Biology subjects

Perkins, J.

Publications and source records attributed to Perkins, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Once in a blue moon: an unexpected evolutionary route to blue floral pigmentation in orchids

Blue flowers are rare in the hyperdiverse orchid family, and the genetic mechanisms enabling their blue delphinidin-based pigmentation remain poorly understood. Within the Australian orchid subtribe Caladeniinae (~350 spp.), repeated transitions from maroon to blue flowers, followed by reversions to maroon, provide a unique opportunity to investigate blue flower evolution. Using phylotranscriptomics, anthocyanin profiling, molecular evolutionary analyses, and gene expression data from 51 species, we reconstructed the genetic changes associated with these transitions. Despite its near-universal role in delphinidin biosynthesis across flowering plants, unexpectedly, we found no evidence for a functional CYP75A-mediated flavonoid 3'5'-hydroxylase (F3'5'H) pathway. Instead, blue-flowered species possess a duplicated CYP75B lineage gene (CYP75B-D) with apparent 5'-hydroxylase activity, a derived D-type dihydroflavonol reductase (DFR), and a distinct anthocyanin biosynthetic pathway co-expression pattern. Phylogenetic analyses suggest that the D-type DFR pre-dated blue flower evolution, representing a permissive evolutionary shift later coupled with the evolution of CYP75B-D. Notably, blue flower evolution coincided with repeated pollinator transitions and major palaeoenvironmental change during the Middle Miocene. Together, these findings reveal an unexpected route to blue floral pigmentation and suggest that its evolution arose through the interaction of molecular innovation, regulatory evolution, and ecological opportunity.

evolutionary biology↗

bioRxiv2026

Porcine epidemic diarrhea virus Whole-Genome Diversity Reveals Divergence of Contemporary Populations in the United States

Porcine epidemic diarrhea virus (PEDV) was introduced into the United States (USA) in 2013 and has circulated ever since. PEDV causes significant losses in the swine industry, with the greatest impact observed during the first years following its introduction into the country. However, the evolutionary dynamics of the virus remain underexplored. Recently, analyses of the Spike protein subunit S1 suggested that the PEDV population currently circulating in the USA represents a fraction of its historical diversity and comprises only two clades restricted to specific geographic regions. These observations were based on a limited set of S1 sequences. Furthermore, our understanding of evolutionary dynamics at the genomic level is even more limited, as complete PEDV genomes have not been generated since 2017. Here, we characterized the evolutionary dynamics of PEDV populations in the USA using complete genomes and assessed the contribution of different evolutionary mechanisms to shaping population structure. We analyzed 338 complete genomes, of which 25 were obtained in this study, together with 623 Spike S1 sequences, of which 41 were obtained in this study. All sequences obtained in this study were assigned to the non-S-INDEL strain. No S-INDEL sequences were recovered in this study, although these viruses continue to circulate in the country. Our analyses revealed that most sequences sampled after 2023 formed a monophyletic clade divergent from sequences collected in previous years, suggesting an ongoing temporal population structuring. Population structure analyses further supported evidence of population differentiation over time. Recombination analyses indicated that sequences belonging to the contemporary clade shared a single recombination event, suggesting that this clade may have emerged through recombination. Time-scaled S1 phylogenies were consistent with previous findings, supporting the circulation of only two contemporary clades; however, one of these clades was detected for the first time outside its previously reported geographic range. Our findings document temporal genetic differentiation in US PEDV populations, consistent with continued viral evolution, and broaden the known geographic distribution of contemporary S1 clades. These results highlight the value of continued genomic surveillance to monitor changes in PEDV diversity and distribution and provide sequence data to inform vaccine research.

microbiology↗

bioRxiv2026

An early-diverging Caladeniinae orchid reveals diversification of terpene and apocarotenoid pathways underlying floral scent evolution

