Biology subjects

Wright, S. J.

Publications and source records attributed to Wright, S. J..

12 recordsLinked to original sources

bioRxiv2026

An Nrf2-Nup214 positive feedback loop sustains the antioxidant response and promotes microbial infection in ticks

Ixodes scapularis ticks are obligate hematophagous ectoparasites that take a single bloodmeal per life stage. During blood digestion, large quantities of heme and iron are released, leading to the production of reactive oxygen species. To counter the oxidative stress, ticks have evolved robust antioxidant systems. We previously found that the antioxidant transcription factor Nrf2 is activated during infection and supports Anaplasma phagocytophilum colonization in ticks. To investigate the Nrf2 regulatory network, we queried promoter regions in the Ixodes genome for Nrf2 binding sites. The gene encoding the nuclear pore complex protein nucleoporin 214 was identified as a target that is induced during Anaplasma infection and putatively regulated by Nrf2. Ixodes nup214 was experimentally validated as an Nrf2-regulated gene through functional luciferase reporter assays, pharmacological manipulation, and RNA interference transcriptional repression. We found that elevated expression of Nup214 leads to binding of the nuclear export protein CRM1, thereby trapping Nrf2 in the nucleus. Increased nuclear retention of Nrf2 prolonged the antioxidant response and functionally supported Anaplasma survival. Our findings uncover a previously unknown mechanism potentiated by Nrf2 that supports Anaplasma infection in ticks. SIGNIFICANCETicks have evolved to rely on host blood for nutrition and development. However, blood feeding comes with drawbacks. During digestion, large quantities of heme and iron are released, which promote the production of reactive oxygen species. To counter this, ticks have evolved robust antioxidant responses to protect themselves against oxidative stress. How tick-transmitted microbes, such as Anaplasma phagocytophilum, withstand the oxidative challenge in the tick is not well understood. Here, we demonstrate that, during infection, host-driven antioxidant defenses coordinated by the transcription factor Nrf2 support Anaplasma infection and persistence in ticks. We show that Nrf2 upregulates the nuclear pore complex protein Nucleoporin 214, which sequesters Nrf2 in the nucleus. The prolonged nuclear retention of Nrf2 enhances the tick antioxidant response, thereby supporting Anaplasma survival in the arthropod vector.

microbiology↗

bioRxiv2025

ATF6 enables pathogen infection in ticks by inducing stomatin and altering cholesterol dynamics

How tick-borne pathogens interact with their hosts has been primarily studied in vertebrates where disease is observed. Comparatively less is known about pathogen interactions within the tick. Here, we report that Ixodes scapularis ticks infected with either Anaplasma phagocytophilum (causative agent of anaplasmosis) or Borrelia burgdorferi (causative agent of Lyme disease) show activation of the ATF6 branch of the unfolded protein response (UPR). Disabling ATF6 functionally restricts pathogen survival in ticks. When stimulated, ATF6 functions as a transcription factor, but is the least understood out of the three UPR pathways. To interrogate the Ixodes ATF6 transcriptional network, we developed a custom R script to query tick promoter sequences. This revealed stomatin as a potential gene target, which has roles in lipid homeostasis and vesical transport. Ixodes stomatin was experimentally validated as a bona fide ATF6-regulated gene through luciferase reporter assays, pharmacological activators, and RNAi transcriptional repression. Silencing stomatin decreased A. phagocytophilum colonization in Ixodes and disrupted cholesterol dynamics in tick cells. Furthermore, blocking stomatin restricted cholesterol availability to the bacterium, thereby inhibiting growth and survival. Taken together, we have identified the Ixodes ATF6 pathway as a novel contributor to vector competence through Stomatin-regulated cholesterol homeostasis. Moreover, our custom, web-based transcription factor binding site search tool "ArthroQuest" revealed that the ATF6-regulated nature of stomatin is unique to blood-feeding arthropods. Collectively, these findings highlight the importance of studying fundamental processes in non-model organisms. IMPORTANCEHost-pathogen interactions for tick-borne pathogens like Anaplasma phagocytophilum (causative agent of Anaplasmosis) have been primarily studied in mammalian hosts. Comparatively less is known about interactions within the tick. Herein, we find that tick-borne pathogens activate the cellular stress response receptor, ATF6, in Ixodes ticks. Upon activation, ATF6 is cleaved and the cytosolic portion translocates to the nucleus to function as a transcription factor that coordinates gene expression networks. Using a custom script in R to query the Ixodes ATF6 regulome, stomatin was identified as an ATF6-regulated target that supports Anaplasma colonization by facilitating cholesterol availability to the bacterium. Moreover, our custom, web-based tool "ArthroQuest" found that the ATF6-regulated nature of stomatin is unique to arthropods. Given that lipid hijacking is common among arthropod-borne microbes, ATF6-mediated induction of stomatin may be a mechanism that is exploited in many vector-pathogen relationships for the survival and persistence of transmissible microbes. Collectively, this study identified a novel contributor to vector competence and highlights the importance of studying molecular networks in non-model organisms.

