Biology subjects

Murphy, K. M.

Publications and source records attributed to Murphy, K. M..

18 recordsLinked to original sources

bioRxiv2026

CD8+ T cells are primed by cDC1 and exacerbate tau-mediated neurodegeneration

There are changes in adaptive immunity in Alzheimers disease (AD) and increases in activated CD8+ T cells in brain correlate with tau pathology1-3. However, which cells mediate T cell priming in tau-mediated neurodegeneration remains unclear. In different conditions such as cancer, viral infections, and autoimmune diseases outside the CNS, conventional type-1 dendritic cells (cDC1) perform antigen cross-presentation to prime CD8+ T cells4,5. We demonstrate that tauopathy mice deficient in cDC1 are markedly protected against tau-mediated neurodegeneration and display a selective decrease in brain CD8+ T cell infiltration and glial reactivity. The remaining CD8+ T cells showed an antigen inexperienced status with less clonal expansion, indicating suboptimal T cell priming. We confirm that brain derived antigens are presented in secondary lymphoid tissues to prime CD8+ T cells. Our study identifies cDC1 cells as critical for CD8+ T cell priming outside the CNS. This priming is required for a large increase of activated CD8+ T cells in the brain which promotes tau-mediated neurodegeneration.

neuroscience↗

bioRxiv2026

Quantifying growth and lodging in Tef (Eragrostis tef) with Uncrewed Aerial Systems (UAS)

Lodging is a major contributor to decreased yield in tef, a staple cereal crop in Ethiopia. Semidwarf varieties have been developed with a goal to increase yield through reduced lodging, but studying lodging susceptibility currently requires a labor-intensive, imprecise, manual scoring method. Here we present workflows for analyzing tef stand height from UAS sensors across time to both predict lodging later in the season with early height and to measure the severity of lodging after a storm event. We compare 3D point clouds generated by photogrammetry from RGB images with those generated from LiDAR to estimate height, demonstrating that they produce similar results, despite differences in cost. Stand height and lodging can both be accurately measured with low-cost UAS, reducing the need for manual measurements and increasing precision and temporal resolution in plant breeding programs. Significance StatementExtreme weather or heavy grain can cause plant stems to bend, a process called lodging. Lodging significantly reduces crop yields globally, particularly in grain crops such as tef (Eragrostis tef). Semidwarf crops have previously been reported to be lodging-resistant, increasing crop yields. Here, we used uncrewed aerial systems (UAS) to measure plant growth, height, and lodging in gene edited semidwarf tef lines, and compared the results to ground-truth data. Using a UAS equipped with a red-green-blue (RGB) camera or LiDAR sensor, we measured plant height and lodging, and found that early-season height measurements could predict future lodging potential. The tools used were contributed to the open-source software PlantCV-Geospatial for community use. This work contributes to a broader understanding of genetic resistance to lodging, providing valuable insights for tef crop improvement and reduces the need for labor-intensive manual measurements.

plant biology↗

bioRxiv2025

PlantCV v4: Image analysis software for high-throughput plant phenotyping

PlantCV is an open-source Python project aimed at developing tools to address a range of image-based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data and the newest release, PlantCV version 4, continues to lower the barrier to entry for users without substantial coding experience through extensive example use-case tutorials and simplified installation. In addition to usability, we document added functionality since the release of PlantCV v2, including support for more image types such as fluorescence, thermal, and hyperspectral data. Finally, we describe the development of a new subpackage focused on morphological trait measurements like leaf angle, and demonstrate its utility as compared to more manual methods of data collection. CORE IDEASO_LIPlantCV is an open-source, open-development, Python-based software package that has a new release for improved functionality and usability to make image analysis flexible and easier for researchers without a coding background. C_LIO_LIPlantCV is now capable of handling new data types that are relevant to researchers, such as thermal and hyperspectral, and has built in functionality for extracting information from these image types. C_LIO_LIThe software project aims to lower the barrier to entry into image analysis for researchers by providing numerous, versioned, interactive tutorials that cover most common use cases, particularly in plant science. C_LI

plant biology↗

bioRxiv2025

Skin lipid chemistry influences host-microbiome-pathogen interactions in snake fungal disease (ophidiomycosis)

