Biology subjects

Shapiro, M.

Publications and source records attributed to Shapiro, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Junctional Nanodomains Organised by Extended Synaptotagmin-1 Underlie Inflammatory Signalling in Sensory Neurons

Endoplasmic reticulum-plasma membrane (ER-PM) junctions coordinate Ca2+ signalling and nociceptor excitability during inflammation, but the molecular scaffold governing assembly of signalling complexes remains unclear. Here, we identify Extended Synaptotagmin-1 (Esyt1) as a key, dynamic regulator of inflammatory pain signalling. In nociceptive DRG neurons, Esyt1 is co-expressed with ANO1 and IP3R1. Time-resolved proximity ligation assays and super-resolution microscopy showed that bradykinin rapidly increased ANO1-Esyt1 nanoscale proximity, while IP3R1-Esyt1 interactions were dynamically reorganised during ANO1-IP3R1 complex formation. Esyt1 knockdown reduced bradykinin-evoked ANO1 activity, impaired store-operated Ca2+ entry (SOCE), decreased STIM1-Orai1 complex formation, and disrupted ER Ca2+ store refilling. Simultaneous imaging of Ca2+ dynamics and ANO1 activity demonstrated functional coupling between SOCE and ANO1 that required Esyt1. Furthermore, in-vivo Esyt1-knockdown significantly reduced bradykinin-induced nocifensive behaviour. Together, these findings identify Esyt1 as a Ca2+-responsive scaffold that organises ER-PM signalling nanodomains and promotes inflammatory pain signalling.

neuroscience↗

bioRxiv2026

Drug-centric knowledge graph: representing therapeutic modality, pharmacology and multiscale biology

Biomedical knowledge graphs link targets to mechanisms, diseases and phenotypes, but target-centered representations omit much of what distinguishes therapeutic interventions. We introduce a drug-centric knowledge graph, whose identity model, schema and information-selection priorities are organized around the therapeutic intervention, and a graph built on this design. Each intervention has one identity, linked through relation types shared by all compounds, including target actions, indications, adverse effects, classifications, half-life and direct links to pathways, Gene Ontology concepts, cells and anatomy, and through modality-specific relation types describing small-molecule chemistry, antibody sequences and formats, protein-therapy sequences and antibody-drug conjugate components. Integrating 38 source resources, the graph contains 166,261 nodes of 27 types, 8,106,906 directed edges of 129 relation types and 18,429 compounds in eight therapeutic categories. Construction combines source-specific extraction, compound-identity resolution, language-model-assisted vocabulary and predicate mapping, confidence scoring and connectivity filtering; an expert-reviewed workflow adds investigational therapeutics without altering the base graph. The design offers a reusable template for representing interventions as structured, multimodal objects.

systems biology↗

bioRxiv2026

In vivo spatial coordination with synthetic paracrine signaling

The immune system uses paracrine signaling to spatially confine potent responses such as inflammation. A bio-orthogonal synthetic paracrine system could enable engineering of analogous multicellular circuits in which different cell types coordinate their functions in a spatially organized fashion. Here, using the plant hormone auxin as a bio-orthogonal chemical signal, we introduce programmable paracrine circuits that distribute sensing and effector functions to different cell types to spatially restrict responses in mouse xenografts. Cells engineered to express auxin biosynthetic genes generated auxin-dense regions with tunable length scales in vivo. This localized signaling ability enabled design of a multicellular sentinel-effector system, in which THP-1 sentinel cells conditionally produce auxin in regions expressing the tumor-specific antigen EGFRvIII, and Jurkat effector cells respond by locally modulating the activity of a chimeric antigen receptor (CAR). This two-cell type system was able to achieve localized activation of engineered effector cells in vivo. These results establish a foundation for engineering multicellular therapeutic systems that focus responses in specific tissue contexts or disease sites.

Synthetic Biology↗

bioRxiv2025

Mapping function in the tree shrew visual system using functional ultrasound imaging.

