Biology subjects

Wright, P.

Publications and source records attributed to Wright, P..

12 recordsLinked to original sources

bioRxiv2026

Development of species-specific real-time PCR assays for the identification of five European Rhinolophus bats.

The detection and monitoring of bat species using non-invasive sampling and molecular techniques has become increasingly popular in recent years. In Europe, these approaches have been applied to identify horseshoe bats of the genus Rhinolophus, which includes five species: R. hipposideros, R. ferrumequinum, R. euryale, R. mehelyi and R. blasii. While species-specific real-time PCR assays exist for R. ferrumequinum and R. hipposideros, no unified panel of real-time PCR assays currently enables the identification of all five European Rhinolophus species from non-invasively collected samples. Here, we developed five species-specific real-time PCR assays, each targeting interspecies nucleotide variation within the mitochondrial cytochrome b gene. To enhance single-base discrimination, RNase H-dependent PCR (rhPCR) primers were employed, incorporating cleavable blocked primers that require perfect complementarity for extension. The assays were applied to droppings non-invasively collected from 18 caves and one church in Serbia and Romania. Of the 149 samples analysed, 131 (88%) yielded successful amplification of Rhinolophus DNA. Detection probabilities for the three species identified in the field ranged from 0.49 to 0.82. Occupancy estimates varied, with R. euryale showing the highest (0.86; UI: 0.69-0.97) and R. mehelyi the lowest (0.23; UI: 0.08-0.43). The assays were capable of detecting up to three species concurrently within a single pooled sample (approximately 15 droppings). These assays are especially valuable for detecting R. mehelyi, given its rarity and uncertain distribution, and offer a robust tool for monitoring Rhinolophus populations across Europe.

ecology↗

bioRxiv2026

X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion Language Models

Causal models of cellular systems hold the promise to empower broad biological discovery, including the systematic identification of novel targets for drug discovery. Predicting how genetic and pathway perturbations reshape gene expression across diverse cellular contexts is a prerequisite for building generalizable cellular foundation models. However, current methods typically fail to extrapolate beyond their training distributions because they rely predominantly on observational expression atlases rather than interventional perturbation data. We present X-Atlas/Pisces, the largest genome-wide CRISPRi Perturb-seq compendium to date, comprising 25.6 million perturbed single-cell transcriptomes across 16 biologically diverse contexts, including widely used cell lines, induced pluripotent stem cells (iPSCs), resting and CD3/CD28 activated Jurkat T lymphoma cells, and multi-lineage differentiating iPSCs. Leveraging this resource, we develop X-Cell, a diffusion language model that predicts perturbation responses by iteratively refining control-to-perturbed state transitions through cross-attention to multi-modal biological priors derived from natural language, protein language models, interaction networks, genetic dependency maps, and morphological profiles. X-Cell outperforms existing state-of-the-art models by up to five-fold on key metrics such as Pearson{Delta} (correlation between predicted and observed perturbation-induced log-fold changes), and demonstrates zero-shot prediction of T cell inactivating perturbations in stimulated Jurkat cells. We scale X-Cell to 4.9 billion parameters (X-Cell-Ultra), the largest causal perturbation model to date. We demonstrate for the first time that perturbation prediction follows power-law scaling with an exponent matching large language models. X-Cell-Ultra demonstrates zero-shot generalization to novel biological contexts, including unseen iPSC-derived melanocyte progenitors and primary human CD4+ T cells from multiple donors, and outperforms all baselines after self-supervised test-time adaptation. These results demonstrate that coordinated scaling of causal perturbation data and model capacity yields foundation models capable of generalizable perturbation prediction across cellular contexts, with potential applications for improving computational target identification, validation, and context-specific therapeutic prioritization.

