Biology subjects

Ryan, L.

Publications and source records attributed to Ryan, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Structure-Function Analysis of an Infantile Rhabdomyosarcoma Fusion-Oncogene Reveals Domain Requirements for Tumorigenesis

Rhabdomyosarcoma is a pediatric soft-tissue sarcoma that reflects impaired skeletal muscle differentiation. Spindle cell/sclerosing rhabdomyosarcoma is a histological subtype found in children and adults. In children under two, spindle cell rhabdomyosarcoma is genetically driven by fusion-oncogenes of transcription factors or co-activators important for skeletal muscle lineage commitment and development. The most common fusion-oncogene in this group is VGLL2::NCOA2, a fusion between vestigial-like family member 2 (VGLL2) and nuclear receptor coactivator 2 (NCOA2). Children with fusion-driven rhabdomyosarcoma are treated with general chemotherapy, surgery, and radiation, which are not specific to the molecular underpinnings, and increase risk of secondary malignancies and premature death. Previously, we showed that VGLL2::NCOA2 is transforming in mouse myoblasts and transgenic zebrafish tumor models. Here, we build on this work by detailing the structure-function relationship of the retained VGLL2::NCOA2 protein domains to define domain requirements and their molecular interactions for tumorigenesis. We created deletion mutants of the VGLL2 vestigial/Tondu (TDU) domain and the NCOA2 activating domains 1 and 2 (AD1 and AD2), and a double mutant lacking the TDU+AD1 domains and assessed their function in a mouse myoblast model. We find that the TDU and AD1 domains support nuclear fusion-oncogene localization, transformation in vitro, and tumorigenesis in a mouse allograft model. Furthermore, transcriptomic analysis demonstrates that the TDU or AD1 mutant VGLL2::NCOA2 drives an upregulation of myogenesis gene sets and supports terminal differentiation. Overall, our results indicate that VGLL2::NCOA2 requires the TDU and AD1 domains for optimal transformation, and that targeting these domains, or their interacting protein partners, represents a therapeutic opportunity.

cancer biology↗

bioRxiv2026

A comparative genomics framework for identifying historical population bottlenecks using olfactory receptor gene evolution

Population bottlenecks reduce genetic diversity, increase the fixation of deleterious mutations and elevate extinction risk. Identifying lineages experiencing bottlenecks is a key goal of conservation genetics, facilitating the allocation of limited resources to at-risk species. Although whole-genome sequencing has improved bottleneck detection by reconstructing demographic history, these methods often require extensive population sampling, limiting their application. Previous studies of species showing population bottlenecks have reported an increased number of pseudogenes in the olfactory receptor (OR) gene family, however whether such evolutionary dynamics can be used as comparative biomarkers of genomic decline remains unknown. By quantifying the number of lineage-specific duplication and pseudogenization events, we introduce the duplication-to-loss ratio (DLR), a comparative metric exploring the rate at which chemosensory gene loss is offset by the generation of novel receptors. We characterize the chemosensory repertoires of 21 felid species, including species with known historical bottlenecks, to establish the utility of this DLR metric. Subsequently, we evaluate its usage across additional mammalian families, specifically Ursidae and Pinnipedia, to determine its utility beyond Felidae. Our DLR metric recovers several felid species with a history of genomic decline, including cheetah (Acinonyx jubatus) and black-footed cat (Felis nigripes), as well as the giant panda (Ailuropoda melanoleuca), polar bear (Ursus maritimus), Hawaiian monk seal (Neomonachus schauinslandi) and northern elephant seal (Mirounga angustirostris). Our results demonstrate the utility of the OR gene repertoire as a scalable, robust biomarker for identifying comparative population decline, prioritising species for conservation genomic investigation using only the reference genome.

genomics↗

bioRxiv2026

Expansion of Olfactory Receptor Family 14 Across Fossorial and Insectivorous Mammals