microbiology↗

bioRxiv2024

Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system

Providencia alcalifaciens is a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. Specific P. alcalifaciens strains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are also pathogenic determinants in P. alcalifaciens is not known. Here we have used P. alcalifaciens 205/92, a clinical isolate, with in vitro and in vivo infection models to investigate P. alcalifaciens-host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS1b is widespread in Providencia spp. and encoded on the chromosome. T3SS1a is encoded on a large plasmid that is present in a subset of P. alcalifaciens strains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS1a in entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS1a or T3SS1b was seen in the calf infection model. However, T3SS1b was required for the rapid killing of Drosophila melanogaster. We propose that the acquisition of two T3SS by horizontal gene transfer has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.

microbiology↗

bioRxiv2024

Disrupting CD38-driven T cell dysfunction restores sensitivity to cancer immunotherapy

A central problem in cancer immunotherapy with immune checkpoint blockade (ICB) is the development of resistance, which affects 50% of patients with metastatic melanoma1,2. T cell exhaustion, resulting from chronic antigen exposure in the tumour microenvironment, is a major driver of ICB resistance3. Here, we show that CD38, an ecto-enzyme involved in nicotinamide adenine dinucleotide (NAD+) catabolism, is highly expressed in exhausted CD8+ T cells in melanoma and is associated with ICB resistance. Tumour-derived CD38hiCD8+ T cells are dysfunctional, characterised by impaired proliferative capacity, effector function, and dysregulated mitochondrial bioenergetics. Genetic and pharmacological blockade of CD38 in murine and patient-derived organotypic tumour models (MDOTS/PDOTS) enhanced tumour immunity and overcame ICB resistance. Mechanistically, disrupting CD38 activity in T cells restored cellular NAD+ pools, improved mitochondrial function, increased proliferation, augmented effector function, and restored ICB sensitivity. Taken together, these data demonstrate a role for the CD38-NAD+ axis in promoting T cell exhaustion and ICB resistance, and establish the efficacy of CD38 directed therapeutic strategies to overcome ICB resistance using clinically relevant, patient-derived 3D tumour models.

cancer biology↗

bioRxiv2023

PERK-mediated antioxidant response is key for pathogen persistence in ticks

A crucial phase in the lifecycle of tick-borne pathogens is the time spent colonizing and persisting within the arthropod. Tick immunity is emerging as a key force shaping how transmissible pathogens interact with the vector. How pathogens remain in the tick despite immunological pressure remains unknown. In persistently infected Ixodes scapularis, we found that Borrelia burgdorferi (Lyme disease) and Anaplasma phagocytophilum (granulocytic anaplasmosis) activate a cellular stress pathway mediated by the endoplasmic reticulum receptor PERK and the central regulatory molecule, eIF2. Disabling the PERK pathway through pharmacological inhibition and RNAi significantly decreased microbial numbers. In vivo RNA interference of the PERK pathway not only reduced the number of A. phagocytophilum and B. burgdorferi colonizing larvae after a bloodmeal, but also significantly reduced the number of bacteria that survive the molt. An investigation into PERK pathway-regulated targets revealed that A. phagocytophilum and B. burgdorferi induce activity of the antioxidant response regulator, Nrf2. Tick cells deficient for nrf2 expression or PERK signaling showed accumulation of reactive oxygen and nitrogen species in addition to reduced microbial survival. Supplementation with antioxidants rescued the microbicidal phenotype caused by blocking the PERK pathway. Altogether, our study demonstrates that the Ixodes PERK pathway is activated by transmissible microbes and facilitates persistence in the arthropod by potentiating an Nrf2-regulated antioxidant environment.

microbiology↗

bioRxiv2023

Functional traits of young seedlings predict trade-offs in seedling performance in three neotropical forests.