Orchids exhibit extraordinary floral diversity, yet the molecular mechanisms underlying floral scent evolution remain poorly understood. Guided by recent phylogenomic reconstruction of the Australian orchid subtribe Caladeniinae, we used Glossodia major, an earlier-diverging food-deceptive lineage, as an evolutionary anchor for investigating floral volatile diversification. Scent-producing petals showed coordinated expression of terpene synthase (TPS), carotenoid and carotenoid cleavage dioxygenase (CCD) pathways. Functional characterisation identified GmTPS-b3, GmTPS-b4 and GmTPS-a1 as contributors to floral monoterpene and sesquiterpene production, while GmCCD1 produced geranylacetone, the dominant floral volatile, from {zeta}-carotene. GmCCD4 and GmCCD7a showed additional, partially overlapping apocarotenoid-forming activities. Integration of tissue-specific expression, enzyme activity and subcellular localisation linked these pathways to the emitted floral bouquet. Functional comparisons with characterised Caladenia homologues revealed biochemical conservation and catalytic and compartmental specialisation, while expression profiling across 31 species identified pollination strategy-associated regulatory divergence in TPSa1 and TPSb3, consistent with corresponding shifts in terpenoid-rich floral scent. We propose that differential modification and deployment of conserved biosynthetic pathways contributed to the attenuation and re-emergence of terpenoid-rich floral scent during Caladeniinae diversification. More broadly, our findings provide candidate mechanistic links between molecular evolution, pollinator-mediated selection and floral diversification.

plant biology↗

bioRxiv2026

An Implantable Wireless Battery-Free Selective Vagus Nerve Stimulator

Objective. Vagus nerve stimulation (VNS) is an established clinical therapy for drug-resistant epilepsy and other inflammatory conditions. However, off-target stimulation can produce unwanted side effects that limit therapeutic stimulation and hinder the development of new neuromodulation therapies. Selective VNS (sVNS) offers a strategy to reduce off-target organ activation; however, this approach is not available in humans, and no implantable or portable devices exist to trial sVNS in the clinical setup. This work aimed to design, manufacture, and validate an implantable wireless, battery-free stimulator with a selectively addressable output stage for targeted current delivery to specific regions of the human vagus nerve (VN). Approach. We developed a near-field communication-controlled, wirelessly powered, battery-free, temporary implantable multichannel stimulation device, compatible with a 15-channel sVNS cuff electrode (14 selective electrode pairs and one circumferential whole-nerve channel). The device was encapsulated for short-term implantation and evaluated through benchtop characterisation, accelerated ageing, and validation in an acute porcine and a pilot human study. Main result. The sVNS device was evaluated in a porcine (n = 4) trial and a first-in-human pilot study (n = 1). Selective bradycardia of 23.28 {+/-} 12.91% was observed in pigs and 7.5% in the human participant. In the human, a clear separation of bradycardic and tachycardic effects was observed, with additional selectivity in laryngeal activity. Cardiac and laryngeal responses were separated by 231{degrees} around the circumference of the nerve. Significance. This work demonstrates the feasibility of wireless battery-free sVNS for cardiac applications using a temporary implantable device. Geometrically selective stimulation has the potential to improve therapeutic efficacy while reducing stimulation-related side effects, and may facilitate future therapies for heart failure and other autonomic disorders.

bioengineering↗

bioRxiv2024

Successful stimulation of myocardial ganglionic plexuses by TAU 20 in the absence of cardiac damage

Atrial fibrillation (AF) is a major healthcare burden worldwide. For AF that is resistant to pharmacological intervention, the standard invasive treatment is a pulmonary vein isolation (PVI) procedure. Ganglionated plexuses (GP) ablation can be used as an adjunctive therapy to PVIs, together reducing the likelihood of AF recurrence. High-frequency stimulation (HFS) is a technique used to identify ectopy-triggering GP sites. However, to locate GP sites, sequential HFS must be delivered over the whole atria. Therefore, ensuring the safety of HFS delivery is integral to avoid causing irreversible damage from excessive pacing. We tested Tau-20 version 2 neural simulator, a prototype of a novel electrophysiological pacing and recording system that has the potential to guide intracardiac AF treatments. Using an ex vivo porcine Langendorff model that closely resembles the anatomy and physiology of a human heart, we confirmed that HFS can successfully trigger AF, indicating that HFS-positive locations contain GP sites. Additionally, we found that the HFS delivered via Tau-20 version 2 did not cause any damage to the heart. These findings evidence that once fully optimised, the Tau-20 system could be suitable for use in clinical settings.

