Biology subjects

Peters, R.

Publications and source records attributed to Peters, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Cargo levels control endosomal PI(3)P homeostasis through direct feedback between SNX17 and MTM1

The sorting of internalised cell surface proteins through the endosomal network is crucial for cellular function. Phosphatidylinositol-3-phosphate (PI(3)P) is a critical lipid identity cue for organising endosomal sorting but there is limited understanding of how PI(3)P homeostasis is regulated. Here, we show that free PI(3)P is segregated into distinct endosomal subdomains and that depletion of the disease-relevant lipid phosphatase Myotubularin1 (MTM1) leads to its accumulation and mis-segregation, impairing cargo recycling. Complementary imaging and reconstitution approaches show that MTM1 recruitment and activity are controlled by binding to the endosomal cargo adaptor SNX17. This interaction is mediated by sorting motifs in the C-Terminal tail of MTM1 and is in competition with the same sorting motifs in cargo that bind to SNX17. This competitive binding mechanistically links cargo sorting to PI(3)P depletion and because SNX17 is itself a PI(3)P effector, establishes negative feedback regulating local PI(3)P levels. Importantly, we demonstrate that this feedback couples endosomal cargo levels to PI(3)P depletion. We propose that cargo levels thereby modulate endosomal phosphoinositide identity through cargo sensitive feedback between SNX17 and MTM1.

cell biology↗

bioRxiv2026

Impact of heat and sex on embryonic brain growth in dragons with temperature induced sex-reversal (Pogona vitticeps, Lacertilia: Agamidae)

Climate warming can influence sex determination and embryonic growth in oviparous reptiles that rely on external temperatures during development. Warmer incubation temperatures can stimulate growth in ectotherms until oxygen supply can no longer keep pace with growth rate; at which point metabolically expensive organs like the brain suffer. We aimed to understand the impact of heat and sex on brain development in central bearded dragons, Pogona vitticeps (Agamidae), a uniquely thermosensitive species that exhibits sex-reversal at warm incubation temperatures. Three sexual phenotypes are possible in P. vitticeps: genetically driven ZW females and ZZ males, with the latter phenotype thermally overridden at incubation temperatures >32C to induce ZZ sex-reversed females. To visualise changes in brain anatomy, we used buffered Lugols iodine to perform contrast-enhanced micro computed tomography (microCT) and synchrotron propagation-based phase-contrast CT scanning. A total of 57 embryos were sampled across developmental stages and incubated at two temperature treatments: cool (28C, n = 26) and warm (36C, n = 21). Using high-resolution models of neuroanatomy, we found that the telencephalic region of the forebrain is significantly larger in individuals with ZZ genotypes (males and sex-reversed females) compared to concordant ZW females. Although incubation temperature significantly influenced growth rate and body size during development, overall brain size was not significantly different across temperature treatments. Our results indicate that the effects of genotypic sex on brain development are more important than thermal influences, and thus the brain may be somewhat buffered to the effects of warm incubation temperatures in this arid-adapted dragon.

neuroscience↗

bioRxiv2026

SMLMFlow: Improving Structural Resolution in Single Molecule Localization Microscopy with Flow Matching

While Single Molecule Localization Microscopy (SMLM) aims to generate precise coordinates of molecular targets in cells, the resulting point clouds are inherently blurred by additive noise sources across the experimental, imaging, and processing workflow. This blurring often limits SMLMs ability to accurately quantify complex assembled structures required to address biological issues, despite reported localization precision down to a couple of nanometers. Here, we present SMLMFlow, a machine learning framework for improving structural resolution in SMLM datasets that combines a graph neural network and a hierarchical transformer with flow matching. We show that SMLMFlow improves structural resolution and downstream quantification across different structures, including filaments and protein nano-clusters, and generalizes to new unseen photophysics models.