Mammals have incredibly diverse olfactory repertoires, reflected in significant copy number variation of olfactory receptor genes across species. As mammals occupy a wide range of habitats and foraging environments, it is expected that such variation is shaped by ecological niche. Indeed, several studies have shown that specific olfactory receptor gene families are associated with habitat and dietary specialization. Despite this, there is currently little known about the ecological factors driving variation of olfactory receptor family 14 (OR14) across mammals. Here, we address this gap by mining mammalian genomes to identify and classify OR14 genes across hundreds of species. By mapping OR14 variation onto dietary and habitat variables, in the context of the mammalian phylogenetic tree, we identify key factors associated with OR14 evolution across mammals. Specifically, we find that OR14 has undergone repeated expansion across independent lineages of fossorial and insectivorous mammals, suggesting that expansion of this gene family may be adaptive and driven by convergent ecological pressures. By performing principal component analysis and k-means clustering based on OR14 subfamily composition, we find that species cluster irrespective of phylogeny. Furthermore, we show that many independent myrmecophagous lineages form a single cluster, providing evidence of convergence at the sequence level, potentially driven by selection for ant/termite rich diets. Together, our results indicate that OR14 plays an important functional role in fossorial and insectivorous mammals, providing a foundation for future studies aimed at deorphaning these receptors.

evolutionary biology↗

bioRxiv2026

GENE-FAM: An automated pipeline for mining gene families and its application to MADS-box genes in Cannabis sativa

Understanding how gene families evolve can offer great insight into adaptation at the phenotypic and ecological levels. This is particularly true in plants, where transcription factor gene families are often targeted for breeding programs to improve the agronomic traits of economically important crops. While recent advances in next generation sequencing have accelerated the wealth of genomics data, there remains a lack of accessible and reproducible genome mining pipelines tailored for gene family characterisation. Here, we address this gap by developing GENE-FAM, an automated, scalable and open-source pipeline designed to mine and predict gene families based on conserved domains and motifs. To illustrate its application, we apply GENE-FAM to annotate MADS-box transcription factor genes across multiple Cannabis sativa genomes. A comprehensive set of MADS-box genes was identified across three C. sativa cultivars, including both previously annotated and newly predicted genes. Through phylogenetic analyses, we confirm that all type II MADS-box gene subfamilies represented in flowering plants are present in C. sativa. Comparing our annotations with those of Arabidopsis thaliana and Solanum lycopersicum revealed that while most MADS type II families are highly conserved, SEPALLATA-like genes have undergone diversification in C. sativa. Together, these results demonstrate the application of GENE-FAM for genome-wide identification and characterisation of gene families in non-model species, revealing novel insights into MADS-box gene family evolution in C. sativa.

genomics↗

bioRxiv2026

SCANBIT facilitates identification of tumor cell populations in scRNAseq data using pseudobulked SNV calls

MotivationSingle cell RNAseq (scRNAseq) is an ideal tool to characterize the heterogeneity within the tumor microenvironment, however, accurate identification of tumor cells can be a challenge. Reference-based methods can be inaccurate, if reference datasets are even available. Current purpose-built methods can be inaccurate, particularly with highly heterogeneous tumor types. Improved methods are needed. We explored the use of genetic variants to distinguish tumor from normal cells within scRNAseq data. ResultsWe characterized the limitations inherent to calling variants from scRNAseq data, quantifying how data sparsity precludes genetic distance calculation between single cells. As a novel workaround, we pooled data from transcriptionally similar cell clusters to call high quality variants and then calculated pairwise differences between cell populations and performed hierarchical clustering. We quantified confidence in genetic divergence between tumor and normal cell populations using bootstrapping. We performed extensive validation to assess accurate identification of tumor cells using ground-truth datasets. Application of our method to human scRNAseq samples highlighted the utility of our approach and revealed how mutational burden influences successful tumor cell identification. Improved cell type assignment in scRNAseq data will facilitate analysis of tumor samples and, in turn, accelerate our understanding of the mechanisms underlying tumor progression and reveal potential biological vulnerabilities that can be exploited to develop improved treatment options. Availability and implementationOur method is publicly available as an R package: SCANBIT (Single Cell Altered Nucleotide Based Inference of Tumor) https://github.com/kidcancerlab/scanBit.

