Biology subjects

Cook, B.

Publications and source records attributed to Cook, B..

9 recordsLinked to original sources

bioRxiv2026

Gene model for the ortholog of raptor in Drosophila erecta

Gene model for the ortholog of raptor in the May 2011 (Agencourt Dere_CAF1/DereCAF1) Genome Assembly (GenBank Accession: GCA_000005135.1) of Drosophila erecta. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

bioRxiv2025

The Anti-Inflammatory Role of GPNMB in Post-Traumatic Osteoarthritis

Osteoactivin (GPNMB) is a transmembrane protein expressed in multiple cell types with known functions in muscle, bone, and neurons, but the role of GPNMB in chondrocytes and cartilage homeostasis remains unknown. Here we show GPNMB/Gpnmb is expressed in human and mouse primary chondrocytes, and that its expression is increased in damaged human cartilage and under pro-inflammatory conditions. We report that recombinant GPNMB treatment inhibits the expression of Mmps (Mmp3, 9, and 13), Adamts4 and Il6 following IL-1{beta}-stimulation in vitro. In vivo, GPNMB function was assessed in a post-traumatic osteoarthritis model, destabilization of the medial meniscus (DMM). Transgenic animals lacking functional GPNMB protein (DBA/2J) developed severe cartilage damage and demonstrated significant increases in pro-inflammatory cytokine expression following DMM. To elucidate the mechanism of action, we demonstrate that GPNMB regulates the MAPK signaling pathway via pERK inhibition in primary murine chondrocytes. Taken together, our results identify a novel anti-inflammatory role for GPNMB in cartilage and chondrocytes and identify GPNMB as a potential therapeutic modality for inflammatory joint diseases.

cell biology↗

bioRxiv2025

Short 5' UTRs serve as a marker for viral mRNA translation inhibition by the IFIT2-IFIT3 antiviral complex

Recognition of "non-self" nucleic acids, including cytoplasmic dsDNA, dsRNA, or mRNAs lacking proper 5 cap structures, is critical for the innate immune response to viruses. Here, we demonstrate that short 5 untranslated regions (UTRs), a characteristic of many viral mRNAs, can also serve as a molecular pattern for innate immune recognition via the interferon-induced proteins IFIT2 and IFIT3. The IFIT2-IFIT3 heterodimer, formed through an intricate domain swap structure resolved by cryo-EM, mediates viral mRNA 5 end recognition, translation inhibition, and ultimately antiviral activity. Critically, 5 UTR lengths <50 nucleotides are necessary and sufficient to sensitize an mRNA to translation inhibition by the IFIT2-IFIT3 complex. Accordingly, diverse viruses whose mRNAs contain short 5 UTRs, such as vesicular stomatitis virus and parainfluenza virus 3, are sensitive to IFIT2-IFIT3-mediated antiviral activity. Our work thus reveals a pattern of antiviral nucleic acid immune recognition that takes advantage of the inherent constraints on viral genome size.

microbiology↗

bioRxiv2024

Characterization of age-associated inflammasome activation reveals tissue specific differences in transcriptional and post-translational inflammatory responses

Aging is associated with systemic chronic, low-grade inflammation, termed inflammaging. This pattern of inflammation is multifactorial and is driven by numerous inflammatory pathways, including the inflammasome. However, most studies to date have examined changes in the transcriptomes that are associated with aging and inflammaging, despite the fact that inflammasome activation is driven by a series of post-translational activation steps, culminating in the cleavage and activation of caspase-1. Here, we utilized transgenic mice expressing a caspase-1 biosensor to examine age-associated inflammasome activation in various organs and tissues to define these post-translational manifestations of inflammaging. Consistent with other studies, we observe increased inflammation, including inflammasome activation, in tissues. However, we note that the degree of inflammasome activation is not uniformly correlated with transcriptional changes commonly used as a surrogate for inflammasome activation in tissues. Furthermore, we used a skull thinning technique to monitor central nervous system inflammasome activation in vivo in aged mice and found that neuroinflammation is significantly amplified in aged mice in response to endotoxin challenge. Together, these data reveal that inflammaging is associated with both transcriptional and post-translational inflammatory pathways that are not uniform between tissues and establish new methodologies for measuring age-associated inflammasome activation in vivo and ex vivo.

immunology↗

bioRxiv2022

Herbarium records provide reliable phenology estimates in the understudied tropics

Plant phenology has been shifting dramatically in response to climate change, a shift that may have significant and widespread ecological consequences. Of particular concern are tropical biomes, which represent the most biodiverse and imperiled regions of the world. However, compared to temperate floras, we know little about phenological responses of tropical plants because long-term observational datasets from the tropics are sparse. Herbarium specimens have greatly increased our phenological knowledge in temperate regions, but similar data have been underutilized in the tropics and their suitability for this purpose has not been broadly validated. Here, we compare phenological estimates derived from field observational data (i.e., plot surveys) and herbarium specimens at various spatial and taxonomic scales to determine whether specimens can provide accurate estimations of reproductive timing and its spatial variation. Here we demonstrate that phenological estimates from field observations and herbarium specimens coincide well. Fewer than 5% of the species exhibited significant differences between flowering periods inferred from field observations versus specimens regardless of spatial aggregation. In contrast to studies based on field records, herbarium specimens sampled much larger geographic and climatic ranges, as has been documented previously for temperate plants, and effectively captured phenological responses across varied environments. Herbarium specimens are verified to be a vital resource for closing the gap in our phenological knowledge of tropical systems. Tropical plant reproductive phenology inferred from herbarium records are widely congruent with field observations, suggesting that they can (and should) be used to investigate phenological variation and their associated environmental cues more broadly across tropical biomes.