We adapted functional ultrasound imaging (fUSI) for awake, head-fixed northern tree shrews and used it to produce functional maps of visual processing at [~]100 {micro}m spatial resolution and [~]100 ms temporal resolution. Using classical retinotopic stimuli, full-field noise, motion localizers, and object versus scrambled object contrasts, we demonstrate robust, spatially specific hemodynamic responses across primary and extrastriate visual cortex, superior colliculus and subcortical structures. fUSI reliably reveals retinotopic reversals, laterality, and stimulus-selective modules, and yields high signal-to-noise %CBV changes that enable single-session mapping and targeting of electrophysiology or perturbations. These mesoscale maps provide a systems-level complement to recent high-density electrophysiological surveys of tree shrew visual cortex, which reported a compressed ventral-stream hierarchy and surprisingly early emergence of object coding in V2 (Lanfranchi et al., 2025). Together, our results establish fUSI as a powerful, scalable tool for functional mapping in the tree shrew, bridging large-scale circuit measurement and single-neuron electrophysiology and accelerating this species utility as a bridge between rodent genetics and primate vision.

neuroscience↗

bioRxiv2025

Harmonic Amplitude-Modulated Singular Value Decomposition for Ultrafast Ultrasound Imaging of Gas Vesicles

Ultrafast nonlinear ultrasound imaging of gas vesicles (GV) contrast agents promises high-sensitivity biomolecular visualization with applications such as targeted molecular imaging of tumor markers or real-time tracking of gene expression. However, separating GV-specific signal from tissue remains challenging and requires the implementation of complex transmit schemes. In this work we introduce harmonic amplitude-modulated singular value decomposition (HAM-SVD), which synergizes pulse inversion (PI) with amplitude-modulated singular value decomposition (AM-SVD) to isolate GV-specific second-harmonic signals. In HAM-SVD, single-cycle plane waves at 9.6 MHz and five tilted angles (at a pulse repetition frequency of 2500 Hz) are transmitted under four duty cycles with alternating polarity. Beamformed IQ data are reshaped along a "space x pressure" matrix and decomposed via SVD; tissue background is cancelled by discarding the first and lowest singular modes, yielding an image comprised solely of pressure-dependent second harmonic signals. HAM-SVD sequence enables wide-field, ultrafast imaging without complex transmit sequences. Validation via simulations, in vitro phantoms, and in vivo rat lower limb experiments demonstrates HAM-SVDs outperformance compared to PI and AM-SVD. HAM-SVD is shown to achieve a 19.16 {+/-} 1.63 dB signal-to-background ratio (SBR) in vivo, surpassing PI (14.19 {+/-} 1.41 dB) and AM-SVD (15.79 {+/-} 1.38 dB). HAM-SVD overcomes limitations of conventional nonlinear techniques (e.g., depth restrictions, tissue clutter) by combining PIs harmonic sensitivity with AM-SVDs adaptive clutter filtering of tissue signals. This approach enhances molecular imaging specificity for GVs and holds potential for ultrasound localization microscopy of slow-flowing agents.

bioengineering↗

bioRxiv2025

Honey bees (Apis mellifera) exhibit seasonal variation in their tolerance to viral infection

Seasonal variation strongly influences honey bee colony dynamics, leading to time-dependent changes in behavioral and physiological phenotypes. However, the extent to which seasonal fluctuations affect the susceptibility and tolerance of honey bees to viral infection remains largely unexplored. To address this, we conducted a longitudinal study in which adult honey bee workers were collected monthly from research colonies and experimentally infected with Israeli acute paralysis virus (IAPV) over the course of a year. Our results showed significant seasonal variation in the mortality and IAPV load of inoculated bees, with bees challenged during the pre-overwintering period (i.e., fall) exhibiting the highest susceptibility and lowest tolerance to IAPV infection compared to bees challenged in spring, summer, or winter. To investigate factors underlying these seasonal differences, we conducted nutrition-based studies that determined: 1) the variation in lipid content of colonies throughout the year and its potential link to our observed trends in IAPV tolerance, and 2) the impact of seasonally collected pollen on the survivorship of IAPV-challenged bees. Our findings support that seasonal changes in honey bee physiology and nutritional status play key roles in influencing honey bee viral tolerance. We conclude that honey bee colonies are particularly vulnerable to viral infection during the pre-overwintering period, most likely as a result of reduced tolerance to pathogen stress when transitioning from a summer to winter worker population. We further hypothesize that this period of increased vulnerability to viral infection, in correlation with other disease factors such as Varroa mite abundance and available forage, likely contributes to the relatively high overwintering losses experienced by beekeepers. Given the recent reports of severe colony losses attributed to honey bee viruses, understanding the relationship between seasonality and viral tolerance in honey bees is crucial for better informing management strategies and improving overwintering success. AUTHOR SUMMARYWe explored how seasonal changes affect the ability of honey bees to withstand viral infections. Previous research has shown that there are physical and behavioral differences between summer and winter bees, but its unclear how these seasonal differences affect a honey bees ability to withstand viral infection. To investigate this, we collected honey bee workers monthly and infected them with Israeli acute paralysis virus (IAPV) over the course of a year. Our results showed that honey bees were most vulnerable to IAPV in the fall (i.e., prior to overwintering), as they showed the highest mortality rates and lowest viral tolerance, based on their IAPV loads, during this time. By following up with nutrition-based studies, we found that seasonal changes in bee nutrition in part explained the seasonal differences we observed in honey bee virus tolerance. Overall, our findings suggest that bees are less tolerant to viral infection during the pre-overwintering period when colonies transition from a summer to a winter worker population. This vulnerable period may help explain the high rates of colony losses experienced by beekeepers nationwide and demonstrates the importance of developing seasonally-dependent disease management strategies.