physiology↗

bioRxiv2023

The effects of genome size on cell size and the functional composition and morphology of leaves: a case study in Rhododendron (Ericaceae)

Background and AimsDespite the predominance of scaling photosynthetic metabolism by two-dimensional leaf surface area, leaves are three-dimensional structures composed of multiple tissues that directly and indirectly influence photosynthetic metabolism. The structure of leaf surfaces for CO2 diffusion and light transmission and the internal volume of tissues that process energy and matter work together to control rates of resource acquisition and turnover. Here we investigate the influence of cell size and packing density on resource acquisition as measured by surface conductance to CO2 and water vapor and on resource turnover as measured by leaf water turnover time. MethodsWe sampled wild and cultivated congeneric species in the genus Rhododendron (Ericaceae) and measured genome size, anatomical traits related to cell sizes and packing densities, and morphological traits related to water content and dry mass allocation. ResultsAmong Rhododendron, anatomical traits related to cell size and morphological traits related to water content and dry mass investment varied largely orthogonally to each other, allowing for many combinations of leaf traits to exist. However, there was a strong, negative relationship between the leaf water residence time ({tau}) and the maximum leaf surface conductance per leaf volume (gmax,vol), both of which are influenced by cell size and cell packing densities. ConclusionsDespite leaf function being controlled by many potential combinations of leaf cell- and tissue-level traits, cell size has a pervasive effect on leaf function. Small cells allow for higher diffusion of CO2 and water vapor per unit leaf volume (gmax,vol) even at constant leaf thickness, but small cells also result in shorter leaf water residence times ({tau}). The strong tradeoff between gmax,vol and ({tau}) illuminates how genome size-cell size allometry influences the fast-slow continuum of plant carbon and water economy.

plant biology↗

bioRxiv2023

Stimulus novelty uncovers coding diversity in visual cortical circuits

Detecting novel stimuli in the environment is critical for learning and survival, yet the neural basis of novelty processing is not understood. To characterize cell type-specific novelty processing, we surveyed the activity of [~]15,000 excitatory and inhibitory neurons in mice performing a visual task with novel and familiar stimuli. Clustering revealed a dozen functional neuron types defined by experience-dependent encoding. Vasoactive-intestinal-peptide (Vip) expressing inhibitory neurons were diverse, encoding novel stimuli, omissions of familiar stimuli, or behavioral features. Distinct Somatostatin (Sst) expressing inhibitory neurons encoded either familiar or novel stimuli. Subsets of excitatory neurons co-clustered with specific Vip or Sst subpopulations, while Sst and Vip inhibitory clusters were non-overlapping. This study establishes that novelty processing is mediated by diverse functional neuron types in the visual cortex.