bioinformatics↗

bioRxiv2026

Coordinated Representational Drift Across the Mouse Cortex

Cortical neurons continuously change their spatial tuning properties over days and weeks, yet how this representational drift is coordinated across distributed cortical networks remains unknown. Using a robotic cranial exoskeleton for chronic widefield calcium imaging with cellular resolution, we tracked over 110,000 unique layer 2/3 neurons across retrosplenial, visual, somatosensory, and motor cortices in mice navigating a figure-8 maze spanning 47 days. Single-neuron spatial tuning properties followed a posterior-to-anterior gradient, with retros-plenial and visual cortices containing the highest proportions of spatially tuned neurons. This was dissociated from local functional coupling, which was strongest in somatosensory cortex. Population activity formed a low-dimensional manifold whose geometry mirrored the structure of the maze. Despite these regional differences, all four regions decorrelated with similar exponential timescales, and session-specific deviations from each regions decay trajectory were correlated across all pairwise region combinations, suggesting that drift was coordinated rather than independent across the dorsal cortex. This coordination persisted after controlling for shared behavioral fluctuations. Furthermore, drift was consistent with an orthogonal transformation of the population code that preserved the geometric relationships between spatial representations across sessions despite continuous drift in single-neuron tuning.

neuroscience↗

bioRxiv2025

Nanoscale spatial-omics via contrastive embedding of single-molecule localisation data

Omics approaches have revolutionised biology, and cells can now be routinely characterised on the genomic, transcriptomic and proteomic levels. However, there is an additional pillar; the (nanoscale) spatial organisation of molecules in the cell - information now accessible through super-resolution microscopy. We present a contrastive learning framework for nanoscale spatial-omics that embeds single-molecule localisation microscopy data into a latent space representing protein architecture directly to enabling comparative analysis. Using simulated and experimental data, we demonstrate its ability to enable new bioanalysis capabilities including assessing changes to cellular nanoscale architecture arising from pharmacological treatments, cell type, fluorophore selection or data-processing workflows. The approach supports downstream tasks such as clustering proteins by nanoscale organisation, mapping dose-response trajectories and identifying batch effects in replicate datasets, establishing contrastive learning as a scalable foundation for nanoscale spatial-omics and providing a platform for comparative phenotyping, quality control, and hypothesis generation.

bioinformatics↗

bioRxiv2025

Quantum Convolutional HLA Immunogenic Peptide Prediction (Q-CHIPP): Next-Generation Neoantigen Prediction with Quantum Neural Networks

The immune system is an intricately evolved series of cellular and protein-protein interactions, which defend the body against pathogens and abnormal cells such as cancer. A key player in the immunologic recognition of non-self is the immune synapse, where T cell receptors (TCRs) scan peptides presented on major histocompatibility complex (MHC) molecules to detect and eliminate cells displaying non-self antigens. While this interaction is vital for vaccine and immunotherapy success, the underlying rules of TCR recognition remain poorly understood. This is only further challenged as the application of predictive models is very limited due to small training datasets. While traditional machine learning models excel at predicting neoantigen binding to MHC, they often struggle to accurately predict immunogenicity. To address these challenges, we developed a quantum computing approach using Quantum Convolutional Neural Networks (QCNNs). Here we present Quantum Convolutional Human Leukocyte Antigen (HLA) Immunogenic Peptide Prediction (Q-CHIPP), the first application of quantum hardware based on training/predicting both MHC binding and immunogenicity in a combinatorial approach. Additionally, we present a large scale use of quantum hardware at scale with 46 qubits. This study underscores how quantum technology can be used for biological modeling and presents a scalable QCNN design with the potential to overcome current computational bottlenecks as quantum hardware advances.

immunology↗

bioRxiv2025

A genetic model for development, physiology and behavior of zebrafish larvae devoid of catecholamines

Dopamine and noradrenaline have conserved roles in control of physiology and behaviors of vertebrates. However, vertebrate genetic systems completely devoid of catecholamines are not available. We have generated a genetic zebrafish model completely devoid of catecholamines by combining mutations in all three genes involved in L-DOPA synthesis: the tyrosine hydroxylase genes th and th2, and tyrosinase tyr. We found catecholamine-deficient zebrafish larvae to be viable and to develop an anatomically normal nervous system including catecholaminergic neuron somata and projections, albeit with reduced cell numbers detected in some clusters. In contrast, selected physiological functions that depend on catecholamines are impaired, including hatching and heart rate regulation upon temperature challenges. Spontaneous locomotion and optomotor behaviors are also impaired. Despite the changes observed, it is surprising that larvae develop a largely normal behavioral repertoire. Our model will be useful to investigate how physiology and neural circuit function are regulated in catecholamine deficient larvae.

