Biology subjects

Gardner, J. M.

Publications and source records attributed to Gardner, J. M..

At least 19 recordsLinked to original sources

bioRxiv2026

LactoTypeDB: a regenerable, type-anchored 16S rRNA gene reference for species-level identification of the Lactobacillaceae in foods

Amplicon surveys of fermented and spoiled foods routinely resolve Lactobacillaceae, the lactic acid bacteria responsible for many food and beverage fermentations, only to genus, whereas registers such as the Inventory of Microbial Food Cultures require species-level identification. This shortfall arises from the 16S rRNA genes limited, region-dependent resolution and from incomplete, non-type-strain-anchored references that silently reassign missing species to their nearest relative. We built LactoTypeDB, a regenerable, type-anchored reference covering 434 of the familys 441 species and all 37 genera and substituted it into the Living Tree Project release LTP 08_2023 the fields default classifier uses. This eliminated species-level misassignment of type strains in all regions tested and cut misassignment of 10,329 other sequences from the same species from 1,374 errors down to 3 when the full-length 16S rRNA gene was used. Applied unmodified to 11,612 V3-V4 distinct sequences from a published survey of two meat production lines, the workflow returned a species for 213 and a genus for 5,926, and flagged 3,495 as undescribed candidates, more than a third of them nearest to Dellaglioa, a genus that includes a meat-spoilage organism tracked in that survey. The ambiguity that remains is the markers, since V3-V4 collapses 417 of the 434 species into 27 groups it cannot separate. For food microbiology laboratories, the practical change is that a species call from this family can now be trusted where the marker allows it, and a sequence matching nothing becomes a candidate worth isolating rather than a limitation to work around.

bioinformatics↗

bioRxiv2026

Stingless bees, turtle ants and tea plants are rich sources of undescribed Lactobacillaceae

Knowledge of the family Lactobacillaceae rests largely on isolates from foods and a few repeatedly sampled hosts. Reference databases give an unrecognised sequence the name of its nearest relative, so a lineage with no entry of its own is renamed rather than flagged. Here we classify the family across the public plant and invertebrate amplicon record to locate the hosts carrying undescribed lineages. Across 3,344 independent 16S rRNA gene amplicon studies, every sequence cluster was tested against a type-strain reference and placed at the deepest rank it supports. Of 204,813 classified clusters, 20,516 were named to species and 127,906 to genus, while 4,741 matched no described species. Six published datasets whose authors could name their Lactobacillaceae only as Lactobacillus, or not at all, are reclassified here. Genera described from one habitat occur far beyond it, three bee-associated genera occurring on Rosaceae and Brassicaceae at several times their rate on wind-pollinated grasses, and we found no published Bombilactobacillus record from a plant. Undescribed lineages concentrate in the least-cultured hosts, reaching 86.1% and 77.4% of studies in the stingless bees Melipona and Tetragonula, and are most divergent in the turtle ant Cephalotes and, among plants, in tea, Camellia. An independent genome-resolved survey of pot honey converges on the same two genera. The primary descriptions of forty-eight species from these hosts specify a supplemented medium, so the hosts carrying undescribed lineages also indicate how to culture them.

microbiology↗

bioRxiv2026

Understanding the impact of sodium sulfide on the invasive growth of wine yeast

Yeasts ability to invade surfaces has important implications for infections and food contamination. Invasive growth in yeast is influenced by genetic and environmental factors. In this exploratory study, we used a systematic experimental design to identify conditions under which sulfide-induced invasive growth can be reliably observed and quantified and investigated the effects of sulfide, gene deletions, and environmental conditions on the invasive behaviour of the wine yeast strain AWRI 796. Sulfide enhanced invasion in the (parent) AWRI 796 strain under nitrogen-limiting conditions, although its effect was obscured by experimental variability and pre-culture conditions. Genetic factors had a major effect on the overall invasive phenotype, with deletion of key genes suppressing invasion. Most gene-deletion mutants did not significantly affect how the colony responded to sulfide. In addition to sulfide and genotype, environmental conditions also influenced invasive behaviour. The pre-2xSLAD pre-culture condition was best for detecting sulfide-induced growth, and later plate washing time and decreased nutrient levels enhanced invasiveness. Our experimental design and findings provide a framework for understanding the determinants of yeast invasiveness, which may inform future studies on filamentous yeast behaviour.