bioinformatics↗

bioRxiv2025

SLAMF1-peptide mediated epigenetic priming reprograms innate immune responses in sepsis

Sepsis is characterized by profound immune dysregulation, including impaired innate immune responses and epigenetic reprogramming of monocytes. However, strategies to therapeutically restore immune function remain limited. Here, we identify a cell-penetrating peptide, P7-Pen, as a modulator of monocyte epigenetic state and inflammatory responsiveness. Using primary human monocytes and peripheral blood mononuclear cells (PBMCs) from healthy donors and sepsis patients, we demonstrate that P7-Pen enhances cytokine production in response to Toll-like receptor stimulation while having minimal effects under basal conditions. P7-Pen treatment increased global histone acetylation, particularly H3 acetylation, and prevented the development of endotoxin tolerance. Transcriptomic and functional analyses revealed restoration of inflammatory gene expression, including TNF, IL6, and IFNB1, in otherwise hyporesponsive cells. Mechanistically, we identified the lysine deacetylase ABHD14B as a direct binding partner of P7-Pen. Silencing of ABHD14B recapitulated the effects of P7-Pen, leading to enhanced histone acetylation and cytokine production. Importantly, P7-Pen selectively potentiated responses to TLR ligands without inducing basal hyperinflammation. Collectively, our findings identify ABHD14B-dependent epigenetic regulation as a key checkpoint in innate immune tolerance and establish P7-Pen as a novel tool to restore immune responsiveness in sepsis.

immunology↗

bioRxiv2025

NINJ1 is activated by Mycobacterium tuberculosis ESX-1 secreted effector EsxA and mediates necrosis of infected human macrophages

Lytic cell death contributes to tissue damage and dissemination during Mycobacterium tuberculosis (Mtb) infection, yet the mechanisms governing plasma membrane rupture (PMR) remain incompletely defined. Here, we identify Ninjurin-1 (NINJ1), a mediator of PMR, as a central effector of macrophage lysis during Mtb infection. Mtb infection induced NINJ1 oligomerization, and genetic deletion or pharmacological inhibition of NINJ1 markedly reduced lactate dehydrogenase (LDH) release. Cytokine secretion was largely preserved in NINJ1-deficient macrophages, with the exception of CXCL10. Unexpectedly, inhibition of pyroptosis, apoptosis, necroptosis, and ferroptosis - individually or in combination - did not prevent NINJ1 activation or PMR, indicating that Mtb-induced membrane rupture proceeds independently of canonical regulated cell death pathways. However, NINJ1 oligomerization and PMR required the Mtb ESX-1 secretion system, identifying a bacterial virulence determinant as a critical upstream trigger. Although osmoprotective PEG partially reduced LDH release, neither calcium signaling nor cell swelling accounted for NINJ1-dependent PMR in Mtb-infected macrophages. Together, these findings establish NINJ1 as a key executioner of Mtb-induced lytic cell death and reveal an ESX-1-dependent pathway of PMR that is uncoupled from canonical host cell death programs. TeaserNINJ1 mediates plasma membrane rupture of macrophages infected with Mycobacterium tuberculosis