developmental biology↗

bioRxiv2024

Computer vision guided rapid and precise automated cranial microsurgeries in rodents

Neuroscientists employ various experimental procedures to interface with the brain to study and perturb the neural activity during behavior. A common procedure that allows such physical interfacing is cranial microsurgery, wherein small to large craniotomies are performed in the overlying skull for insertion of neural interfaces or implantation of optically clear windows for long-term cranial observation. Performing craniotomies is, however, a skilled task that requires significant time and practice and further needs to be carried out precisely to ensure that the procedure does not cause damage to the underlying brain and dura. Here, we present a computer vision-guided craniotomy robot (CV-Craniobot) that utilizes machine learning to accurately estimate the dorsal skull anatomy from optical coherence tomography (OCT) images. Instantaneous information of the skull morphology is used by a robotic mill to rapidly and precisely remove the skull from a desired craniotomy location. We show that the CV-Craniobot can perform small (2 - 4 mm diameter) craniotomies with near 100% success rates within 2 minutes and large craniotomies encompassing most of the dorsal cortex in less than 5 minutes. Thus, the CV-Craniobot enables rapid and precise craniotomies, significantly reducing surgery time as compared to human practitioners and eliminating the need for long training.

neuroscience↗

bioRxiv2024

Thermoneutral Housing has Limited Effects on Social Isolation-Induced Bone Loss in Male C57BL/6J Mice

Social isolation stress has numerous known negative health effects, including increased risk for cardiovascular disease, dementia, as well as overall mortality. The impacts of social isolation on skeletal health, however, have not been thoroughly investigated. We previously found that four weeks of social isolation through single housing led to a significant reduction in trabecular and cortical bone in male, but not female, mice. One possible explanation for these changes in male mice is thermal stress due to sub-thermoneutral housing. Single housing at room temperature ([~]20-25{degrees}C)--below the thermoneutral range of mice ([~]26-34{degrees}C)--may lead to cold stress, which has known negative effects on bone. Therefore, the aim of this study was to test the hypothesis that housing mice near thermoneutrality, thereby ameliorating cold-stress, will prevent social isolation-induced bone loss in male C57BL/6J mice. 16-week-old mice were randomized into social isolation (1 mouse/cage) or grouped housing (4 mice/cage) at either room temperature ([~]23{degrees}C) or in a warm temperature incubator ([~]28{degrees}C) for four weeks (N=8/group). As seen in our previous studies, isolated mice at room temperature had significantly reduced bone parameters, including femoral bone volume fraction (BV/TV), bone mineral density (BMD), and cortical thickness. Contrary to our hypothesis, these negative effects on bone were not ameliorated by thermoneutral housing. Social isolation increased glucocorticoid-related gene expression in bone and Ucp1 and Pdk4 expression in BAT across temperatures, while thermoneutral housing increased percent lipid area and decreased Ucp1 and Pdk4 expression in BAT across housing conditions. Overall, our data suggest social isolation-induced bone loss is not a result of thermal stress from single housing and provides a key insight into the mechanism mediating the effects of isolation on skeletal health. Lay SummarySocial isolation is a major public health concern and is known to increase the risk for many diseases, including heart disease and dementia. The impact of social isolation on bone health, however, has not been well-studied. We previously found that four weeks of social isolation reduces bone in male mice. Isolated mice may experience more cold stress than mice housed in groups, as we commonly keep laboratory mice at temperatures below their ideal range, which could lead to bone loss. The aim of our study was therefore to test if housing mice at warmer temperatures, within their ideal temperature range, prevents isolation-induced bone loss in male mice. We found that housing mice at warmer temperatures did not fully prevent isolation-induced bone loss. We also found social isolation increased the expression of genes related to glucocorticoid signaling in bone across temperatures, as well as genes associated with mitochondrial metabolism within fat tissue. Overall, our results show that social isolation-induced bone loss is likely not a result of cold stress from single housing and provide insight into the mechanisms by which isolation causes bone loss.