pathology↗

bioRxiv2025

The positionally conserved long non-coding RNA DANCR is an essential regulator of zebrafish development and a human melanoma oncogene

Long non-coding RNAs (lncRNAs) can regulate gene expression. Some are essential for organismal development and physiology and can contribute to diseases including cancer. Whilst most lncRNAs exhibit little sequence similarity, conservation of lncRNA transcription relative to neighbouring protein-coding genes suggests potential functional significance. Most positionally equivalent lncRNAs are uncharacterized and it remains unclear whether they exert similar roles in distant species. Here, we identified syntenic melanoma-associated lncRNAs predicted to be components of the MITF gene regulatory network in human melanoma, with positionally equivalent transcripts in zebrafish. We prioritized Differentiation Antagonizing Non-Protein Coding RNA (DANCR), a cancer-associated lncRNA critical for maintaining somatic progenitor cells in human models, for functional investigation. Dancr is a multi-exonic, cytoplasmically-enriched lncRNA transcribed from syntenic regions in the human and zebrafish genomes. MITF and c-MYC, key melanoma transcription factors, regulate human DANCR expression and melanoma patients with high DANCR display significantly decreased survival. DANCR is a melanoma oncogene that controls cancer-associated gene expression networks and promotes human melanoma cell proliferation and migration. Zebrafish dancr is dynamically expressed across multiple different cell types in the developing embryo, regulates genes involved in cell death, and is essential for embryonic development. Our work suggests that cancer-critical lncRNAs such as DANCR, expressed from similar regions in vertebrate genomes, may regulate related genes and processes involved in both embryonic development and tumorigenesis across species.

cancer biology↗

bioRxiv2024

Genomics of experimental adaptive radiation in the cryptic coloration of feather lice

1A major challenge faced by living organisms is adaptation to novel environments. This process is poorly understood because monitoring genetic changes in natural populations is difficult. One way to simplify the task is to focus on organisms that can be studied in captivity under conditions that remain largely natural. Feather lice (Insecta, Phthiraptera, Ischnocera) are host-specific parasites of birds that live, feed, and breed solely on feathers. Birds defend themselves against lice, which damage feathers, by killing them with their beaks during bouts of preening. In response, feather lice have evolved background-matching cryptic coloration to help them avoid preening. We experimentally manipulated the color backgrounds of host-specific pigeon lice (Columbicola columbae) by confining them to different colored breeds of rock pigeon (Columba livia) over a period of four years (ca. 60 louse generations). Over the course of the experiment, we sampled lice from pigeons every six months for genomic resequencing, and then calculated allele frequency differences and trajectories to identify putative genomic sites under selection. We documented many loci that changed in response to selection for color. Most loci putatively under selection were unshared among replicate populations of lice, indicating that independent adaptation of distinct lineages to the same novel environment resulted in similar phenotypes driven by different genotypes.

evolutionary biology↗

bioRxiv2024

Novel immunotherapy for multiple solid cancers using an Anti-HVEM blocking monoclonal antibody