neuroscience↗

bioRxiv2022

Organotopic organisation of the cervical vagus nerve

Despite detailed characterization of fascicular organization of somatic nerves, the functional anatomy of fascicles evident in human and large mammal cervical vagus nerve is unknown. The vagus nerve is a prime target for intervention in the field of electroceuticals due to its extensive distribution to the heart, larynx, lungs, and abdominal viscera. However, current practice of the approved vagus nerve stimulation (VNS) technique is to stimulate the entire nerve. This produces indiscriminate stimulation of non-targeted effectors and undesired side effects. Selective neuromodulation is now a possibility with a spatially-selective vagal nerve cuff. However, this requires the knowledge of the fascicular organization at the level of cuff placement to inform selectivity of only the desired target organ or function. We imaged function over milliseconds with fast neural electrical impedance tomography and selective stimulation, and found consistent spatially separated regions within the nerve correlating with the three fascicular groups of interest, suggesting organotopy. This was independently verified with structural imaging by tracing anatomical connections from the end organ with microCT and the development of an anatomical map of the vagus nerve. This confirmed organotopic organization. Here we show, for the first time, localized fascicles in the porcine cervical vagus nerve which map to cardiac, pulmonary and recurrent laryngeal function (N=4). These findings pave the way for improved outcomes in VNS as unwanted side effects could be reduced by targeted selective stimulation of identified organ-specific fascicles and the extension of this technique clinically beyond the currently approved disorders to treat heart failure, chronic inflammatory disorders and more.

neuroscience↗

bioRxiv2021

Learning from unexpected events in the neocortical microcircuit

Scientists have long conjectured that the neocortex learns the structure of the environment in a predictive, hierarchical manner. According to this conjecture, expected, predictable features are differentiated from unexpected ones by comparing bottom-up and top-down streams of information. It is theorized that the neocortex then changes the representation of incoming stimuli, guided by differences in the responses to expected and unexpected events. In line with this conjecture, different responses to expected and unexpected sensory features have been observed in spiking and somatic calcium events. However, it remains unknown whether these unexpected event signals occur in the distal apical dendrites where many top-down signals are received, and whether these signals govern subsequent changes in the brains stimulus representations. Here, we show that both somata and distal apical dendrites of cortical pyramidal neurons exhibit distinct unexpected event signals that systematically change over days. These findings were obtained by tracking the responses of individual somata and dendritic branches of layer 2/3 and layer 5 pyramidal neurons over multiple days in primary visual cortex of awake, behaving mice using two-photon calcium imaging. Many neurons in both layers 2/3 and 5 showed large differences between their responses to expected and unexpected events. Interestingly, these responses evolved in opposite directions in the somata and distal apical dendrites. These differences between the somata and distal apical dendrites may be important for hierarchical computation, given that these two compartments tend to receive bottom-up and top-down information, respectively.

neuroscience↗

bioRxiv2020

CoBRA: Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis - from differential peak calling to pathway analysis

ChIP-seq and ATAC-seq have become essential technologies used as effective methods of measuring protein-DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates correct normalization between samples, adjustment of copy number variations, and integration of new downstream analysis tools. Here we present CoBRA, a modularized computational workflow which quantifies ChIP and ATAC-seq peak regions and performs unsupervised and supervised analysis. CoBRA provides a comprehensive state-of-the-art ChIP and ATAC-seq analysis pipeline that is usable by scientists with limited computational experience. This enables researchers to gain rapid insight into protein-DNA interactions and chromatin accessibility through sample clustering, differential peak calling, motif enrichment, comparison of sites to a reference DB and pathway analysis. Code availability: https://bitbucket.org/cfce/cobra

bioinformatics↗

bioRxiv2020

PROTECTIVE ANTIBODIES AGAINST HPIV3 INFECTION

Human parainfluenza virus type III (HPIV3) is a common respiratory pathogen that afflicts children and can be fatal in vulnerable populations, including the immunocompromised. Unfortunately, an effective vaccine or therapeutic is not currently available, resulting in tens of thousands of hospitalizations per year. In an effort to discover a protective antibody against HPIV3, we screened the B cell repertoires from peripheral blood, tonsils, or spleen from healthy children and adults. These analyses yielded five monoclonal antibodies that potently neutralized HPIV3 in vitro. These HPIV3 neutralizing antibodies targeted two non-overlapping epitopes of the HPIV3 F protein, with most targeting the apex. Importantly, prophylactic administration of one of these antibodies, named PI3-E12, resulted in potent protection against HPIV3 infection in cotton rats. Additionally, PI3-E12 could also be used therapeutically to suppress HPIV3 in immunocompromised animals. These results demonstrate the potential clinical utility of PI3-E12 for the prevention or treatment of HPIV3 in both immunocompetent and immunocompromised individuals.