microbiology↗

bioRxiv2025

NR0B1 alters the 9-cis-retinoic acid response in Ewing Sarcoma cells

Pediatric cancers are often characterized by relatively low DNA mutation rates and are frequently driven instead by alterations in gene expression programs. In Ewing Sarcoma (EwS), these changes result from the activity of an oncogenic fusion transcription factor, EWS::FLI1, which alters the enhancer landscape and rewires transcriptional programs to promote oncogenic transformation. Among the targets directly activated by EWS::FLI1, NR0B1 has emerged as a potentially targetable transcription co-regulator and as a manifold for widespread alterations in downstream gene expression programs mediated by members of the ligand-inducible nuclear receptor superfamily of transcription factors. We have dissected the gene regulatory activity of NR0B1 in EwS models, showing its role in altering the basal gene expression programs of nuclear receptors COUP-TFII, EAR2, RXRa, and TR4. Additionally, we show that NR0B1 impacts the EwS response to retinoids, particularly 9-cis-retinoic acid signaling in part through RXRa. Our findings suggest NR0B1 silencing or inhibition offer a means of achieving a more potent response to retinoids, which may activate differentiation programs, decrease EwS gene expression signatures, and limit in vitro transformation phenotypes. Taken together, our study presents evidence of NR0B1 acting canonically as a nuclear receptor co-regulator in EwS, revealing a potential pathway to treatment of this aggressive cancer by combining NR0B1 inhibition with therapeutic nuclear receptor ligands.

cancer biology↗

bioRxiv2025

Lactate Blocks Tertiary Lymphoid Structure Formation by Inhibiting B Cell Chemotaxis

Tertiary lymphoid structures (TLS) and B cell infiltration are strong predictors of immunotherapy success across cancers, including triple-negative breast cancer (TNBC). However, immune-cold TNBCs often lack both features. Here, we identify a tumor-intrinsic mechanism that actively suppresses B cell recruitment. Despite evidence of B cell responses in cancer-associated lymph nodes (cLNs), B cells fail to infiltrate TNBC tumors or form TLS. This exclusion is not simply due to chemokine deficiency as exogenous chemokine addition fails to restore B cell migration. Using fractionation and metabolic profiling, we identify lactate as a dominant tumor-secreted metabolite that directly impairs B cell chemotaxis by disrupting mitochondrial metabolism. In vivo, combining lactate inhibition with engineered chemokine secretion promotes cLN-derived B cell infiltration and enables TLS formation, particularly when coupled with CD40 stimulation. Transcriptomics analyses across several human cancer datasets strengthen the association between high glycolytic activity with poor B-cell infiltration in chemokine-rich tumors. Together, our findings reveal lactate as a key metabolic barrier to B cell trafficking and TLS induction, suggesting that metabolic reprogramming may provide an avenue to convert "immune-cold" tumors into TLS-rich, immunologically responsive microenvironments.

cancer biology↗

bioRxiv2025

SMART: A Spatio-Molecular Atlas of Response Trajectories in Triple-Negative Breast Cancer

A major challenge in treating Triple-Negative Breast Cancer (TNBC) lies in its molecular, morphological and clinical heterogeneity, which hampers accurate prediction of responses to neoadjuvant treatment. To address this, we introduce SMART: Spatio-Molecular Atlas of Response Trajectories, a comprehensive, multimodal resource compiled from 129 TNBC samples across 89 patients, obtained before, during, and after neoadjuvant chemotherapy (NACT). SMART comprises of 5,096 high quality manually selected spatial transcriptomic profiles enriched for epithelial, immune, or stromal compartments; paralleled with histological annotations, imagebased network analysis and protein expression. Seven novel spatial epithelial archetypes (EAs), seven tumour-immune microenvironments (TIMEs) and their co-localisation patterns were defined, revealing an opposing prevalence of functionally divergent EAs between response groups and the prognostic significance of B-cell enriched TIMEs, in particular those surrounding histologically normal epithelium adjacent to the tumour. The SMART dataset and analytical tools are publicly available via the PharosAI platform, providing the research community with the most comprehensive, manually annotated spatio-molecular transcriptomics atlas of NACT-treated TNBC to date.