microbiology↗

bioRxiv2026

Fezf2 regulates differentiation of Aire-expressing and post-Aire mimetic epithelial populations maintaining thymic homeostasis

Fezf2 has been proposed to serve principally as a transcriptional regulator of broad self-antigen expression in medullary thymic epithelial cells (mTECs). Here, we demonstrate an additional function for Fezf2 as a developmental regulator of TEC lineage commitment. Fezf2 deficiency in the thymus led to a relative expansion of lung mimetic and Ccl21+ immature mTECs at the expense of MHCII-hi Aire-expressing and all other mimetic populations. Consistent with this, the disruption of mTEC development had functional consequences, including alterations in tuft-associated iNKT polarization and microfold-associated B-cell class switching. In addition, high-resolution transcriptomics revealed that Fezf2 and Aire regulate distinct transcriptional programs, with Fezf2 driving both activation and repression of a more limited set of tissue-restricted genes compared to the broad gene activation program observed for Aire. Pure transcriptional repression at Fezf2 target loci was sufficient to partially rescue mTEC development in global Fezf2-/- (tKO) mice, potentially through suppression of Lifr expression and modulation of downstream Stat3 signaling tone. These results expand our understanding of Fezf2 in mTEC biology, highlighting transcriptional repression as a required functional facet for adult steady-state lineage patterning across the mTEC compartment.

immunology↗

bioRxiv2025

Development and validation of an ultra-low-cost, open source normothermic ex vivo organ perfusion platform

BackgroundNormothermic ex vivo organ perfusion (NEVOP) promises to catalyze organ preservation, therapeutic discovery, and organ-specific disease modeling. Existing technology platforms remain inaccessible for research due to restricted access to commercial organ perfusion devices, high costs of both devices and proprietary consumables, and steep technical learning curves. Additionally, the available technology is not optimized to perfuse smaller organs such as the kidney. MethodsTo overcome these barriers, a custom NEVOP circuit was developed using recycled, repurposed, and low-cost components. Porcine kidneys and autologous blood were used to iteratively optimize circuit design. A porcine kidney autotransplantation protocol was adapted to evaluate in vivo kidney function after ex vivo perfusion. To pilot the flexibility of this system as a multi-organ platform for ex vivo human biology, non-transplantable human donor kidney, spleen, and pancreas specimens were stably perfused using human blood products and analyzed. ResultsAn ultra low-cost NEVOP system engineered to perfuse porcine kidneys and diverse human organs (kidney, pancreas, and spleen) sustained viable organs for up to 24 hours with evidence of both function and viability. Key innovations included a parallel flow resistor to facilitate low-flow perfusion in non-heparinized organs and a containment bag with adjustable magnets to provide vascular stability and recycling of venous overflow. The circuit costs less than 1,500USD to construct, and porcine kidneys perfused for 24 hours on this platform demonstrated healthy in vivo function upon autotransplantation. ConclusionsCustom NEVOP platforms constitute novel and potentially transformative research platforms which use low-cost and readily available materials. Paired with access to non-transplantable research organs from altruistic donors, this model provides a road map for investigators to advance biomedical discovery and human ex vivo biology.

bioengineering↗

bioRxiv2025

Quantifying the effects of cell death and agar density on yeast colony biofilms using an extensional flow mathematical model

We use a combination of experiments, mathematical modelling, and parameter estimation to better understand how agar density affects colony biofilm growth of the yeast species Saccharomyces cerevisiae. We obtained 15 total experimental replicates on rectangular plates filled with 0.6%, 0.8%, 1.2%, and 2.0% agar. In the experiments, we measured the horizontal expansion over time, the number of living cells, and the colony-biofilm aspect ratio. These measurements quantify the colony-biofilm size, composition, and shape, respectively. We modelled colony-biofilm expansion using a thin-film extensional-flow mathematical model. By fitting five unknown model parameters to mean experimental data, we show that nutrient uptake decreases and biofilm-substratum adhesion strength increases with an increase in agar density. Sensitivity analysis, fitting to individual replicates, and synthetic-data analysis confirmed that increased biofilm-substratum adhesion is the most consistent effect of increased agar density. This finding aligns with similar results reported for bacteria, and suggests that substratum properties are important for yeast-colony-biofilm growth.