Within host-microbiome-pathogen systems, the host chemical microenvironment is often overlooked despite its inherent role in host physiology. We used a multifaceted experimental approach encompassing culture-dependent and independent methods, metagenomic and genomic data, and deep neural network modeling to assess the impact of host skin lipid chemistry and the bacterial microbiome on the growth of Ophidiomyces ophidiicola (ophidiomycosis, snake fungal disease). Results suggest that host skin lipid chemistry (e.g., oleic acid, squalene) and bacteria isolated from wild snake skins (e.g., Chryseobacterium sp. and Stenotrophomonas maltophilia) suppress O. ophidiicola growth. Notably, the O. ophidiicola genome contains biosynthetic gene clusters (BGCs) that encode metabolites that may suppress host lipid production, facilitating fungal pathogenicity. The contrastive deep neural network produced a near-perfect alignment of snake skin lipid and microbiome profiles for both individual snakes and disease states. BGCs from bacterial genomes isolated from snake skin overlap with metagenome profiles from wild snakes and correlate with disease state. We highlight antifungal activity found in the diverse lipid milieu of snake skin and bacterial-fungal interactions (BFIs) that structure the skin microbiome. Our results illustrate a strong relationship among a fungal pathogen, the microbiome, and host skin lipid chemistry.

microbiology↗

bioRxiv2024

Morphometric Identification of Parvalbumin-Positive Interneurons: A Data-Driven Approach

Traditionally, anatomical studies of parvalbumin-positive (PV+) labelled interneurons describe them as a homogeneous population of neurons. In contrast, recent single-cell RNAseq studies have identified multiple transcriptomically distinct categories of PV+ cells. That difference between a single anatomical category of PV+ neurons and multiple transcriptomic categories presents a problem in understanding the role of these neurons in cortical function. One gap that might contribute to this discrepancy is that PV+ morphology is typically addressed using qualitative descriptions and simple quantifications, while single-cell RNAseq studies use big data and high dimensional analyses. PV+ neurons play critical roles in the experience-dependent development of the cortex and are often involved in disease-related changes associated with neurodegenerative and neuropsychiatric disorders. Here, we developed a modern data-driven analysis pipeline to quantify PV+ morphology. We quantified 97 morphometric features from 14274 PV+ neurons and applied unsupervised clustering that identified 13 different PV+ morphologies. We extended the analysis to compare PV+ dendritic arbour patterns and cell body morphologies. Finally, we compared the morphologies of PV+ neurons with the cell body morphologies of neurons expressing various genes associated with PV+ transcriptomic cell types. This approach identified a range of PV+ morphologies similar to the number of transcriptomic categories. It also found that the PV+ morphologies have cortical area, laminar, and transcriptomic biases that might contribute to cortical function.

neuroscience↗

bioRxiv2023

Cell-extrinsic effects of Irf2 on cDC2 development

Characterization of the functional effects of cDC2s in vivo requires model systems in which cDC2s are depleted. Previous literature has reported a loss of cDC2s in mice lacking the transcription factor IRF21,2. We sought to further characterize the cDC2 defect in these animals. Here, we find that the requirement for IRF2 in cDC2 development and survival is cell-extrinsic and correlated to the development of dermatitis in the Irf2-/- model system. We also find that Flt3L-mediated in vitro development of cDC1s and cDC2s, but not pDCs, is abrogated in Irf2-/- bone marrow, as well as in wild-type bone marrow cultured with IFN. Loss of interferon (IFN) signaling in Irf2-/- mice restored cDC2 development in vivo and cDC1 and cDC2 development in vitro. We therefore conclude that IRF2 is required for cDC2 development in a cell-extrinsic manner dependent on IFN signaling.

immunology↗

bioRxiv2022

WDFY4 deficiency in NOD mice abrogates autoimmune diabetes and insulitis

The events that initiate autoimmune diabetes in NOD mice remain poorly understood. CD4 and CD8 T cells are both required but whether either cell initiates disease is unclear. To test whether CD4 T cell infiltration into islet required damage to {beta} cells induced by autoreactive CD8 T cells, we selectively inactivated Wdfy4 in NOD mice (NOD.Wdfy4-/-) using CRISPR/Cas9 targeting. Similar to C57BL/6 Wdfy4-/- mice NOD.Wdfy4-/- mice develop type 1 conventional dendritic cells (cDC1) that are unable to cross-present cell-associated antigens required to activate CD8 T cells. By contrast, cDC1 from heterozygous Wdfy4+/- mice can cross-present normally. Heterozygous NOD.Wdfy4+/- mice develop diabetes similar to NOD mice, but NOD.Wdfy4-/- mice neither develop diabetes nor prime autoreactive CD8 T cells in vivo. By contrast, NOD.Wdfy4-/- mice can process and present MHC-II-restricted autoantigens and can activate {beta} cell specific CD4 T cells in lymph nodes, and yet do not develop CD4 T cell infiltration in islets. These results indicate that the priming of autoreactive CD8 T cells in NOD mice requires cross-presentation by cDC1. Further, autoreactive CD8 T cells are required not only to develop diabetes, but to recruit autoreactive CD4 T cells into islets of NOD mice, perhaps in response to progressive {beta} cell damage.

immunology↗

bioRxiv2022

A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize (Zea mays).