immunology↗

bioRxiv2020

Imaging fascicular organization of peripheral nerves with fast neural Electrical Impedance Tomography (EIT)

Imaging of the compound action potential (CAP) in fascicles in peripheral nerves could help avoid side effects in neuromodulation by selective stimulation of identified fascicles. Existing methods have low resolution, limited imaging depth, or are invasive. We propose fast neural electrical impedance tomography (EIT), which allows fascicular CAP imaging with a high resolution of [~]200 m, <1 ms. This uses a non-penetrating flexible cuff electrode array with 14 circumferential electrodes. This has been validated in rat sciatic nerve by comparison to micro-computed tomography (microCT) and histology with fluorescent dextran tracers (n=5). With EIT, there were reproducible localized changes in tissue impedance in response to stimulation of individual fascicles (tibial, peroneal and sural). The reconstructed EIT images corresponded to microCT scans and neural tracer histology, with significant separation between the fascicles (p<0.01), and no significant difference between techniques. The standard deviation from the mean fascicle position for EIT was 86 m (6% of nerve diameter). This suggests fast neural EIT can reliably image the functional fascicular anatomy of the nerves and so aid selective neuromodulation.

bioengineering↗

bioRxiv2020

Subthreshold repertoire and threshold dynamics of midbrain dopamine neuron firing in vivo.

The firing pattern of ventral midbrain dopamine neurons is controlled by afferent and intrinsic activity to generate prediction error signals that are essential for reward-based learning. Given the absence of intracellular in vivo recordings in the last three decades, the subthreshold membrane potential events that cause changes in dopamine neuron firing patterns remain unknown. By establishing stable in vivo whole-cell recordings of >100 spontaneously active midbrain dopamine neurons in anaesthetized mice, we identified the repertoire of subthreshold membrane potential signatures associated with distinct in vivo firing patterns. We demonstrate that dopamine neuron in vivo activity deviates from a single spike pacemaker pattern by eliciting transient increases in firing rate generated by at least two diametrically opposing biophysical mechanisms: a transient depolarization resulting in high frequency plateau bursts associated with a reactive, depolarizing shift in action potential threshold; and a prolonged hyperpolarization preceding slower rebound bursts characterized by a predictive, hyperpolarizing shift in action potential threshold. Our findings therefore illustrate a framework for the biophysical implementation of prediction error and sensory cue coding in dopamine neurons by tuning action potential threshold dynamics.

neuroscience↗

bioRxiv2019

MicroCT optimisation for imaging fascicular anatomy in peripheral nerves

Vagus nerve stimulation (VNS) is a promising therapy for treatment of various conditions resistant to standard therapeutics. However, due to the lack of understanding of the fascicular organisation of the vagus nerve, VNS leads to unwanted off-target effects. Micro-computed tomography (microCT) can be used to trace fascicles from periphery and image fascicular anatomy. In this work we optimised the microCT protocol of the rat sciatic and subsequent pig vagus nerves.\n\nAfter differential staining, the optimal staining time was selected and scanning parameters were altered in subsequent scans. Scans were reconstructed, visualised in ImageJ and fascicles segmented with a custom algorithm in Matlab to determine ultimate parameters for tracking of the nerve. Successful segmentation for tracking of individual fascicles was achieved after 24 hours and 120 hours of staining with Lugols solution (1% total iodine) for rat sciatic and pig vagus nerves, respectively, and the following scanning parameters: 4 {micro}m voxel size, 35 kVp energy, 114 {micro}A current, 4 W power, 0.25 fps in 4 s exposure time, 3176 projections and a molybdenum target.\n\nThe optimised microCT protocol allows for segmentation and tracking of the fascicles within the nerve. This will be used to scan the full length of the pig, and possibly, the human vagus nerves. The resulting segmentation map of the functional anatomical organisation of the vagus nerve will enable selective VNS ultimately allowing for the avoidance of the off-target effects and improving its therapeutic efficacy.