systems biology↗

bioRxiv2026

Taste Papillae-associated Salivary Gland Ducts Contribute to Immune Surveillance

The lingual surface is composed of a tough epithelium that affords effective protection from the resident and food-borne microbiota. The circumvallate taste papillae (CVP) in the back of the tongue are associated with underlying minor salivary glands called von Ebners gland (VEG) that drains its secretions into the trenches of the papillae. The taste buds are exposed to the lingual surface through taste pores, to enable interaction with tastants. These openings may be exploited by pathogens for infection. Mucosa-associated lymphoid tissue (MALT) such as those in the gut epithelium, tonsils and lachrymal and salivary ducts possess specialized cells called microfold (M) cells that transport luminal microbes and present them to underlying immune cells, which then initiate an appropriate immune response. Our previous work indicated that type II taste cells might mediate similar immune surveillance akin to M cells and that CVP is patrolled by large population of immune cells. Using single cell RNASeq (scRNASeq) of CVP, we discovered that the duct cells of the VEG strongly express markers for M cells. The ducts were capable of transcytosing fluorescently labelled E. coli and fluorescent nanobeads, which are then taken up by underlying immune cells. We propose that taste and duct cell-mediated immune surveillance might be crucial for preventing infection of taste papillae and for maintaining taste function, and conversely, this pathway might be hijacked by microbes for infection.

immunology↗

bioRxiv2025

X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models

The rapid expansion of massively parallel sequencing technologies has enabled the development of foundation models to uncover novel biological findings. While these have the potential to significantly accelerate scientific discoveries by creating AI-driven virtual cell models, their progress has been greatly limited by the lack of large-scale high-quality perturbation data, which remains constrained due to scalability bottlenecks and assay variability. Here, we introduce "Fix-Cryopreserve-ScRNAseq" (FiCS) Perturb-seq, an industrialized platform for scalable Perturb-seq data generation. We demonstrate that FiCS Perturb-seq exhibits high sensitivity and low batch effects, effectively capturing perturbation-induced transcriptomic changes and recapitulating known biological pathways and protein complexes. In addition, we release X-Atlas: Orion edition (X-Atlas/Orion), the largest publicly available Perturb-seq atlas. This atlas, generated from two genome-wide FiCS Perturb-seq experiments targeting all human protein-coding genes, comprises eight million cells deeply sequenced to over 16,000 unique molecular identifiers (UMIs) per cell. Furthermore, we show that single guide RNA (sgRNA) abundance can serve as a proxy for gene knockdown (KD) efficacy. Leveraging the deep sequencing and substantial cell numbers per perturbation, we also show that stratification by sgRNA expression can reveal dose-dependent genetic effects. Taken together, we demonstrate that FiCS Perturb-seq is an efficient and scalable platform for high-throughput Perturb-seq screens. Through the release of X-Atlas/Orion, we highlight the potential of FiCS Perturb-seq to address current scalability and variability challenges in data generation, advance foundation model development that incorporates gene-dosage effects, and accelerate biological discoveries.

genomics↗

bioRxiv2024

Mispacking of the F87 sidechain drives aggregation-promoting conformational fluctuations in the subunit interfaces of the transthyretin tetramer

Aberrant formation and deposition of human transthyretin (TTR) aggregates causes transthyretin amyloidosis. To initialize aggregation, transthyretin tetramers must first dissociate into monomers that partially unfold to promote entry into the aggregation pathway. The native TTR tetramer (T) is stabilized by docking of the F87 sidechain into an interfacial cavity enclosed by several hydrophobic residues including A120. We have previously shown that an alternative tetramer (T*) with mispacked F87 sidechains is more prone to dissociation and aggregation than the native T state. However, the molecular basis for the reduced stability in T* remains unclear. Here we report characterization of the A120L mutant, where steric hindrance is introduced into the F87 binding site. The X-ray structure of A120L shows that the F87 sidechain is displaced from its docking site across the subunit interface. In A120S, a naturally occurring pathogenic mutant that is less aggregation-prone than A120L, the F87 sidechain is correctly docked, as in the native TTR tetramer. Nevertheless, 19F-NMR aggregation assays show an elevated population of a monomeric aggregation intermediate in A120S relative to a control containing the native A120, due to accelerated tetramer dissociation and slowed monomer tetramerization. The mispacking of the F87 sidechain is associated with enhanced exchange dynamics for interfacial residues. At 298 K, the T* populations of various naturally occurring mutants fall between 4-7% ({Delta}G [~] 1.5- 1.9 kcal/mol), consistent with the free energy change expected for undocking and solvent exposure of one of the four F87 sidechains in the tetramer ({Delta}G [~] 1.6 kcal/mol). Our data provide a molecular-level picture of the likely universal F87 sidechain mispacking in tetrameric TTR that promotes interfacial conformational dynamics and increases aggregation propensity.