biophysics↗

bioRxiv2025

Agent-based modelling and time series inference of filamentous yeast colonies

The bakers yeast Saccharomyces cerevisiae can form invasive filamentous colonies with non-uniform spatiotemporal patterns. We aimed to better understand how individual cellular actions give rise to colony-scale patterns. We used an off-lattice agent-based model to simulate colony growth, and used a neural likelihood estimator (NLE) to infer parameters for experimental photographs. Li et al. [1] used approximate Bayesian computation (ABC) to infer parameters using coarse summary statistics obtained from a single time point averaged across experimental replicates. The NLE overcomes the computational expense of ABC, allowing us to infer the parameters of individual colonies from a full time series of experimental photographs. To demonstrate the capabilities of our model and inference technique, we tested extensively on synthetic data and then predicted yeast growth under three different experimental conditions. As before, the proportion of total colony growth above which pseudohyphal growth is permitted was a key parameter that contributed to colony morphology. Since our NLE-based approach incorporates time series data, it yielded better parameter estimates and more accurate predictions compared to our ABC-based method. This updated approach improved understanding of how the probability that a stated cell produces a pseudohyphal cell influences colony morphology. In this way, the model also has the potential to generate hypotheses, which can be tested through biological experiments to increase the understanding of the basis for different growth patterns in yeast.

cell biology↗

bioRxiv2025

Modelling the emergence of spiral colony morphology in the yeast Magnusiomyces magnusii

Yeast species have several adaptations that enable them to survive in harsh environments. These adaptations include biofilm formation, where the secretion of extracellular polymeric substances can protect the cells from a hostile environment, or, under nutrient-limited conditions, pseudohyphal or hyphal growth, where the colony can send out long tendrils to explore the environment and seek nutrients. Recently, we observed a spiral colony morphology emerge in an isolate of the hyphae-forming yeast Magnusiomyces magnusii grown under laboratory conditions. We use an off-lattice agent-based model (ABM) that simulates colony development to investigate the hypothesis that bias in the angle between successive hyphal segments causes the spiral morphology. The model involves biologically-motivated rules of hyphal extension, with key model parameters including the colony size at the onset of hyphal filaments, and the angle between the penultimate and the apical segments. Using one example of an experimentally-grown colony, we use a sequential neural likelihood method to perform likelihood-free Bayesian inference to infer the model parameters. Our results indicate a mean angle between hyphal segments of 2.3{whitebullet} [1.1{whitebullet}, 3.6{whitebullet}] (95% credible interval). To confirm the models applicability to colony growth, we use biologically-feasible parameter values to yield morphologies observed in M. magnusii experiments.

microbiology↗

bioRxiv2025

Blocking Osteoprotegerin Reprograms Cancer Associated Fibroblast to Promotes Immune Infiltration into the Tumor Microenvironment

AbstractThe stromal compartment of many solid tumors plays a critical role in shaping an immunosuppressive microenvironment that limits the effectiveness of immune-based therapies1. Among stromal constituents, cancer-associated fibroblasts (CAFs) have emerged as key regulators of antitumor immunity2-5. Here, we identify a distinct subset of CAFs in both murine and human stroma-rich cancers that secrete osteoprotegerin (OPG)-- a soluble decoy receptor that neutralizes receptor activator of nuclear factor kappa-B ligand (RANKL) and TNF-related apoptosis-inducing ligand (TRAIL), both of which are involved in T cell function. In vitro, OPG directly impairs CD8 T cell-mediated killing of target cells. In murine models of pancreatic and breast cancer, antibody-mediated blockade of OPG promotes robust immune infiltration into the tumor microenvironment, leading to significant tumor regression. Stromal profiling revealed that OPG blockade induces a shift in CAF cells--reducing immunosuppressive OPG fibroblasts while expanding interferon-responsive fibroblasts, thus recalibrating the tumor stroma toward a pro-immunogenic landscape. These findings uncover a previously unrecognized mechanism of stromal immune suppression and highlight OPG as a stromal immune checkpoint controlling CD8 T cell infiltration. Targeting OPG may offer a novel therapeutic strategy to convert immunologically "cold" tumors into T cell-infiltrated, tumor microenvironment.