physiology↗

bioRxiv2024

Nano-org, a functional resource for single-molecule localisation microscopy data

We present a publicly accessible, curated, and functional resource, termed "nano-org", containing single-molecule localisation microscopy (SMLM) data representing the nanoscale distributions of proteins in cells. Nano-org is searchable by comparing the statistical similarity of the datasets it contains. This unique functionality allows the resource to be used to understand the relationships of nanoscale architectures between proteins, cell types or conditions, enabling a new field of spatial nano-omics.

biophysics↗

bioRxiv2024

Vortex light field microscopy: 3D spectral single-molecule imaging with a twist

We introduce vortex light field microscopy (VLFM), a novel method for snapshot 3D spectral single-molecule localization microscopy. Inspired by the azimuthal phase profile of optical vortices, we place an azimuthally oriented prism array immediately after the microlens array in a Fourier light field microscope (FLFM). This innovative arrangement causes the axial position and spectral peak for a point emitter to be encoded in the radial and azimuthal displacement of point-spread-function (PSF) respectively. This enables simultaneous detection of 3D position and emission peak of individual fluorophores with 25 nm spatial precision and 3 nm spectral precision over a 4 m depth of field (DOF). We illustrate the spectral scalability of our method by performing four-color 3D single particle tracking of freely diffusing fluorescent beads, and two-color 3D dSTORM imaging of microtubules and mitochondria in fixed COS-7 cells, without the need for spectrally distinct fluorophores.

biophysics↗

bioRxiv2024

Pan-cortical cellular imaging in freely behaving mice using a miniaturized micro-camera array microscope (mini-MCAM)

Understanding how circuits in the brain simultaneously coordinate their activity to mediate complex ethnologically relevant behaviors requires recording neural activities from distributed populations of neurons in freely behaving animals. Current miniaturized imaging microscopes are typically limited to imaging a relatively small field of view, precluding the measurement of neural activities across multiple brain regions. Here we present a miniaturized micro-camera array microscope (mini-MCAM) that consists of four fluorescence imaging micro-cameras, each capable of capturing neural activity across a 4.5 mm x 2.55 mm field of view (FOV). Cumulatively, the mini-MCAM images over 30 mm2 area of sparsely expressed GCaMP6s neurons distributed throughout the dorsal cortex, in regions including the primary and secondary motor, somatosensory, visual, retrosplenial, and association cortices across both hemispheres. We demonstrate cortex-wide cellular resolution in vivo Calcium (Ca2+) imaging using the mini-MCAM in both head-fixed and freely behaving mice.

neuroscience↗

bioRxiv2024

Epg5 links proteotoxic stress due to defective autophagic clearance and epileptogenesis in Drosophila and Vici Syndrome patients

Epilepsy is a common neurological condition that arises from dysfunctional neuronal circuit control due to either acquired or innate disorders. Autophagy is an essential neuronal housekeeping mechanism, which causes severe proteotoxic stress when impaired. Autophagy impairment has been associated to epileptogenesis through a variety of molecular mechanisms. Vici Syndrome (VS) is the paradigmatic congenital autophagy disorder in humans due to recessive variants in the ectopic P-granules autophagy tethering factor 5 (EPG5) gene that is crucial for autophagosome-lysosome fusion and ultimately for effective autophagic clearance. VS is characterized by a wide range of neurodevelopmental, neurodegenerative, and neurological features, including epilepsy. Here, we used Drosophila melanogaster to study the importance of epg5 in development, ageing, and seizures. Our data indicate that proteotoxic stress due to impaired autophagic clearance and seizure-like behaviors correlate and are commonly regulated, suggesting that seizures occur as a direct consequence of proteotoxic stress and age-dependent neurodegenerative progression in epg5 Drosophila mutants, in the absence of evident neurodevelopmental abnormalities. We provide complementary evidence from EPG5-mutated patients demonstrating an epilepsy phenotype consistent with Drosophila predictions and propose autophagy stimulating diets as a feasible approach to control EPG5-related pharmacoresistant seizures.