cancer biology↗

bioRxiv2025

Rab11FIP2 controls NLRP3 inflammasome activation through Rab11b

Membrane trafficking through the trans-Golgi network has recently been shown to guide activation of the NLRP3 inflammasome. The GTPases Rab11a and Rab11b, and their effector molecule Rab11-FIP2, are regulators of endosome trafficking and retrograde transport. Rab11-FIP2 binds phosphatidylinositol species including PI4P, enriched in the trans-Golgi network and peripheral endosomes following NLRP3 inflammasome activation. We here demonstrate that Rab11-FIP2 and Rab11b, but not Rab11a, control caspase-1 mediated cleavage of pro-IL-1{beta} and GSDMD, and pyroptotic cell death in human macrophages. Rab11-FIP2 also controlled LPS stimulated IKK{beta} activation by TAK1 and IKK{beta} mediated NLRP3 translocation to the trans-Golgi network. Furthermore, we show that NLRP3 bound Rab11-FIP2 via its KMKK motif and that Rab11-FIP2 interacts with NLRP3 via its N-terminal C2-domain. The formation of PI4P positive endosomes and ASC-specks were also controlled by Rab11-FIP2. Collectively our results demonstrate that Rab11-FIP2 and Rab11b control NLRP3 inflammasome activation on early endosomes in human macrophages.

immunology↗

bioRxiv2025

Novel SLAMF1-derived peptide induces apoptosis in multiple myeloma cells by targeting IRF4 transcription factor for degradation

Multiple myeloma (MM) is the second most common hematological cancer. It remains incurable, highlighting the urgent need for novel therapeutic targets and treatment strategies. In this study, we investigated a panel of peptides derived from a functional motif of Signaling Lymphocytic Activation Molecule Family 1 (SLAMF1) with single amino acid substitutions and found that several of them exhibited potent anti-cancer activity by inducing MM cell death. The most potent peptide P7N4 significantly reduced the viability of both IL-6-dependent and -independent human myeloma cell lines (HMCLs), proteasome inhibitor-resistant MM cells, and primary MM cells, while exerting minimal effects on healthy blood cells. Furthermore, P7N4 enhanced the efficacy of the chemotherapeutic agent melphalan. When combined with the proteasome inhibitor bortezomib, P7N4 potentiated the anti-cancer effect of bortezomib in a highly aggressive murine MM model. Mechanistically, P7N4 induced apoptosis in MM cells by disrupting key pro-survival pathways, leading to reduction in IRF4, MYC, and {beta}-catenin levels, as well as inhibition of Akt and ERK1/2 phosphorylation. Furthermore, in peptide-sensitive HMCL, P7N4 significantly altered the expression of IRF4-associated genes. These effects were likely mediated by direct interaction of peptide with IRF4, targeting this transcription factor for degradation. Overall, our findings established P7N4 as a promising therapeutic candidate for MM, warranting further optimization and in-depth mechanistic studies.

cancer biology↗

bioRxiv2025

A novel TIRAP-MyD88 inhibitor blocks TLR7- and TLR8-induced type I IFN responses

Endosomal toll-like receptors TLR7 and TLR8 are critical sensors of microbial RNA that initiate antiviral and antibacterial immune responses through type I interferon (IFN) and proinflammatory cytokine production. While TIRAP is traditionally associated with plasma membrane TLR signaling, recent evidence suggests it also contributes to signaling via endosomal TLRs. Here, we examined the role of TIRAP in TLR7/8 signaling using P7-Pen, a novel SLAMF1-derived peptide that disrupts the TIRAP-MyD88 interaction. In primary human monocytes and a whole blood model, P7-Pen inhibited TLR7- and TLR8-induced expression and secretion of IRF5-regulated cytokines IFN{beta}, IL-12p40, and IL-12p70, without effect on TNF or IL-6. Mechanistically, P7-Pen blocked TIRAP recruitment to the TLR8-MyD88 complex, leading to reduced late-stage IRAK1 activation, Akt and IKK/{beta} phosphorylation, and downstream IRF5 dimerization and nuclear translocation. Inhibition of Staphylococcus aureus-induced cytokine production by P7-Pen was associated with reduced bacterial phagocytosis, impairing endosomal delivery of bacterial RNA. Notably, P7-Pen failed to inhibit murine TLR7 responses, which correlated with a lack of TIRAP recruitment to MyD88 in mouse macrophages following TLR7 ligand stimulation, highlighting species-specific differences in TLR signaling mechanisms. These findings support a noncanonical role for TIRAP in regulating IRF5-dependent signaling downstream of human TLR7 and TLR8, and demonstrate that selective disruption of TIRAP recruitment by a SLAMF1-derived peptide effectively attenuates IFN{beta} production. This strategy may hold therapeutic potential in diseases characterized by dysregulated type I IFN responses, such as systemic lupus erythematosus and chronic infections.