O_LIUnderstanding the mechanisms that promote the coexistence of hundreds of species over small areas in tropical forest remains a challenge. Many tropical tree species are presumed to be functionally equivalent shade tolerant species that differ in performance trade-offs between survival in shade and the ability to quickly grow in sunlight. C_LIO_LIVariation in plant functional traits related to resource acquisition is thought to predict variation in performance among species, perhaps explaining community assembly across habitats with gradients in resource availability. Many studies have found low predictive power, however, when linking trait measurements to species demographic rates. C_LIO_LISeedlings face different challenges recruiting on the forest floor and may exhibit different traits and/or performance trade-offs than older individuals face in the eventual adult niche. Seed mass is the typical proxy for seedling success, but species also differ in cotyledon strategy (reserve vs photosynthetic) or other seedling traits. These can cause species with the same average seed mass to have divergent performance in the same habitat. C_LIO_LIWe combined long-term studies of seedling dynamics with functional trait data collected at a standard developmental stage in three diverse neotropical forests to ask whether variation in coordinated suites of traits predicts variation among species in demographic performance. C_LIO_LIAcross hundreds of species in Ecuador, Panama, and Puerto Rico, we found seedlings displayed correlated suites of leaf, stem, and root traits, which strongly correlated with seed mass and cotyledon strategy. Variation among species in seedling functional traits, seed mass, and cotyledon strategy were strong predictors of trade-offs in seedling growth and survival. C_LIO_LIOur findings highlight the importance of cotyledon strategy in addition to seed mass as a key component of seed and seedling biology. These results also underscore the importance of matching the ontogenetic stage of the trait measurement to the stage of demographic dynamics. C_LIO_LISynthesis: With strikingly consistent patterns across three tropical forests, we find strong evidence for the promise of functional traits to provide mechanistic links between seedling form and demographic performance. C_LI

ecology↗

bioRxiv2022

Density dependence generates spatial overdispersion in adult tropical trees

For species to coexist, performance must decline as the density of conspecific individuals increases. Although evidence for such Conspecific Negative Density Dependence (CNDD) exists in forests, the spatial repulsion it should produce has not been demonstrated in adults. Here we show that in comparison to a null model of stochastic birth, death and limited dispersal, the adults of dozens of tropical forest tree species show almost ubiquitous and strong spatial repulsion, some to surprising distances of ~100 meters. We use simulations to show such strong repulsion can only occur if CNDD considerably exceeds Heterospecific Negative Density Dependence, an even stronger condition required for coexistence, and that large-scale repulsion can indeed result from small-scale CNDD. These results highlight the power of limited dispersal spatial null models. One-Sentence SummarySpatial distributions of tropical trees reflect a strong negative effect of conspecifics, exceeding that of heterospecifics

ecology↗

bioRxiv2021

Multi-scale phenological niches in diverse Amazonian plant communities

Phenology has long been hypothesized as an avenue for niche partitioning or interspecific facilitation, both promoting species coexistence. Tropical plant communities exhibit striking diversity in reproductive phenology, but many are also noted for large synchronous reproductive events. Here we study whether the phenology of seed fall in such communities is non-random, what are the temporal scales of phenological patterns, and ecological factors that drive reproductive phenology. We applied multivariate wavelet analyses to test for phenological synchrony versus compensatory dynamics (i.e. anti-synchronous patterns where one species decline is compensated by the rise of another) among species and across temporal scales. We used data from long-term seed rain monitoring of hyperdiverse plant communities in the western Amazon. We found significant synchronous whole-community phenology at multiple time scales, consistent with shared environmental responses or positive interactions among species. We also observed both compensatory and synchronous phenology within groups of species likely to share traits (confamilials) and seed dispersal mechanisms. Wind-dispersed species exhibited significant synchrony at ~6 mo scales, suggesting these species share phenological niches to match seasonality of wind. Our results suggest that community phenology is shaped by shared environmental responses but that the diversity of tropical plant phenology may partly result from temporal niche partitioning. The scale-specificity and time-localized nature of community phenology patterns highlights the importance of multiple and shifting drivers of phenology. Open research statementData are provided as private-for-peer review. Code and data can be found at https://github.com/pakdamie/treephenology which is currently public. This submission does not use novel code.

ecology↗

bioRxiv2019

Predicting kinase inhibitors using bioactivity matrix derived informer sets

Prediction of compounds that are active against a desired biological target is a common step in drug discovery efforts. Virtual screening methods seek some active-enriched fraction of a library for experimental testing. Where data are too scarce to train supervised learning models for compound prioritization, initial screening must provide the necessary data. Commonly, such an initial library is selected on the basis of chemical diversity by some pseudo-random process (for example, the first few plates of a larger library) or by selecting an entire smaller library. These approaches may not produce a sufficient number or diversity of actives. An alternative approach is to select an informer set of screening compounds on the basis of chemogenomic information from previous testing of compounds against a large number of targets. We compare different ways of using chemogenomic data to choose a small informer set of compounds based on previously measured bioactivity data. We develop this Informer-Based-Ranking (IBR) approach using the Published Kinase Inhibitor Sets (PKIS) as the chemogenomic data to select the informer sets. We test the informer compounds on a target that is not part of the chemogenomic data, then predict the activity of the remaining compounds based on the experimental informer data and the chemogenomic data. Through new chemical screening experiments, we demonstrate the utility of IBR strategies in a prospective test on two kinase targets not included in the PKIS. Using limited training data in both retrospective and prospective tests, bioactivity fingerprints based on chemogenomic data outperform chemical fingerprints in predicting active compounds in both standard virtual screening metrics and accurate identification of hits from novel chemical classes. Author SummaryIn the early stages of drug discovery efforts, computational models are used to predict activity and prioritize compounds for experimental testing. New targets commonly lack the data necessary to build effective models, and the screening needed to generate that experimental data can be costly. We seek to improve the efficiency of the initial screening phase, and of the process of prioritizing compounds for subsequent screening. We choose a small informer set of compounds based on publicly available prior screening data on distinct (though related) targets. We then use experimental data on these informer compounds to predict the activity of other compounds in the set against the target of interest. Computational and statistical tools are needed to identify informer compounds and to prioritize other compounds for subsequent phases of screening. Using limited training data, we find that selection of informer compounds on the basis of bioactivity data from previous screening efforts is superior to the traditional approach of selection of a chemically diverse subset of compounds. We demonstrate the success of this approach in retrospective tests on the Published Kinase Inhibitor Sets (PKIS) chemogenomic data and in prospective experimental screens against two additional non-human kinase targets.