cancer biology↗

bioRxiv2025

Transient Dietary Changes Modulate Inflammatory Disease Trajectory in the Lean State

Obesity potently alters immune responses across various inflammatory contexts1-7. However, it is unclear whether a transient high-fat diet (HFD) can affect immune function despite minimal effects on body weight. Here, we demonstrate that a short-term HFD regimen significantly exacerbates disease severity in a model of experimental psoriasis, comparable to what is observed in obese mice on long-term HFD. We find that a critical 4-day window of HFD coinciding with disease onset is sufficient to overactivate the immune response, leading to worsened disease outcomes. Mechanistically, we identify the CD4+ T cell compartment as an essential mediator of HFD-induced disease severity. Within the compartment, we functionally validate that disease exacerbation is driven by increased differentiation of a pathogenic population of T helper 17 (TH17) cells8 expressing IL1R1 (interleukin-1 receptor, type I)9, which is triggered by localized activation of the NLRP3 (NOD-, LRR-, and pyrin domain-containing protein 3) inflammasome10. This brief window of HFD at disease onset leads to immune-dependent sensitization, as disease severity is increased upon a subsequent flare, despite complete recovery and under a low-fat diet (LFD) regimen. Our data indicate that transient dietary changes during the initial stages of an inflammatory event can rewire the immune milieu, profoundly influencing disease progression and inflammatory memory11. This phenomenon may have broad implications for conditions where obesity, and not diet itself, is considered the primary risk factor.

immunology↗

bioRxiv2025

PISA: a versatile interpretation tool for visualizing cis-regulatory rules in genomic data

Sequence-to-function neural networks learn cis-regulatory sequence rules driving many types of genomic data. Interpreting these models to relate the sequence rules to underlying biological processes remains challenging, especially for complex genomic readouts such as MNase-seq, which maps nucleosome occupancy but is confounded by experimental bias. We introduce pairwise influence by sequence attribution (PISA), an interpretation tool that combinatorially decodes which bases contributed to the readout at a specific genomic coordinate. PISA visualizes the effects of transcription factor motifs, detects undiscovered motifs with complex contribution patterns, and reveals experimental biases. By learning the bias for MNase-seq, PISA enables unprecedented nucleosome prediction models, allowing the de novo discovery of nucleosome-positioning motifs and their longrange chromatin effects, as well as the design of sequences with altered nucleosome configurations. These results show that PISA is a versatile tool that expands our ability to train and interpret sequence-to-function neural networks on genomics data and understand the underlying cis-regulatory code.

genomics↗

bioRxiv2025

Comparative analysis of human and mouse ovaries across age

Mouse is a tractable model for human ovarian biology, however its utility is limited by incomplete understanding of how transcription and signaling differ interspecifically and with age. We compared ovaries between species using 3D-imaging, single-cell transcriptomics, and functional studies. In mice, we mapped declining follicle numbers and oocyte competence during aging; in human ovaries, we identified cortical follicle pockets and density changes. Oocytes had species-specific gene expression patterns during growth that converged toward maturity. Age-related transcriptional changes were greater in oocytes than granulosa cells across species, although mature oocytes change more in humans. We identified ovarian sympathetic nerves and glia; nerve density increased in aged human ovaries and, when ablated in mice, perturbed folliculogenesis. This comparative atlas defines shared and species-specific hallmarks of ovarian biology.

genomics↗

bioRxiv2025

Accidental and Regulated Cell Death in Yeast Colony Biofilms

The yeast species Saccharomyces cerevisiae is one of the most intensively studied organisms on the planet due to being an excellent eukaryotic model organism in molecular and cell biology. In this work, we investigate the growth and morphology of yeast colony biofilms, where proliferating yeast cells reside within a self-produced extracellular matrix. This research area has garnered significant scientific interest due to its applicability in the biological and biomedical sectors. A central feature of yeast colony biofilm expansion is cellular demise, which is onset by one of two independent mechanisms: either accidental cell death (ACD) or regulated cell death (RCD). In this article, we generalise a recently developed continuum model for the nutrient-limited growth of a yeast colony biofilm to include the effects of ACD and RCD. This new model involves a system of four coupled nonlinear reaction-diffusion equations for the yeast-cell density, the nutrient concentration, and two species of dead cells. Numerical solutions of the spatially one and two-dimensional governing equations reveal the impact that ACD and RCD have on expansion speed, morphology and cell distribution within the colony biofilm. Our results show good qualitative agreement with our own experiments.