immunology↗

bioRxiv2024

Raver1 links Ripk1 RNA splicing to caspase-8-mediated pyroptotic cell death, inflammation, and pathogen resistance

Multiple cell death and inflammatory signaling pathways converge on two critical factors: receptor interacting serine/threonine kinase 1 (RIPK1) and caspase-8. Careful regulation of these molecules is critical to control apoptosis, pyroptosis and inflammation. Here we discovered a pivotal role of Raver1 as an essential regulator of Ripk1 pre-mRNA splicing, expression, and functionality, and the subsequent caspase-8-dependent inflammatory cell death. Macrophages from Raver1-deficient mice exhibit altered splicing of Ripk1, accompanied by diminished cell death and reduced activation of caspase-8, Gasdermin D and E, caspase-1, as well as decreased interleukin-18 (IL-18) and IL-1{beta} production. These effects were triggered by Yersinia bacteria, or by restraining TAK1 or IKK{beta} in the presence of LPS, TNF family members, or IFN{gamma}. Consequently, animals lacking Raver1 showed heightened susceptibility to Yersinia infection. Raver1 and RIPK1 also controlled the expression and function of the C-type lectin receptor Mincle. Our study underscores the critical regulatory role of Raver1 in modulating innate immune responses and highlights its significance in directing in vivo and in vitro inflammatory processes. SignificanceCaspase-8 and the kinase RIPK1 are at focal points of several inflammation and cell death pathways. Thus, a careful regulation of their actions is needed. Our work identifies the RNA splicing factor Raver1 as a critical factor directing the splicing of Ripk1 in order to modulate RIPK1/caspase-8-driven pyroptosis, apoptosis and inflammation. Raver1 is central for macrophage responses to Yersinia bacteria, initiated after blockade of kinases TAK1 and IKK, measured as activation of RIPK1, caspase-8, Gasdermin D, caspase-3, IL-1{beta} and IL-18. Importantly, Raver1 is necessary for host resistance to Yersinia infection in vivo. We propose that Raver1 is key for correct tuning of RIPK1-caspase-8 dependent processes.

immunology↗

bioRxiv2023

Transcriptional signatures associated with waterlogging stress responses and aerenchyma formation in barley root tissue

The negative impact of soil waterlogging on crop production is expected to increase due higher frequencies of extreme rainfall events arising from climate change. Consequently, understanding the molecular mechanisms that enable plants to mitigate waterlogging stress is critical for breeding programmes, particularly in the case of waterlogging-susceptible crop species, such as barley (Hordeum vulgare). Aerenchyma formation is a key morphological adaptation allowing plants to cope with waterlogging stress and hypoxic conditions, however, the genetic regulation of its development in barley remains largely unresolved. In this study, two barley cultivars with contrasting waterlogging tolerance (Franklin and Yerong) were subjected to waterlogging stress, followed by analysis of phenotypic traits including root aerenchyma formation, and transcriptomic profiling of root tissue samples. Differential expression analyses identified genes transcriptionally responsive to 24 and 72 h of waterlogging in both cultivars, and highlighted metabolic adaptations, regulation of ROS signalling and management of stress responses as key elements of the waterlogging response. The results revealed large intra-individual variations in root aerenchyma formation, and these variations were exploited to isolate 81 candidate aerenchyma-associated genes from the generated RNA-seq datasets. Network analyses suggest the involvement of the DNA damage response gene, DRT100 and cell wall modifying genes, XHT16 and XHT15 as regulatory hub genes in aerenchyma formation. Collectively, the generated data provide insights into transcriptional signatures associated with the barley root responses to waterlogging and aerenchyma formation, informing our understanding of strategies that plants employ to cope with the negative impacts of heavy rainfall.