Two major groups of maize (Zea mays) specialized metabolites, termed kauralexins and dolabralexins, serve as known or predicted diterpenoid defenses against pathogens, herbivores, and other environmental stressors. To consider physiological roles of the recently discovered dolabralexin pathway, we examined dolabralexin structural diversity, tissue-specificity, and stress-elicited production in a defined biosynthetic pathway mutant. Metabolomics analyses support a larger number of dolabralexin pathway products than previously known. We identified dolabradienol as a previously undetected pathway metabolite and characterized its enzymatic production. Transcript and metabolite profiling showed that dolabralexin biosynthesis and accumulation predominantly occurs in primary roots and shows quantitative variation across genetically diverse inbred lines. Generation and analysis of CRISPR-Cas9-derived loss-of- function Kaurene Synthase-Like 4 (Zmksl4) mutants demonstrated dolabralexin production deficiency, thus supporting ZmKSL4 as the diterpene synthase responsible for the conversion of geranylgeranyl pyrophosphate precursors into dolabradiene and downstream pathway products. Zmksl4 mutants further display altered root-to-shoot ratios and root architecture in response to water deficit, consistent with an interactive role of maize dolabralexins in plant vigor during abiotic stress.

plant biology↗

bioRxiv2021

The conventional dendritic cell 1 subset primes CD8+ T cells and traffics tumor antigen to drive anti-tumor immunity in the brain

The central nervous system (CNS) antigen presenting cell (APC) which primes anti-tumor CD8+ T cell responses remains undefined. Elsewhere, the conventional dendritic cell 1 (cDC1) performs this role. However, steady-state brain cDC1 are rare; cDC localize to choroid plexus and dura. Using preclinical glioblastoma models and cDC1-deficient mice, we explored the role of cDC1 in CNS anti-tumor immunity. We determined that cDC1 mediate checkpoint blockade-induced survival benefit and prime neoantigen-specific CD8+ T cells against brain tumors. We observed that cDC, including cDC1, isolated from the tumor, the dura, and the CNS-draining cervical lymph nodes harbored a traceable fluorescent tumor-antigen. In patient samples, we observed several APC subsets (including the CD141+ cDC1-equivalent) infiltrating glioblastomas, meningiomas, and dura. In these same subsets, we identified a tumor-specific fluorescent metabolite of 5- aminolevulinic acid, which labels tumor cells during fluorescence-guided glioblastoma resection. Together, these data elucidate the specialized behavior of cDC1 and suggest cDC1 play a significant role in CNS anti-tumor immunity. One Sentence SummaryCNS cDC1 engage in previously undefined behavior to establish immune responses against brain tumors.

immunology↗

bioRxiv2021

BCL6-dependent TCF-1+ progenitor cells maintain effector and helper CD4 T cell responses to persistent antigen

Shortly after priming, the fate of activated CD4 T cells is segregated into BCL6+ follicular helper T (Tfh) and BCL6- effector (Teff) cells. However, it remains unknown how these subsets are sustained in the presence of chronic antigen stimulation. Using a combination of single cell- and population-based approaches, we show that in chronic viral infection, activated CD4 T cells differentiate into BCL6-dependent TCF-1+ progenitor cells with superior capacity to expand and give rise to both Teff and Tfh. They share properties with progenitor-exhausted CD8 T cells and are required for the continued generation of Teff cells as antigen persists. In response to tumors, an analogous CD4 T cell population develops in draining lymph nodes. Our study reveals the heterogeneity and plasticity of CD4 T cells upon encountering persistent antigen and highlights their population dynamics through a stable bipotent intermediate state.

immunology↗

bioRxiv2021

A Practical Guide to Sparse Clustering for Studying Molecular Development of the Human Brain