neuroscience↗

bioRxiv2023

High-density volumetric super-resolution microscopy

Volumetric super-resolution microscopy typically encodes the 3D position of single-molecule fluorescence into a 2D image by changing the shape of the point spread function (PSF) as a function of depth. However, the resulting large and complex PSF spatial footprints reduce temporal resolution by requiring lower labelling densities to avoid overlapping fluorescent signals. We quantitatively compare the density dependence of single-molecule light field microscopy (SMLFM) to other 3D PSFs (astigmatism, double helix and tetrapod) showing that SMFLM enables an order-of-magnitude speed improvement compared to the double helix PSF by resolving overlapping emitters through parallax. We then experimentally demonstrate the high accuracy (>99.2 {+/-} 0.1%, 0.1 locs m-2) and sensitivity (>86.6 {+/-} 0.9%, 0.1 locs m-2) of SMLFM at point detection through whole-cell (scan-free) imaging and tracking of single membrane proteins in live primary B cells. We also exemplify high density volumetric imaging (0.15 locs m-2) in dense cytosolic tubulin datasets.

biophysics↗

bioRxiv2023

POLCAM: Instant molecular orientation microscopy for the life sciences

Current methods for single-molecule orientation localization microscopy (SMOLM) require optical setups and algorithms that can be prohibitively slow and complex, limiting the widespread adoption for biological applications. We present POLCAM, a simplified SMOLM method based on polarized detection using a polarization camera, that can be easily implemented on any wide-field fluorescence microscope. To make polarization cameras compatible with single-molecule detection, we developed theory to minimize field of view errors, used simulations to optimize experimental design, and developed a fast algorithm based on Stokes parameter estimation which can operate over 1000 fold faster than the state of the art, enabling near instant determination of molecular anisotropy. To aid in the adoption of POLCAM, we developed open-source image analysis software, and a website detailing hardware installation and software use. To illustrate the potential of POLCAM in the life sciences, we applied our method to study alpha-synuclein fibrils, the actin cytoskeleton of mammalian cells, fibroblast-like cells and the plasma membrane of live human T cells.

biophysics↗

bioRxiv2022

Measuring the similarity of SMLM-derived point-clouds

Single-molecule localisation microscopy produces data in the form of point-clouds. Here, we present a tool for assessing the similarity of two such point-clouds, which, unlike measures such as co-localisation, is insensitive to differences that are not preserved between data sets. The presented method can determine whether two point-clouds were generated from the same conditions and can identify from which of two experimental conditions an unseen point-cloud was likely derived.

biophysics↗

bioRxiv2022

An ACAT inhibitor regulates SARS-CoV-2 replication and antiviral T cell activity

The severity of disease following infection with SARS-CoV-2 is determined by viral replication kinetics and host immunity, with early T cell responses and/or suppression of viraemia driving a favourable outcome. Recent studies have uncovered a role for cholesterol metabolism in the SARS-CoV-2 life cycle and in T cell function. Here we show that blockade of the enzyme Acyl-CoA:cholesterol acyltransferase (ACAT) with Avasimibe inhibits SARS-CoV-2 entry and fusion independent of transmembrane protease serine 2 expression in multiple cell types. We also demonstrate a role for ACAT in regulating SARS-CoV-2 RNA replication in primary bronchial epithelial cells. Furthermore, Avasimibe boosts the expansion of functional SARS-CoV-2-specific T cells from the blood of patients sampled in the acute phase of infection. Thus, re-purposing of available ACAT inhibitors provides a compelling therapeutic strategy for the treatment of COVID-19 to achieve both antiviral and immunomodulatory effects.

immunology↗

bioRxiv2022

Establishing a reproducible approach for the controllable deposition and maintenance of plants cells with 3D bioprinting

Capturing cell-to-cell and cell-to-environment signals in a defined 3 dimensional (3D) microenvironment is key to study cellular functions, including cellular reprogramming towards tissue regeneration. A major challenge in current culturing methods is that these methods cannot accurately capture this multicellular 3D microenvironment. In this study, we established the framework of 3D bioprinting with plant cells to study cell viability, cell division, and cell identity. We established long-term cell viability for bioprinted Arabidopsis root cells and soybean meristematic cells. To analyze the large image datasets generated during these long-term viability studies, we developed an open source high-throughput image analysis pipeline. Furthermore, we showed the cell cycle re-entry of the isolated Arabidopsis and soybean cells leading to the formation of microcalli. Finally, we showed that the identity of isolated cells of Arabidopsis roots expressing endodermal markers maintained longer periods of time. The framework established in this study paves the way for a general use of 3D bioprinting for studying cellular reprogramming and cell cycle re-entry towards tissue regeneration.

plant biology↗