INTRODUCTIONImmune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, yet their efficacy remains limited. Therefore, there is a clear need for new anti-tumor agents. HVEM (Herpes Virus Entry Mediator) plays a regulatory role in immunity, making it a promising cancer therapeutic target. EXPERIMENTAL DESIGNWe have developed Anti-4CB1, a fully human HVEM-BTLA and HVEM-CD160 blocking mAb and tested its anti-tumor activity in various in-vitro, ex-vivo and in-vivo models, alone or in combination with Anti-PD1. Finally, we analyzed HVEM expression in serum samples and melanoma tumor tissues and its correlation with HVEM and PD1 blockade treatment response. RESULTSIn-vitro assays demonstrated enhanced melanoma cell killing by autologous TILs in the presence of Anti-4CB1. In addition, Anti-4CB1 significantly increased cytotoxicity by up to 233% in a variety of ex-vivo cancer tissue samples of different indications. Notably, Anti-4CB1 demonstrated effectiveness in samples where Anti-PD1 was ineffective. In addition, significant anti-tumor activity at 10 mg/kg in combination with Anti-PD1 (TGI 95% p=0.0001) or at 25 mg/kg as monotherapy (TGI 50% p=0.0096) was demonstrated in a colon carcinoma transgenic mice model. Moreover, significant anti-tumor activity was observed in a mouse ImmunoGraft model (TGI 53% p=0.0102 as monotherapy). Finally, we demonstrated that HVEM expression correlated with response to Anti-HVEM and Anti-PD1 treatments. DISCUSSIONWe describe the development of Anti-4CB1, a fully human anti-HVEM mAb, blocking HVEM-BTLA and HVEM-CD160 human interactions and enhancing lymphocytes cytotoxicity against various cancer cells ex-vivo. In-vivo, Anti-4CB1 showed promising anti-tumor effects, particularly in combination with Anti-PD1, suggesting its therapeutic potential. Finally, HVEM expression may serve as a predictive marker for Anti-HVEM and Anti-PD1 treatments response, offering potential diagnostic utility in patient selection for these immunotherapies. These results support Anti-4CB1 potential as an anti-cancer therapeutic agent. Translational RelevanceThe discovery of immune checkpoint inhibitors (ICIs), marks a significant breakthrough in cancer therapy. However, despite the remarkable success of current ICIs targeting CTLA4 and PD1/PD-L1 pathways, a significant proportion of patients fail to respond or develop resistance. Therefore, the search for novel ICIs is crucial for advancing cancer immunotherapy. Anti-HVEM emerged as a promising candidate, as we demonstrate in ex-vivo and in-vivo models, its ability to block the HVEM-BTLA interaction, resulting in enhanced antitumor immune responses in solid tumors, alone or in combination with existing ICIs, to improve treatment outcomes. Moreover, the correlation between HVEM expression and treatment responses highlight its potential as an attractive target for biomarker-driven therapies. Investigating HVEM as an ICI offers a promising path to expand therapeutic options, personalize treatment approaches, address the evolving challenges in cancer immunotherapy and improve patient outcomes.

cancer biology↗

bioRxiv2024

Adult honey bee queens consume pollen and nectar

Despite the queens crucial reproductive role in honey bee colonies, queen diet and feeding behavior remain remarkably enigmatic, with most studies assuming they are solely fed nutritious glandular secretions (i.e., royal jelly) by workers. This colors our understanding of basic honey bee biology and how governmental agencies assess pesticide risk. We hypothesized that adult queens also consume honey and pollen. Through experiments with queenright laboratory microcolonies fed with marked diets, we demonstrate that queens are fed pollen and nectar by workers and can also feed directly. We then measured pollen content in mature, unmanipulated queens sacrificed from 43 conventional field colonies from two distinct geographical regions. Similar to workers, we found pollen in almost all queens guts, though at expectedly lower quantities than in young workers. These findings suggest queens have a more complex, dynamic diet than previously thought, raising new questions about how dietary habits and feeding behaviors influence pesticide risk and other aspects of queen biology.

ecology↗

bioRxiv2024

Nonlinear Singular Value Decomposition Beamforming for Ultrasound Imaging of Gas Vesicles