Studying the molecular development of the human brain presents unique challenges for selecting a data analysis approach. The rare and valuable nature of human postmortem brain tissue, especially for developmental studies, means the sample sizes are small (n), but the use of high throughput genomic and proteomic methods measure the expression levels for hundreds or thousands of variables (e.g. genes or proteins (p)) for each sample. This leads to a data structure that is high dimensional (p >> n) and introduces the curse of dimensionality, which poses a challenge for traditional statistical approaches. In contrast, high dimensional analyses, especially cluster analyses developed for sparse data, have worked well for analyzing genomic datasets where p >> n. Here we explore applying a lasso-based clustering method developed for high dimensional genomic data with small sample sizes. Using protein and gene data from the developing human visual cortex, we compared clustering methods. We identified an application of sparse K-means clustering (Robust Sparse K-means Clustering (RSKC)) that partitioned samples into age-related clusters that reflect lifespan stages from birth to aging. RSKC adaptively selects a subset of the genes or proteins contributing to partitioning samples into age-related clusters that progress across the lifespan. This approach addresses a problem in current studies that could not identify multiple postnatal clusters. Moreover, clusters encompassed a range of ages like a series of overlapping waves illustrating that chronological- and brain-age have a complex relationship. In addition, a recently developed workflow to create plasticity phenotypes (Balsor et al., 2020) was applied to the clusters and revealed neurobiologically relevant features that identified how the human visual cortex changes across the lifespan. These methods can help address the growing demand for multimodal integration, from molecular machinery to brain imaging signals, to understand the human brains development.

neuroscience↗

bioRxiv2020

cDC1 Coordinate Innate and Adaptive Responses in the Omentum required for T cell Priming and Memory

The omentum in the peritoneal cavity contains fat associated lymphoid clusters (FALCs) whose role in the response to microbial challenge are poorly understood. After intraperitoneal immunization with Toxoplasma gondii, type I dendritic cells (cDC1) were critical to induce innate sources of IFN-{gamma} required to recruit monocytes to the FALCs. The migration of infected peritoneal macrophages into T and B cell rich areas of the FALCs allowed the TCR-induced activation of parasite-specific T cells. Unexpectedly, cDC1 were not required for T cell priming but rather supported the expansion of parasite-specific CD8+ T cells. An agent-based mathematical model predicted that the lack of cDC1 would impact the early proliferative burst, and we confirmed that cDC1 were required for optimal T cell expression of nutrient uptake receptors and cell survival. These studies highlight that cDC1 in the FALCs have distinct roles in the co-ordination of the innate and adaptive responses to microbial challenge.

immunology↗

bioRxiv2020

Genetic elucidation of complex biochemical traits mediating maize innate immunity

Specialized metabolites constitute key layers of immunity underlying crop resistance; however, challenges in resolving complex pathways limit our understanding of their functions and applications. In maize (Zea mays) the inducible accumulation of acidic terpenoids is increasingly considered as a defense regulating disease resistance. To understand maize antibiotic biosynthesis, we integrated association mapping, pan-genome multi-omic correlations, enzyme structure-function studies, and targeted mutagenesis. We now define ten genes in three zealexin (Zx) gene clusters comprised of four sesquiterpene synthases and six cytochrome P450s that collectively drive the production of diverse antibiotic cocktails. Quadruple mutants blocked in the production of {beta}-macrocarpene exhibit a broad-spectrum loss of disease resistance. Genetic redundancies ensuring pathway resiliency to single null mutations are combined with enzyme substrate-promiscuity creating a biosynthetic hourglass pathway utilizing diverse substrates and in vivo combinatorial chemistry to yield complex antibiotic blends. The elucidated genetic basis of biochemical phenotypes underlying disease resistance demonstrates a predominant maize defense pathway and informs innovative strategies for transferring chemical immunity between crops.

plant biology↗

bioRxiv2020

Constructing plasticity phenotypes to classify experience-dependent development of the visual cortex

Many neural mechanisms regulate experience-dependent plasticity in the visual cortex (V1) and new techniques for quantifying large numbers of proteins or genes are transforming how plasticity is studied into the era of big data. With those large data sets comes the challenge of extracting biologically meaningful results about visual plasticity from data-driven analytical methods designed for high-dimensional data. In other areas of neuroscience, high-information content methodologies are revealing more subtle aspects of neural development and individual variations that give rise to a richer picture of brain disorders. We have developed an approach for studying V1 plasticity that takes advantage of the known functions of many synaptic proteins for regulating visual plasticity and using that to rebrand the results of high-dimensional analyses into a plasticity phenotype. Here we provide a primer for analyzing experience-dependent plasticity in V1 using example R code to identify high-dimensional changes in a group of proteins. We describe using PCA to classify high-dimensional plasticity features and use them to construct a plasticity phenotype. In the examples, we show how the plasticity phenotype can be visualized and used to identify neurobiological features in V1 that change during development or after different visual rearing conditions. We include an R package "v1hdexplorer" that aggregates the various coding packages and custom visualization scripts written in R Studio.

neuroscience↗

bioRxiv2019

Recovery of glutamatergic and GABAergic protein expression in visual cortex after monocular deprivation