microbiology↗

bioRxiv2023

Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains

A key aspect of nutrient absorption is the exquisite division of labor across the length of the small intestine, with individual classes of micronutrients taken up at different positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum, and ileum. By examining fine-scale longitudinal segmentation of the mouse and human small intestines, we identified transcriptional signatures and upstream regulatory factors that define five domains of nutrient absorption, distinct from the three traditional sections. Spatially restricted expression programs were most prominent in nutrient-absorbing enterocytes but initially arose in intestinal stem cells residing in three regional populations. While a core signature was maintained across mice and humans with different diets and environments, domain properties were influenced by dietary changes. We established the functions of Ppar- and Cdx1 in patterning lipid metabolism in distal domains and generated a predictive model of additional transcription factors that direct domain identity. Molecular domain identity can be detected with machine learning, representing the first systematic method to computationally identify specific intestinal regions in mice. These findings provide a foundational framework for the identity and control of longitudinal zonation of absorption along the proximal:distal small intestinal axis.

genomics↗

bioRxiv2023

Dual α-globin and truncated erythropoietin receptor knock-in restores hemoglobin production in α-thalassemia major-derived hematopoietic stem and progenitor cells

Alpha-thalassemia is an autosomal recessive disease with increasing worldwide prevalence. The molecular basis is due to mutation or deletion of one or more duplicated -globin genes, and disease severity is directly related to the number of allelic copies compromised. The most severe form, -thalassemia major (TM), results from loss of all four copies of -globin and has historically resulted in fatality in utero. However, in utero transfusions now enable survival to birth. Postnatally, patients face challenges similar to {beta}-thalassemia, including severe anemia and erythrotoxicity due to imbalance of {beta}-globin and -globin chains. While curative, hematopoietic stem cell transplantation (HSCT) is limited by donor availability and potential transplant-related complications. Despite progress in genome editing treatments for {beta}-thalassemia, there is no analogous curative option for patients suffering from -thalassemia. To address this, we designed a novel Cas9/AAV6-mediated genome editing strategy that integrates a functional -globin gene into the {beta}-globin locus in TM patient-derived hematopoietic stem and progenitor cells (HSPCs). Incorporation of a truncated erythropoietin receptor transgene into the -globin integration cassette dramatically increased erythropoietic output from edited HSPCs and led to the most robust production of -globin, and consequently normal hemoglobin. By directing edited HSPCs toward increased production of clinically relevant RBCs instead of other divergent cell types, this approach has the potential to mitigate the limitations of traditional HSCT for the hemoglobinopathies, including low genome editing and low engraftment rates. These findings support development of a definitive ex vivo autologous genome editing strategy that may be curative for -thalassemia. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/555926v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1b63dacorg.highwire.dtl.DTLVardef@18b25a1org.highwire.dtl.DTLVardef@53835corg.highwire.dtl.DTLVardef@d52bf5_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Nucleoside-driven specificity of DNA Methyltransferase

We have studied adenosine binding specificities of two bacterial DNA methyltransferase Taq methyltransferase (M.TaqI), and HhaI methyltransferase (M.HhaI). While these DNA methyltransferases have similar cofactor binding pocket interactions, experimental data showed different specificity for novel cofactors ((SNM) (S-guanosyl-L-methionine (SGM), S-cytidyl-L-methionine (SCM), S-uridyl-L-methionine (SUM)). Protein dynamics corroborate the experimental data on the cofactor specificities. For M.TaqI the specificity for S-adenosyl-L-methionine (SAM) is governed by the tight binding on the nucleoside part of the cofactor, while for M.HhaI the degree of freedom of the nucleoside chain allows the acceptance of other bases. The experimental data proves a catalytically productive methylation by M.HhaI binding pocket for all the SNM. Our results suggest a new route for successful design of unnatural SNM analogues for methyltransferases as a tool for cofactor engineering. Table of Content O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/513954v2_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@2562aforg.highwire.dtl.DTLVardef@71de9forg.highwire.dtl.DTLVardef@1cead77org.highwire.dtl.DTLVardef@1de8682_HPS_FORMAT_FIGEXP M_FIG TOC: Methylation by DNA methyltransferase is nucleobase dependent. While M.Taq1 is specific for SAM, M.HhaI is promiscuous for other SAM analogs C_FIG

biochemistry↗

bioRxiv2021

Antigen presentation by type 3 innate lymphoid cells instructs the differentiation of gut microbiota-specific regulatory T cells