Ultrasound imaging holds significant promise for the observation of molecular and cellular phenomena through the utilization of acoustic contrast agents and acoustic reporter genes. Optimizing imaging methodologies for enhanced detection represents an imperative advancement in this field. Most advanced techniques relying on amplitude modulation scheme such as cross amplitude modulation (xAM) and ultrafast amplitude modulation (uAM) combined with Hadamard encoded multiplane wave transmissions have shown efficacy in capturing acoustic signals of gas vesicles (GVs). Nonetheless, uAM sequence requires odd- or even-element transmissions leading to imprecise amplitude modulation emitting scheme, and the complex multiplane wave transmission scheme inherently yields overlong pulse durations. xAM sequence is limited in terms of field of view and imaging depth. To overcome these limitations, we introduce an innovative ultrafast imaging sequence called nonlinear singular value decomposition (SVD) beamforming. Our method demonstrated a contrast imaging sensitivity comparable to the current gold-standard xAM and uAM, while requiring 4.8 times less pulse transmissions. With similar number of transmit pulses, nonlinear SVD beamforming outperforms xAM and uAM in terms of an improvement in signal-to-background ratio of + 4.78 {+/-} 0.35 dB and + 8.29 {+/-} 3.52 dB respectively. Additionally, our method provides a higher flexibility in terms of the selection of acoustic pressure amplitude compared to the other methods. Furthermore, it shows a significant potential for application in the realm of ultrasound localization microscopy (ULM), where it stands poised to facilitate the more precise extraction of nonlinear signatures originating from contrast agents.

biophysics↗

bioRxiv2024

Inhibition of CD226 Co-Stimulation Suppresses Diabetes Development in the NOD Mouse by Augmenting Tregs and Diminishing Effector T Cell Function

Aims/hypothesisImmunotherapeutics targeting T cells are crucial for inhibiting autoimmune disease progression proximal to disease onset in type 1 diabetes. A growing number of T cell-directed therapeutics have demonstrated partial therapeutic efficacy, with anti-CD3 (-CD3) representing the only regulatory agency-approved drug capable of slowing disease progression through a mechanism involving the induction of partial T cell exhaustion. There is an outstanding need to augment the durability and effectiveness of T cell targeting by directly restraining proinflammatory T helper type 1 (Th1) and type 1 cytotoxic CD8+ T cell (Tc1) subsets, while simultaneously augmenting regulatory T cell (Treg) activity. Here, we present a novel strategy for reducing diabetes incidence in the NOD mouse model using a blocking monoclonal antibody targeting the type 1 diabetes-risk associated T cell co-stimulatory receptor, CD226. MethodsFemale NOD mice were treated with anti-CD226 between 7-8 weeks of age and then monitored for diabetes incidence and therapeutic mechanism of action. ResultsCompared to isotype-treated controls, anti-CD226 treated NOD mice showed reduced insulitis severity at 12 weeks and decreased disease incidence at 30 weeks. Flow cytometric analysis performed five weeks post-treatment demonstrated reduced proliferation of CD4+ and CD8+ effector memory T cells in spleens of anti-CD226 treated mice. Phenotyping of pancreatic Tregs revealed increased CD25 expression and STAT5 phosphorylation following anti-CD226, with splenic Tregs displaying augmented suppression of CD4+ T cell responders in vitro. Anti-CD226 treated mice exhibited reduced frequencies of islet-specific glucose-6-phosphatase catalytic subunit related protein (IGRP)-reactive CD8+ T cells in the pancreas, using both ex vivo tetramer staining and single-cell T cell receptor sequencing (scTCR-seq) approaches. 51Cr-release assays demonstrated reduced cell-mediated lysis of beta-cells by anti-CD226-treated autoreactive cytotoxic T lymphocytes. Conclusions/interpretationCD226 blockade reduces T cell cytotoxicity and improves Treg function, representing a targeted and rational approach for restoring immune regulation in type 1 diabetes. Research in ContextO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIThe co-stimulatory receptor CD226 is upregulated upon activation and is highly expressed on NK cell subsets, myeloid cells, and effector T cells. C_LIO_LIA single nucleotide polymorphism in CD226 (rs763361; C>T) results in a Gly307Ser missense mutation linked to genetic susceptibility for type 1 diabetes. C_LIO_LIGlobal knockout of Cd226 and conditional Cd226 knockout in FoxP3+ Tregs reduced insulitis severity and diabetes incidence in NOD mice, indicating a crucial role for CD226 in disease pathogenesis. C_LI What is the key question?O_LICan CD226 blockade reduce T cell cytotoxicity and improve Treg function to diminish diabetes incidence in NOD mice? C_LI What are the new findings?O_LIAnti-CD226 treatment reduced insulitis, decreased disease incidence, and inhibited splenic CD4+ and CD8+ effector memory T cell proliferation. C_LIO_LIPancreatic Tregs from anti-CD226 treated mice exhibited increased CD25 expression; splenic Tregs displayed augmented STAT5 phosphorylation and suppressive capacity in vitro. C_LIO_LIAnti-CD226 treatment reduced IGRP-specific pancreatic CD8+ T cell frequencies, and reduced autoreactive CD8+ T cell-mediated lysis of beta-cells in vitro. C_LI How might this impact on clinical practice in the foreseeable future?O_LICD226 blockade could reduce autoreactive T cell cytotoxicity, enhance Treg function, and slow disease progression in high-risk or recent-onset type 1 diabetes cases. C_LI