biophysics↗

bioRxiv2024

Characterization of an amyloidogenic intermediate of transthyretin by NMR relaxation dispersion

The aggregation pathway of transthyretin (TTR) proceeds through rate-limiting dissociation of the tetramer and partial misfolding of the monomers, which assemble into amyloid structures through a downhill polymerization mechanism. The structural features of the aggregation-prone monomeric intermediate are poorly understood. Characterization of amyloidogenic intermediates is challenging due to their propensity to aggregate at concentrations necessary for structural studies. NMR relaxation dispersion offers a unique opportunity to characterize these intermediates when they exchange on favorable timescales with NMR-visible ground states. To characterize the structural transitions associated with tetramer dissociation, we have analyzed ground-state chemical shift differences between the native tetramer and an engineered monomer in which the critical F87 side chain is replaced by glutamate. The secondary structure and overall fold of the F87E monomer is similar to that of the tetramer except for {beta}-strand H. This strand populates two conformations, where it is either docked on the protein core or is displaced from the edge of the {beta}-sheet formed by {beta}-strands D, A, G, and H (DAGH {beta}-sheet) and is dynamically disordered. Chemical shift differences derived from analysis of 1H/15N single, double and zero quantum relaxation dispersion data provide insights into the structure of a low-lying excited state that exchanges with the ground state of the F87E monomer at a rate of 3800 s-1. Disruption of the subunit interfaces of the TTR tetramer leads to destabilization of edge strands in both {beta}-sheets of the F87E monomer. Conformational fluctuations are propagated through the entire hydrogen bonding network of the DAGH {beta}-sheet, from the inner {beta}-strand H, which forms the strong dimer interface in the TTR tetramer, to outer strand D which is unfolded in TTR fibrils. Fluctuations are also propagated from the AB loop in the weak dimer interface to the EF helix, which undergoes structural remodeling in fibrils. The conformational fluctuations in both regions are enhanced at acidic pH where amyloid formation is most favorable. The relaxation dispersion data provide insights into the conformational dynamics of the amyloidogenic state of monomeric TTR that predispose it for structural remodeling and progression to amyloid fibrils.

biophysics↗

bioRxiv2024

Advancements in monitoring: a comparison of traditional and application-based tools for measuring outdoor recreation

Outdoor recreation has experienced a boom in recent years. While outdoor recreation provides wide-ranging benefits to human well-being and is an important feature of many protected and non-protected areas, there are growing concerns about the sustainability of recreation with the increased pressures placed on ecological systems and visitor experiences. These concerns emphasize the need for managers to access accurate and timely recreation data at scales that match the growing recreation footprint. Here, we compare spatial and temporal patterns of winter and summer recreation use using traditional and application-based tools across the Columbia and Canadian Rocky Mountains of western Canada. We demonstrate how recreation use can be estimated using traditional and application-based tools, although their accuracy and utility varies across space, season and activity type. Cameras and counters captured similar broad-scale patterns in count estimates of pedestrians and all recreation activities. Application-based data provided detailed spatiotemporal information on recreation use, but datasets were biased towards specific recreation types and did not represent the full recreation population. For instance, Strava Metro data was more suited for capturing broad-scale spatial patterns in biking than pedestrian recreation. Traditional tools including aerial surveys and participatory mapping captured coarser information on the intensity and extent of recreation, with the former tool capturing areas with low recreation intensity and the latter tool suited for capturing recreation information across large spatial and temporal scales. Application-based data should be supplemented with data from traditional tools including cameras or trail counters to identify biases in data and fill in data gaps. We provide a comparison of each tool for measuring recreation use, highlight each tools strengths and limitations, and suggest how to use these tools to address real-world monitoring and management scenarios. Our research contributes towards a better understanding of what tools are available to measure recreation and can help direct managers in selecting which tool, or combinations of tools, to use that can expand the rigor and scope of recreation research. This information can support decision-making and lead to the protection of ecological systems while allowing for high-quality recreation experiences. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=159 HEIGHT=200 SRC="FIGDIR/small/579662v1_ufig1.gif" ALT="Figure 1"> View larger version (76K): org.highwire.dtl.DTLVardef@95b5a7org.highwire.dtl.DTLVardef@c926d7org.highwire.dtl.DTLVardef@151296org.highwire.dtl.DTLVardef@1773d13_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2023