The mutualistic relationship of gut-resident microbiota and cells of the host immune system promotes homeostasis that ensures maintenance of the microbial community and of a poised, but largely non-aggressive, immune cell compartment1, 2. Consequences of disturbing this balance, by environmental or genetic factors, include proximal inflammatory conditions, like Crohns disease, and systemic illnesses, both metabolic and autoimmune. One of the means by which this equilibrium is achieved is through induction of both effector and suppressor or regulatory arms of the adaptive immune system. In mice, Helicobacter species induce regulatory (iTreg) and follicular helper (Tfh) T cells in the colon-draining mesenteric lymph nodes under homeostatic conditions, but can instead induce inflammatory Th17 cells when iTreg cells are compromised3, 4. How Helicobacter hepaticus and other gut bacteria direct T cells to adopt distinct functions remains poorly understood. Here, we investigated which cells and molecular components are required to convey the microbial instruction for the iTreg differentiation program. We found that antigen presentation by cells expressing ROR{gamma}t, rather than by classical dendritic cells, was both required and sufficient for iTreg induction. These ROR{gamma}t+ cells, likely to be type 3 innate lymphoid cells (ILC3) and/or a recently-described population of Aire+ cells termed Janus cells5, require the MHC class II antigen presentation machinery, the chemokine receptor CCR7, and v integrin, which activates TGF-{beta}, for iTreg cell differentiation. In the absence of any of these, instead of iTreg cells there was expansion of microbiota-specific pathogenic Th17 cells, which were induced by other antigen presenting cells (APCs) that did not require CCR7. Thus, intestinal commensal microbes and their products target multiple APCs with pre-determined features suited to directing appropriate T cell differentiation programs, rather than a common APC that they endow with appropriate functions. Our results illustrate the ability of microbiota to exploit specialized functions of distinct innate immune system cells, targeting them to achieve the desired composition of equipoised T cells, thus maintaining tolerance.

immunology↗

bioRxiv2021

Single-Cell Multiomics Defines Tolerogenic Extrathymic Aire-Expressing Populations with Unique Homology to Thymic Epithelium

The Autoimmune Regulator (Aire) gene, well defined for its role in medullary thymic epithelial cells (mTECs) and immune self-tolerance, is also expressed in extrathymic Aire-expressing cells (eTACs) in the secondary lymphoid organs. eTACs have been shown to be hematopoietic antigen presenting cells (APCs) and potent inducers of immune tolerance (1-3). However, the precise identity and function of these cells remain unclear. Here, we use high-dimensional single-cell multiomics and functional approaches to define eTACs at the transcriptional, genomic, and proteomic level. We find that eTACs consist of two similar cell types: CCR7+ Aire-expressing migratory dendritic cells (AmDCs) and a unique Aire-hi population co-expressing Aire and RAR-related orphan receptor gamma-t (ROR{gamma}t). The latter, which have significant transcriptional and genomic homology to migratory dendritic cells (migDCs) and mTECs, we term Janus cells (JCs). All eTACs, and JCs in particular, have a highly accessible chromatin structure and high levels of broad gene expression, including tissue-specific antigens, as well as remarkable transcriptional and genomic homology to thymic medullary epithelium. As in the thymus, Aire expression in eTACs is also dependent on RANK-RANK-ligand interactions. Furthermore, lineage-tracing shows that JCs are not precursors to the majority of AmDCs. Finally, self-antigen expression by eTACs is sufficient to mediate negative selection of T cells escaping thymic selection and can prevent autoimmune diabetes in non-obese diabetic mice. This transcriptional, genomic, and functional symmetry between a hematopoietic Aire-expressing population in the periphery and an epithelial Aire-expressing population in the thymus suggests that a core biological program may influence self-tolerance and self-representation across the spectrum of immune development.

immunology↗