immunology↗

bioRxiv2024

TrajectoryGeometry suggests cell fate decisions involve branches rather than bifurcations

AO_SCPLOWBSTRACTC_SCPLOWDifferentiation of multipotential progenitor cells is a key process in the development of any multi-cellular organism and often continues throughout its life. It is often assumed that a bi-potential progenitor develops along a (relatively) straight trajectory until it reaches a decision point where the trajectory bifurcates. At this point one of two directions is chosen, each direction representing the unfolding of a new transcriptomic programme. However, we have lacked quantitative means for testing this model. Accordingly, we have developed the R package TrajectoryGeometry. Applying this to published data we find several examples where, rather than bifurcate, developmental pathways branch. That is, the bipotential progenitor develops along a relatively straight trajectory leading to one of its potential fates. A second relatively straight trajectory branches off from this towards the other potential fate. In this sense only cells that branch off to follow the second trajectory make a "decision". Our methods give precise descriptions of the genes and cellular pathways involved in these trajectories. We speculate that branching may be the more common behaviour and may have advantages from a control-theoretic viewpoint.

developmental biology↗

bioRxiv2023

An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon

Variation in pigment patterns within and among vertebrate species reflects underlying changes in cell migration and function that can impact health, reproductive success, and survival. The domestic pigeon (Columba livia) is an exceptional model for understanding the genetic changes that give rise to diverse pigment patterns, as selective breeding has given rise to hundreds of breeds with extensive variation in plumage color and pattern. Here, we map the genetic architecture of a suite of pigmentation phenotypes known as piebalding. Piebalding is characterized by patches of pigmented and non-pigmented feathers, and these plumage patterns are often breed-specific and stable across generations. Using a combination of quantitative trait locus mapping in F2 laboratory crosses and genome-wide association analysis, we identify a locus associated with piebalding across many pigeon breeds. This shared locus harbors a candidate gene, EDNRB2, that is a known regulator of pigment cell migration, proliferation, and survival. We discover multiple distinct haplotypes at the EDNRB2 locus in piebald pigeons, which include a mix of protein-coding, noncoding, and structural variants that are associated with depigmentation in specific plumage regions. These results identify a role for EDNRB2 in pigment patterning in the domestic pigeon, and highlight how repeated selection at a single locus can generate a diverse array of stable and heritable pigment patterns. AUTHOR SUMMARYBoth wild and domestic birds show striking variation in pigment patterning, and these pigment patterns can play critical roles in mate choice, communication, and camouflage. Despite the importance of pigment patterning for survival and reproductive success, the mechanisms that control pigment patterning remain incompletely understood. In domestic pigeons, artificial selection has given rise to a wide array of pigmentation patterns within a single species, including a suite of phenotypes called "piebalding" that is characterized by regional loss of feather pigment. Here, we took advantage of the wide array of distinct piebalding phenotypes in domestic pigeons to map the genetic basis of region-specific loss of plumage pigment. Rather than focusing on a single piebalding pattern, we sought to broadly understand genetic control of regional pigment loss by examining several breeds with different piebalding patterns. We compared the genomes of piebald and non-piebald pigeons using both genetic crosses and genome-wide association studies, and identified several genetic changes affecting the endothelin receptor gene EDNRB2. Our findings highlight how independent mutations at a single locus can drive diversification of plumage pigment patterning within a species.

genetics↗

bioRxiv2023

Effects of focused ultrasound in a "clean" mouse model of ultrasonic neuromodulation