A collection of glutamatergic and GABAergic proteins participate in regulating experience-dependent plasticity in the visual cortex (V1). Many studies have characterized changes to those proteins caused by monocular deprivation (MD) during the critical period (CP), but less is known about changes that occur when MD stops. We measured the effects of 3 types of visual experience after MD (n=24, 10 male and 14 female); reverse occlusion (RO), binocular deprivation (BD), or binocular vision, on the expression of synaptic proteins in V1 including glutamatergic and GABAergic receptor subunits. Synapsin expression was increased by RO but not affected by the other treatments. BD shifted the balance between glutamatergic and GABAergic receptor subunits to favor GABAA1. In contrast, BV shifted expression to favor the glutamatergic mechanisms by increasing NMDAR and decreasing GABAA1 subunits. None of the conditions returned normal expression levels to all of the proteins, but BV was the closest.

neuroscience↗

bioRxiv2019

Toxoplasma gondii infection drives conversion of NK Cells into ILC1s

Innate lymphoid cells (ILCs) were originally classified based on their cytokine profiles, placing natural killer (NK) cells and ILC1s together, but recent studies support their separation into different lineages at steady-state. However, tumors may induce NK cell conversion into ILC1-like cells that are limited to the tumor microenvironment and whether this conversion occurs beyond this environment remains unknown. Here we describe Toxoplasma gondii infection converts NK cells into cells resembling steady-state ILC1s that are heterogeneous and distinct from both steady-state NK cells and ILC1s in uninfected mice. Most toxoplasma-induced ILC1s were Eomes-dependent, indicating that NK cells can give rise to Eomes- Tbet-dependent ILC1-like cells that circulate widely and persist independent of ongoing infection. Moreover, these changes appear permanent, as supported by epigenetic analyses. Thus, these studies markedly expand current concepts of NK cells, ILCs, and their potential conversion.

immunology↗

bioRxiv2019

A primer on high-dimensional data analysis workflows for studying visual cortex development and plasticity

New techniques for quantifying large numbers of proteins or genes are transforming the study of plasticity mechanisms in visual cortex (V1) into the era of big data. With those changes comes the challenge of applying new analytical methods designed for high-dimensional data. Studies of V1, however, can take advantage of the known functions that many proteins have in regulating experience-dependent plasticity to facilitate linking big data analyses with neurobiological functions. Here we discuss two workflows and provide example R code for analyzing high-dimensional changes in a group of proteins (or genes) using two data sets. The first data set includes 7 neural proteins, 9 visual conditions, and 3 regions in V1 from an animal model for amblyopia. The second data set includes 23 neural proteins and 31 ages (20d-80yrs) from human post-mortem samples of V1. Each data set presents different challenges and we describe using PCA, tSNE, and various clustering algorithms including sparse high-dimensional clustering. Also, we describe a new approach for identifying high-dimensional features and using them to construct a plasticity phenotype that identifies neurobiological differences among clusters. We include an R package "v1hdexplorer" that aggregates the various coding packages and custom visualization scripts written in R Studio.

neuroscience↗

bioRxiv2019

Classification of visual cortex plasticity phenotypes following treatment for amblyopia

Monocular deprivation (MD) during the critical period (CP) has enduring effects on visual acuity and the functioning of the visual cortex (V1). This experience-dependent plasticity has become a model for studying the mechanisms, especially glutamatergic and GABAergic receptors, that regulate amblyopia. Less is known, however, about treatment-induced changes to those receptors and if those changes differentiate treatments that support the recovery of acuity versus persistent acuity deficits. Here we use an animal model to explore the effects of 3 visual treatments started during the CP (n=24, 10 male and 14 female); binocular vision (BV) that promotes good acuity versus reverse occlusion (RO) and binocular deprivation (BD) that causes persistent acuity deficits. We measured recovery of a collection of glutamatergic and GABAergic receptor subunits in V1 and modeled recovery of kinetics for NMDAR and GABAAR. There was a complex pattern of protein changes that prompted us to develop an unbiased data-driven approach for these high-dimensional data analyses to identify plasticity features and construct plasticity phenotypes. Cluster analysis of the plasticity phenotypes suggests that BV supports adaptive plasticity while RO and BD promote a maladaptive pattern. The RO plasticity phenotype appeared more similar to adults with high expression of GluA2 and the BD phenotypes were dominated by GABAA1, highlighting that multiple plasticity phenotypes can underlie persistent poor acuity. After 2-4 days of BV the plasticity phenotypes resembled normals, but only one feature, the GluN2A:GluA2 balance, returned to normal levels. Perhaps, balancing Hebbian (GluN2A) and homeostatic (GluA2) mechanisms is necessary for the recovery of vision.

neuroscience↗