however, much less is known about rhythm generation in soft-bodied terrestrial animals. Here we explored how muscarinic acetylcholine receptor (mAChR) dependent rhythm generating networks are distributed in the central nervous system (CNS) of soft-bodied Drosophila larvae. We measured fictive motor patterns in isolated CNS preparations using a combination of Ca2+ imaging and electrophysiology while manipulating mAChR signalling pharmacologically. Bath application of the mAChR agonist oxotremorine potentiated rhythm generation in distal regions of the isolated CNS, whereas application of the mAChR antagonist scopolamine suppressed rhythm generation in these regions. Oxotremorine raised baseline Ca2+ levels and potentiated rhythmic activity in isolated posterior abdominal CNS segments as well as isolated anterior brain and thoracic regions, but did not induce rhythmic activity in isolated anterior abdominal segments. Bath application of scopolamine to reduced preparations lowered baseline Ca2+ levels and abolished rhythmic activity. These results suggest the presence of a bimodal gradient of rhythmogenicity in the larval CNS, with mAChR dependent rhythm generating networks in distal regions separated by medial segments with severely reduced rhythmogenic abilities. This work furthers our understanding of motor control in soft-bodied locomotion and provides a foundation for study of rhythm generating networks in an emerging genetically tractable locomotor system.

neuroscience↗

bioRxiv2021

Regulation of coordinated muscular relaxation by a pattern-generating intersegmental circuit

Typical patterned movements in animals are achieved through combinations of contraction and delayed relaxation of groups of muscles. However, how intersegmentally coordinated patterns of muscular relaxation are regulated by the neural circuits remain poorly understood. Here, we identify Canon, a class of higher-order premotor interneurons, that regulates muscular relaxation during backward locomotion of Drosophila larvae. Canon neurons are cholinergic interneurons present in each abdominal neuromere and show wave-like activity during fictive backward locomotion. Optogenetic activation of Canon neurons induces relaxation of body wall muscles, whereas inhibition of these neurons disrupts timely muscle relaxation. Canon neurons provide excitatory outputs to inhibitory premotor interneurons. Canon neurons also connect with each other to form an intersegmental circuit and regulate their own wave-like activities. Thus, our results demonstrate how coordinated muscle relaxation can be realized by an intersegmental circuit that regulates its own patterned activity and sequentially terminates motor activities along the anterior-posterior axis.

neuroscience↗

bioRxiv2020

Segment-Specific Optogenetic Stimulation in Drosophila melanogaster with Linear Arrays of Organic Light-Emitting Diodes

Optogenetics allows light-driven, non-contact control of neural systems, but light delivery remains challenging, in particular when fine spatial control of light is required to achieve local specificity. Here, we employ organic light-emitting diodes (OLEDs) that are micropatterned into linear arrays to obtain precise optogenetic control in Drosophila melanogaster larvae expressing the light-gated activator CsChrimson and the inhibitor GtACR2 within their peripheral sensory system. Our method allows confinement of light stimuli to within individual abdominal segments, which facilitates the study of larval behaviour in response to local sensory input. We show controlled triggering of specific crawling modes and find that targeted neurostimulation in abdominal segments switches the direction of crawling. More broadly, our work demonstrates how OLEDs can provide tailored patterns of light for photo-stimulation of neuronal networks, with future implications ranging from mapping neuronal connectivity in cultures to targeted photo-stimulation with pixelated OLED implants in vivo.

neuroscience↗

bioRxiv2018

Long term impact of intensive post graduate laboratory training at the Cold Spring Harbor Neurobiology of Drosophila summer course

Intensive postgraduate courses provide an opportunity for junior and senior level scientists to learn concepts and techniques that will advance their training and research programs. It is commonly assumed that short intensive courses have positive impacts within fields of research; however, these assumptions are rarely tested. Here we describe the framework of a long running postgraduate summer course at Cold Spring Harbor and attempt to quantify the impact made over its history. For over three decades, the Drosophila Neurobiology: Genes, Circuits & Behavior Summer Course at Cold Spring Harbor Laboratories (CSHL) has provided participants with intense instruction on a wide variety of topics and techniques in integrative neuroscience using Drosophila as a model organism. Students are introduced to the latest approaches for studying nervous system development, activity and connectivity, as well as complex behaviors and diseases. The course has a long history of successful alumni, many of whom describe participation in the course as foundational to their training. Student surveys of recent participants indicate a high level of satisfaction, improved career outcomes, and direct impact on publications. Analysis of student success reveals that over 64% of participants obtain independent faculty positions. Further, we describe ongoing efforts to enhance diversity and encourage access to scientific research at undergraduate-focused institutions. Together, our findings suggest that laboratory-intensive postgraduate courses provide a highly effective mechanism for scientific training that has lasting positive impacts on trainees.

scientific communication and education↗