Recent studies on ultrasonic neuromodulation (UNM) in rodents have shown that focused ultrasound (FUS) can activate peripheral auditory pathways, leading to off-target and brain-wide excitation, which obscures the direct activation of the target area by FUS. To address this issue, we developed a new mouse model, the double transgenic Pou4f3+/DTR x Thy1-GCaMP6s, which allows for inducible deafening using diphtheria toxin and minimizes off-target effects of UNM while allowing effects on neural activity to be visualized with fluorescent calcium imaging. Using this model, we found that the auditory confounds caused by FUS can be significantly reduced or eliminated within a certain pressure range. At higher pressures, FUS can result in focal fluorescence dips at the target, elicit non-auditory sensory confounds, and damage tissue, leading to spreading depolarization. Under the acoustic conditions we tested, we did not observe direct calcium responses in the mouse cortex. Our findings provide a cleaner animal model for UNM and sonogenetics research, establish a parameter range within which off-target effects are confidently avoided, and reveal the non-auditory side effects of higher-pressure stimulation.

neuroscience↗

bioRxiv2023

Drosophila AHR limits tumor growth and stem cell proliferation in the intestine

The aryl hydrocarbon receptor (AHR) plays important roles in intestinal homeostasis, limiting tumour growth and promoting differentiation in the intestinal epithelium. Spineless, the Drosophila homolog of AHR, has only been studied in the context of development but not in the adult intestine. Here, we show that spineless is upregulated in the adult intestinal epithelium after infection with Pseudomonas entomophila (P.e.). Spineless knockdown increased stem cell proliferation following infection-induced injury. Spineless overexpression limited intestinal stem cell proliferation and reduced survival after infection. In two tumour models, using either Notch RNAi or constitutively active Yorkie, Spineless suppressed tumour growth and doubled the lifespan of tumour-bearing flies. At the transcriptional level it reversed the gene expression changes induced in Yorkie tumours, counteracting cell proliferation and altered metabolism. These findings demonstrate a new role for Spineless in the adult Drosophila midgut and highlight the evolutionarily conserved functions of AHR/Spineless in the control of proliferation and differentiation of the intestinal epithelium.

cancer biology↗

bioRxiv2022

Hippocampal and Medial Prefrontal Cortical Maps Represent Episodes and Rules in a Common Task Space

Memory helps us adapt to changing circumstances but needs guidance to retrieve relevant episodes. Episodic memory requires the hippocampus, the prefrontal cortex (PFC) guides memory retrieval, but how their representations interact is unclear. Using state-space analysis of neuronal spiking, we found CA1 and PFC activity within and between rats formed similar, low-dimensional, region-specific "shapes" representing different tasks tested in the same maze. Task shapes were organized by behaviorally salient variables including time and maze start and goal locations. PFC predicted CA1 representations when both regions were needed to solve a spatial memory task, but not in a cue approach task that required neither region. Task demands imposed common dimensions on CA1 and PFC maps whose topologies distinguished episodic and rule-related computations.

animal behavior and cognition↗

bioRxiv2022

A branching model of cell fate decisions in the enteric nervous system

How neurogenesis and gliogenesis are coordinated during development and why mature glial cells often share properties with neuroectodermal progenitors remains unclear. Here, we have used single cell RNA sequencing to map the regulatory landscape of neuronal and glial differentiation in the mammalian enteric nervous system (ENS). Our analysis indicates that neurogenic trajectories branch directly from a linear gliogenic axis defined by autonomic neural crest cells adopting sequential states as they progressively lose their strong neurogenic bias and acquire properties of adult enteric glia. We identify gene modules associated with transcriptional programs driving enteric neurogenesis and cell state transitions along the gliogenic axis. By comparing the chromatin accessibility profile of autonomic neural crest and adult enteric glia we provide evidence that the latter maintain an epigenetic memory of their neurogenic past. Finally, we demonstrate that adult enteric glia maintain neurogenic potential and are capable of generating enteric neurons in certain contexts by activating transcriptional programs employed by early ENS progenitors. Our studies uncover a novel configuration of enteric neurogenesis and gliogenesis that enables the coordinate development of ENS lineages and provides a mechanistic explanation for the ability of enteric glia to be functionally integrated into the adult intestine and simultaneously maintain attributes of early ENS progenitors.

neuroscience↗