plant biology↗

bioRxiv2023

Cortical circuitry mediating inter-areal touch signal amplification

Sensory cortical areas are often organized into topographic maps which represent the sensory epithelium1,2. Individual areas are richly interconnected3, in many cases via reciprocal projections that respect the topography of the underlying map4,5. Because topographically matched cortical patches process the same stimulus, their interaction is likely central to many neural computations6-10. Here, we ask how topographically matched subregions of primary and secondary vibrissal somatosensory cortices (vS1 and vS2) interact during whisker touch. In the mouse, whisker touch-responsive neurons are topographically organized in both vS1 and vS2. Both areas receive thalamic touch input and are topographically interconnected4. Volumetric calcium imaging in mice actively palpating an object with two whiskers revealed a sparse population of highly active, broadly tuned touch neurons responsive to both whiskers. These neurons were especially pronounced in superficial layer 2 in both areas. Despite their rarity, these neurons served as the main conduits of touch-evoked activity between vS1 and vS2 and exhibited elevated synchrony. Focal lesions of the whisker touch-responsive region in vS1 or vS2 degraded touch responses in the unlesioned area, with whisker-specific vS1 lesions degrading whisker-specific vS2 touch responses. Thus, a sparse and superficial population of broadly tuned touch neurons recurrently amplifies touch responses across vS1 and vS2.

neuroscience↗

bioRxiv2023

Evolutionary constraint and innovation across hundreds of placental mammals

Evolutionary constraint and acceleration are powerful, cell-type agnostic measures of functional importance. Previous studies in mammals were limited by species number and reliance on human-referenced alignments. We explore the evolution of placental mammals, including humans, through reference-free whole-genome alignment of 240 species and protein-coding alignments for 428 species. We estimate 10.7% of the human genome is evolutionarily constrained. We resolve constraint to single nucleotides, pinpointing functional positions, and refine and expand by over seven-fold the catalog of ultraconserved elements. Overall, 48.5% of constrained bases are as yet unannotated, suggesting yet-to-be-discovered functional importance. Using species-level phenotypes and an updated phylogeny, we associate coding and regulatory variation with olfaction and hibernation. Focusing on biodiversity conservation, we identify genomic metrics that predict species at risk of extinction.

genomics↗

bioRxiv2022

Columnar scale lesions in barrel cortex degrade tactile discrimination but not detection

Primary sensory cortices typically display functional topography, suggesting that even small cortical volumes may underpin perception of specific stimuli. Because traditional loss-of-function approaches have a relatively large radius of effect (>1 mm), the behavioral necessity of smaller cortical volumes remains unclear. In the mouse primary vibrissal somatosensory cortex (vS1), barrels with a radius of [~]150 m receive input predominantly from a single whisker, partitioning vS1 into a topographic map of well-defined columns. Here, we train animals implanted with a cranial window over vS1 to perform single-whisker perceptual tasks. We then use high-power laser exposure centered on the barrel representing the spared whisker to produce lesions with an average volume of [~]2 barrels. These columnar scale lesions impair performance on object location discrimination tasks without disrupting vibrissal kinematics. Animals with degraded discrimination performance can immediately perform a detection task with high accuracy. Animals trained de novo on both simple and complex detection tasks showed no behavioral deficits following columnar scale lesions. Thus, vS1 barrels are necessary for performing object location discrimination but not simple or complex object detection behaviors.

neuroscience↗