neuroscience↗

bioRxiv2019

A Petascale Automated Imaging Pipeline for Mapping Neuronal Circuits with High-throughput Transmission Electron Microscopy

Serial-section electron microscopy is the method of choice for studying cellular structure and network connectivity in the brain. We have built a pipeline of parallel imaging using transmission electron automated microscopes (piTEAM) that scales this technology and enables the acquisition of petascale datasets containing local cortical microcircuits. The distributed platform is composed of multiple transmission electron microscopes that image, in parallel, different sections from the same block of tissue, all under control of a custom acquisition software (pyTEM) that implements 24/7 continuous autonomous imaging. The suitability of this architecture for large scale electron microscopy imaging was demonstrated by acquiring a volume of more than 1 mm3 of mouse neocortex spanning four different visual areas. Over 26,500 ultrathin tissue sections were imaged, yielding a dataset of more than 2 petabytes. Our current burst imaging rate is 500 Mpixel/s (image capture only) per microscope and net imaging rate is 100 Mpixel/s (including stage movement, image capture, quality control, and post processing). This brings the combined burst acquisition rate of the pipeline to 3 Gpixel/s and the net rate to 600 Mpixel/s with six microscopes running acquisition in parallel, which allowed imaging a cubic millimeter of mouse visual cortex at synaptic resolution in less than 6 months.

neuroscience↗

bioRxiv2019

Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil

The application of environmental DNA (eDNA) metabarcoding as a biomonitoring tool has greatly increased in the last decade. However, most studies have focused on aquatic macro-organisms in temperate areas (e.g., fishes). We apply eDNA metabarcoding to detect the mammalian community in two high-biodiversity regions of Brazil, the Amazon and Atlantic Forest. We identified critically endangered and endangered mammalian species in the Atlantic Forest and Amazon respectively and found congruence with species identified via camera trapping in the Atlantic Forest. In light of our results, we highlight the potential and challenges of eDNA monitoring for mammals in these high biodiverse areas.

ecology↗

bioRxiv2018

Biological variation in the sizes, shapes and locations of visual cortical areas in the mouse

Visual cortex is organized into discrete sub-regions or areas that are arranged into a hierarchy and serve different functions in the processing of visual information. In our previous work, we noted that retinotopic maps of cortical visual areas differed between mice, but did not quantify these differences or determine the relative contributions of biological variation and measurement noise. Here we quantify the biological variation in the size, shape and locations of 11 visual areas in the mouse. We find that there is substantial biological variation in the sizes of visual areas, with some visual areas varying in size by two-fold across the population of mice.

neuroscience↗

bioRxiv2018

Ventral tegmental area astrocytes orchestrate avoidance and approach behavior

The ventral tegmental area (VTA) is a heterogeneous midbrain structure, containing neurons and astrocytes, that coordinates approach and avoidance behaviors by integrating activity from numerous afferents. Within neuron-astrocyte networks, astrocytes control signals from distinct afferents in a circuit-specific manner, but whether this capacity scales up to drive motivated behavior has been undetermined. Using genetic and optical dissection strategies in vitro and during behavior we report that VTA astrocytes tune glutamatergic signaling selectively on local inhibitory neurons to drive a functional circuit for learned avoidance. In this circuit, VTA astrocytes facilitate excitation of local GABA neurons to increase inhibition of dopamine neurons. The increased inhibition of dopamine neurons elicits real-time and learned avoidance behavior that is sufficient to impede expression of learned preference for reward. Despite the large number of functions performed by astrocytes, loss of one glutamate transporter (GLT-1) from VTA astrocytes selectively blocks these avoidance behaviors and spares preference for reward. Thus, VTA astrocytes selectively regulate excitation of local GABA neurons to drive a distinct learned avoidance circuit that opposes learned approach behavior.

neuroscience↗