Transcriptomic profiling reveals a pro-nociceptive role for Angiotensin II in inflammatory bowel disease

ObjectiveVisceral pain is a leading cause of morbidity in inflammatory bowel disease (IBD), contributing significantly to reduced quality of life. Currently available analgesics often lack efficacy or have intolerable side-effects, driving the need for a more complete understanding of the mechanisms causing pain. MethodsWhole transcriptome gene expression analysis was performed by bulk RNA sequencing of colonic biopsies from patients with ulcerative colitis (UC) and Crohns disease (CD) reporting abdominal pain and compared with non-inflamed control biopsies. Putative pro-nociceptive mediators were identified based on pathway analysis of differentially expressed genes in IBD tissue and single cell gene expression in colonic neurons. Pro-nociceptive activity of identified mediators was assessed in assays of sensory neuron and colonic afferent activity. ResultsRNA sequencing analysis highlighted a 7.6-fold increase in the expression of angiotensinogen transcripts, Agt, the precursor to angiotensin II (Ang II), in samples from UC patients (p = 3.2x10-8). Consistent with the marked expression of the angiotensin AT1 receptor in colonic neurons, Ang II elicited an increase in intracellular Ca2+ in capsaicin-sensitive, voltage gated sodium channel subtype NaV1.8-positive sensory neurons. Ang II also evoked action potential discharge in high-threshold colonic nociceptors. These effects were inhibited by the AT1 receptor antagonist valsartan. ConclusionFindings from our study identify AT1 receptor-mediated colonic nociceptor activation as a novel pathway of visceral nociception in IBD patients with UC. This work highlights the potential utility of angiotensin receptor blockers, such as valsartan, as treatments for pain in IBD.

neuroscience↗

bioRxiv2022

Mink on the brink: Comparing survey methods for detecting a Critically Endangered carnivore, the European mink Mustela lutreola

Monitoring rare and elusive species is critical in guiding appropriate conservation management measures. Mammalian carnivores are challenging to monitor directly, due to their generally nocturnal and solitary lifestyle, and relatively large home ranges. The European mink Mustela lutreola is a Critically Endangered, small, semi-aquatic carnivore and is one of the most threatened mammal species in Europe. In northern Spain, the European mink population is monitored regionally using different methods and approaches, making assessment of national population status difficult. There is an urgent need to 1) assess the efficacy of survey methods, and 2) identify a standard monitoring methodology that can be deployed rapidly and inexpensively over large areas of the minks range. We deployed four methods - camera trapping, hair tubes, live trapping, and environmental DNA (eDNA) from water samples - to compare the probability of detecting European mink when present at 25 sampling sites within five 10x10km squares, and the economic cost and time required for each method. All four methods successfully detected European mink but the probability of detection varied by method. Camera trapping and hair tubes had the highest probability of detection; however, eDNA and live trapping detected mink in one 10x10km square where the latter two methods did not. For future European mink monitoring programmes, we recommend a combination of at least two methods, and suggest that camera traps or hair tubes are combined with live trapping or eDNA (depending on the scale and aims of the study), to gather critical information on distribution, occupancy and conservation status.