ecology↗

bioRxiv2020

Confinement size determines the architecture of Ran-induced microtubule networks

The organization of microtubules (MTs) within cells is critical for its internal organization during interphase and mitosis. During mitotic spindle assembly, MTs are made and organized around chromosomes in a process regulated by RanGTP. The role of RanGTP has been explored in Xenopus egg extracts, which are not limited by a cell membrane. Here, we investigated whether cell-sized confinements affect the assembly of RanGTP-induced MT networks in Xenopus egg extracts. We used microfluidics to encapsulate extract within monodisperse extract-in-oil droplets. Importantly, we find that the architecture of Ran-induced MT networks depends on the droplet diameter and the Ran concentration, and differs from structures formed in bulk extract. Our results highlight that both MT nucleation and physical confinement play critical roles in determining the spatial organization of the MT cytoskeleton. STATEMENT OF SIGNIFICANCEDuring cell division, chromosomes are segregated by the mitotic spindle, whose framework consists of up to hundreds of thousands of microtubules (MTs). Spindle MTs are generated via several pathways, one of which is regulated by RanGTP. Yet, how Ran-induced MTs self-organize within cell-sized confinement remains unclear. This work reports unexpected architectures of Ran-induced MT networks confined in cell-sized droplets, which depend on the droplet diameter and the RanGTP concentration. Thus, MT nucleation and confinement together give rise to specific MT network architectures, which are otherwise not observed in unconfined assays. The findings provide a simple strategy to engineer the architectures of MT networks and could have direct implications in nucleation-controlled soft material processing.

biophysics↗

bioRxiv2019

Cargo and Cell Specific Differences in Extracellular Vesicle Populations Identified by Multiplexed Immunofluorescent Analysis

Extracellular vesicles (EVs) are implicated in a wide variety of biological activities, have been implicated in the pathogenesis of numerous diseases, and have been proposed to serve as potential biomarkers of disease in human patients and animal models. However, characterization of EV populations is often performed using methods that do not account for heterogeneity of EV populations and require comparatively large sample sizes to facilitate analysis. Here, we describe an imaging-based method that allows for the multiplexed characterization of EV populations at the single EV level following centrifugation of EV populations directly onto cover slips, allowing comprehensive analysis of EV populations with relatively small samples. We observe that canonical EV markers are present on subsets of EVs which differ substantially in a producer cell and cargo specific fashion, including differences in EVs containing different HIV-1 proteins previously reported to be incorporated into pathogenic EVs. We also describe a lectin binding assay to interrogate EVs based on their glycan content, which we observe to change in response to pharmacological modulation of secretory autophagy pathways. These studies collectively reveal that multiplexed analysis of EV populations using fluorescent microscopy can reveal differences in specific EV populations that may be used to understand the biogenesis of specific EV populations or to interrogate small subsets of EVs of interest within larger EV populations.

cell biology↗

bioRxiv2019

Learning may help pollinators find their host plants in polluted landscapes

Pollination strongly contributes to food production, and often relies on pollinating insects. However, atmospheric pollution may interfere with pollination by disrupting floral plumes that pollinators use to navigate to flowers.\n\nIn this study, we examine the impacts of pollution-induced elevated ozone levels on the composition of a floral blend of Nicotiana alata and examine the response of innate and trained Manduca sexta to the ozone-altered blend.\n\nOzone exposure altered the floral blend of N. alata, and disrupted the innate attraction of naive M. sexta to the altered blend. However, associative learning can offset this disruption in attraction. Moths that were enticed with visual cues to an artificial flower emitting an ozonated blend learned to associate this blend with a nectar reward after just one rewarded experience. More importantly, moths that were rewarded while experiencing the unozonated floral blend of their host subsequently found the ozonated floral blend of the same host attractive, most likely due to experience-based reinforcement of ozone-insensitive cues in the blend.\n\nThe attraction of moths to both unaltered and ozonated plumes is critical for tolerating polluted landscapes. At the host plant, where moths feed, floral emissions are relatively pure. As floral odors travel away from the host, however, they become degraded by pollution. Therefore, targeting the flower requires recognizing both conditions of the odor. The ability to generalize between the pure and ozone-altered scents may enable pollinators like M. sexta to maintain communication with their flowers and reduce the impact anthropogenic oxidants may have on plant-pollinator systems.

animal behavior and cognition↗

bioRxiv2018

Roles for tubulin recruitment and self-organization by TOG domain arrays in Microtubule plus-end tracking and polymerase

The XMAP215/Stu2/Alp14 microtubule polymerases utilize Tumor Overexpressed Gene (TOG) domain arrays to accelerate microtubule plus-end polymerization. Structural studies suggest a microtubule polymerase model in which TOG arrays recruit four {beta}-tubulins, forming large square assemblies; an array of TOG1 and TOG2 domains may then unfurl from the square state to polymerize two {beta}-tubulins into protofilaments at microtubule ends. Here, we test this model using two biochemically characterized classes of fission yeast Alp14 mutants. Using in vitro reconstitution and in vivo live cell imaging, we show that {beta}-tubulins recruited by TOG1 and TOG2 domains serve non-additive roles in microtubule plus-end tracking and polymerase activities. Alp14 mutants with inactivated square assembly interfaces have defects in processive plus-end tracking and poor microtubule polymerase, indicating a functional role for square assemblies in processive tracking. These studies provide functional insights into how TOG1 and TOG2 domain arrays recruit tubulins and promote polymerase at microtubule plus ends.

biochemistry↗