pharmacology and toxicology↗

bioRxiv2018

Comparative metabolomics of forest communities: Species differences in foliar chemistry are greater in the tropics.

Interspecific variation in the secondary metabolites of plants constrains host specificity of insect herbivores and microbial pathogens. The intensity and specificity of these plant-pest interactions is widely believed to increase towards the Equator, leading to the prediction that secondary metabolites should differ more among co-occurring plant species in tropical communities than in temperate communities. To evaluate this prediction, we quantified metabolomic similarity for 203 tree species that represent >89% of all individuals in large forest plots in Maryland and Panama. We constructed molecular networks based on mass spectrometry of all 203 species, quantified metabolomic similarity for all pairwise combinations of species, and evaluated how pairwise metabolomic similarity varies phylogenetically. Leaf metabolomes exhibited clear phylogenetic signal for the temperate plot, with high similarity among congeneric species. In contrast, leaf metabolomes lacked phylogenetic signal for the tropical plot, with low similarity among congeners. Our results suggest that species differences in secondary chemistry comprise important axes of niche differentiation among tropical trees, especially within species-rich genera, and that the contribution of species differences in secondary chemistry to niche differences increases towards the equator in forest tree communities.

ecology↗

bioRxiv2017

Unifying intra- and inter-specific variation in tropical tree mortality

Tree death is a fundamental process driving population dynamics, nutrient cycling, and evolution within plant communities. While past research has identified factors influencing tree mortality across a variety of scales, these distinct drivers are yet to be integrated within a unified predictive framework. In this study, we use a cross-validated Bayesian framework coupled with classic survival analysis techniques to derive instantaneous mortality functions for 203 tropical rainforest tree species at Barro Colorado Island (BCI) Panama. Specifically, we develop mortality functions that not only integrate individual, species, and temporal effects, but also partition the contributions of growth-dependent and growth-independent effects on the overall instantaneous mortality rate. We show that functions that separate mortality rates into growth-dependent and growth-independent hazards, use stem diameter growth rather than basal-area growth, and attribute the effect of wood density to growth-independent mortality outperform alternative formulations. Moreover, we show that the effect of wood density - a prominent trait known to influence tree mortality - explains only 22% of the total variability observed among species. Lastly, our analysis show that growth-dependent processes are the predominant contributor to rates of tree mortality at BCI. Combined, this study provides a framework for predicting individual-level mortality in highly diverse tropical forests. It also highlights how little we know about the causes of species-level and temporal plot-scale effects needed to effectively predict tree mortality.

ecology↗

bioRxiv2017

Decomposing leaf mass into photosynthetic and structural components explains divergent patterns of trait variation within and among plant species

O_LIAcross the global flora, interspecific variation in photosynthetic and metabolic rates depends more strongly on leaf area than leaf mass. In contrast, intraspecific variation in these rates is strongly mass-dependent. These contrasting patterns suggest that the causes of variation in leaf mass per area (LMA) may be fundamentally different within vs. among species. C_LIO_LIWe developed a statistical modeling framework to decompose LMA into two conceptual components - metabolic LMAm (which determines photosynthetic capacity and dark respiration) and structural LMAs (which determines leaf toughness and potential leaf lifespan) - using leaf trait data from tropical forests in Panama and a global leaf-trait database. C_LIO_LIDecomposing LMA into LMAm and LMAs improves predictions of leaf trait variation (photosynthesis, respiration, and lifespan). We show that strong area-dependence of metabolic traits across species can result from multiple factors, including high LMAs variance and/or a slow increase in photosynthetic capacity with increasing LMAm. In contrast, strong mass-dependence of metabolic traits within species results from LMAm increasing from sunny to shady conditions. LMAm and LMAs were nearly independent of each other in both global and Panama datasets. C_LIO_LISynthesis: Our results suggest that leaf functional variation is multi-dimensional and that biogeochemical models should treat metabolic and structural leaf components separately. C_LI

ecology↗