ecology↗

bioRxiv2021

Positive feedback promotes terrestrial emergence behaviour in an amphibious fish

Major ecological transitions such as the invasion of land by aquatic vertebrates have been hypothesised to be facilitated by positive feedback between habitat choice and phenotypic plasticity. We tested whether aquatic hypoxia, emergence behaviour, and plastic changes in gill surface area could create such a positive feedback loop and drive an amphibious fish to spend increasing amounts of time out of water. We found that terrestrially acclimated amphibious mangrove rivulus Kryptolebias marmoratus were more sensitive to, and less tolerant of, aquatic hypoxia relative to water-acclimated fish, which are necessary trade-offs for positive feedback to occur. Next, we acclimated fish to normoxic or hypoxic water with the opportunity to emerge for 7d to test the predictions that fish in hypoxic conditions should regularly leave water, reduce gill surface area, and become less hypoxia tolerant. Consistent with these predictions, fish in severe hypoxia spent almost 50% of the time out of water and coverage of the gill lamellae by an inter-lamellar cell mass almost doubled. Hypoxia acclimated fish were also more sensitive to acute aquatic hypoxia (emergence at higher oxygen levels), and lost equilibrium faster in hypoxic water compared to control fish. Thus, we show that a positive feedback loop develops in amphibious fish where emergence behaviour begets further emergence behaviour, driven by gill remodelling which reduces aquatic respiratory function. Such a scenario may explain how amphibious behaviour has repeatedly evolved in fishes that occupy hypoxic aquatic habitats despite the associated challenges of life on land.

physiology↗

bioRxiv2021

eIF6 rebinding dynamically couples ribosome maturation and translation

Protein synthesis is a cyclical process consisting of translation initiation, elongation, termination and ribosome recycling. The release factors SBDS and EFL1 (both mutated in the leukaemia predisposition disorder Shwachman-Diamond syndrome) license entry of nascent 60S ribosomal subunits into active translation by evicting the anti-association factor eIF6 from the 60S intersubunit face. Here, we show that in mammalian cells, eIF6 holds all free cytoplasmic 60S subunits in a translationally inactive state and that SBDS and EFL1 are the minimal components required to recycle these 60S subunits back into additional rounds of translation by evicting eIF6. Increasing the dose of eIF6 in mice in vivo impairs terminal erythropoiesis by sequestering post-termination 60S subunits in the cytoplasm, disrupting subunit joining and attenuating global protein synthesis. Our data reveal that ribosome maturation and recycling are dynamically coupled by a mechanism that is disrupted in an inherited leukaemia predisposition disorder.

cell biology↗

bioRxiv2020

Using a bistable animal opsin for switchable and scalable optogenetic inhibition of neurons

There is no consensus on the best optogenetic tool for neuronal inhibition. Lamprey parapinopsin ( Lamplight) is a Gi/o-coupled bistable animal opsin that can be activated and deactivated by short and long wavelength light, respectively. Since native mechanisms of neuronal inhibition frequently employ Gi/o signalling, we asked here whether Lamplight could be used for optogenetic silencing. We show that short (405nm) and long (525nm) wavelength pulses repeatedly switch Lamplight between stable signalling active and inactive states, and that combining these wavelengths can be used to achieve intermediate levels of activity. We demonstrate that these properties can be applied to produce switchable and scalable neuronal hyperpolarisation, and suppression of spontaneous spike firing in the mouse hypothalamic suprachiasmatic nucleus. We show that expressing Lamplight in (predominantly) ON bipolar cells can photosensitise retinas following advanced photoreceptor degeneration, and that 405 and 525nm stimuli can produce responses of opposite sign in output neurons of the retina. Lamplight-driven responses to both activating (405nm) and deactivating (525nm) light can occur within 500ms and be elicited by intensities at least 10x below threshold for available inhibitory optogenetic tools. We conclude that Lamplight can co-opt endogenous signalling mechanisms to allow optogenetic inhibition that is scalable, sustained and rapidly reversible.

neuroscience↗