Biology subjects

Hudson, L.

Publications and source records attributed to Hudson, L..

6 recordsLinked to original sources

bioRxiv2026

Lysine Demethylase 4A (KDM4A) Maintains Basal Body Architecture and Protects Against Ciliary Destabilization

Primary cilia are sensory organelles essential for signaling and defects in formation, maintenance or structure underlie diverse ciliopathies. Here, we identify lysine demethylase 4A (KDM4A) as a previously unrecognized mediator of ciliogenesis. Using genetic depletion and pharmacologic inhibition, we show that KDM4A is required for cilia assembly and maintenance. Super-resolution imaging reveals KDM4A localization at the basal body, where it distinctively wraps around the centrioles. We uncover a direct interaction between KDM4A and Rootletin (CROCC), a structural protein mediating centriole cohesion, and demonstrate that KDM4A loss increases inter-centriolar distances, implicating basal body architecture in ciliary failure. Together, these findings define a demethylase-centrosome axis that integrates KDM4A activity with organelle biology, revealing new mechanisms underlying ciliogenesis.

cell biology↗

bioRxiv2025

Structural Plasticity of RRE Stem-Loop II Modulates Nuclear Export of HIV-1 RNA

The Rev Response Element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 infection. However, our structural understanding of this crucial virological process remains limited. In this study, we determined several crystal structures of an intact RRE stem-loop II in two distinct conformations, performed negative-staining electron microscopy and molecular dynamics simulations, and revealed that this three-way junction RNA exhibits remarkable structural plasticity. Through in vitro Rev-binding and in vivo Rev-activity assays using various stem-loop II mutants designed to favor one of the conformers, we demonstrated that the structural plasticity of stem-loop II modulates Rev binding and oligomerization. Our findings illuminate emerging perspectives on RRE dynamics-based regulation of HIV-1 RNA nuclear export and provide a framework for developing anti-HIV drugs that target specific RRE conformations.

biophysics↗

bioRxiv2025

Phenological turnover matters when making trait-based predictions of plant-pollinator interactions

1. Understanding the processes determining species interactions is key to predicting and safeguarding ecological networks under rapid environmental change. One approach to estimating interactions is to use morphologies of taxa interacting across trophic levels to reveal suites of traits they are more likely to interact with (i.e. a trait niche). 2. Previous work studying these morphological trait niches has typically used interactions between species that are pooled in space and time. However, species assemblages, and the traits of individuals within species, can change across even small landscapes over a season, leading to morphological trait space being dynamically reshaped. Therefore, it is unclear how morphological trait turnover affects our inferences of trait niches, and our ability to answer this is in part limited by a lack of individual-level trait data. 3. Here, we directly address this by studying a montane Arctic plant-pollinator community over five growing seasons (>1,300 hours of fieldwork). Specifically, we linked every recorded plant-bumblebee interaction with the traits of the bee individual involved (n = 1,150), to investigate 1) whether plant taxa (n = 10) exhibited bee trait niches by interacting with specific regions of multidimensional trait space of visiting bumblebees, and 2) how our inference of these trait niches was affected by considering bumblebee trait turnover and plant taxon turnover. 4. When not considering turnover (interactions in space and time are pooled), plant taxa demonstrated bee trait niches. However, next we considered how bee trait space is reshaped over the elevational and seasonal gradient (especially with the emergence of different castes), and how this reshaping co-occurs with different spatiotemporal ranges of the plant taxa. From this we found the degree to which plant taxa exhibited trait niches declined significantly, and that seasonal reshaping of bee trait space was the primary driver of this trend. 5. Overall, in highly dynamic systems, like the Arctic, overlooking community turnover could mask and even overestimate the ability of morphology to explain interactions. Hence, determining how morphological traits of individual interaction partners are in phenological synchrony at localised scales will be fundamental to understanding the role morphology plays in underpinning plant-pollinator interactions.

ecology↗

bioRxiv2022

DNA-encoded library (DEL)-enabled discovery of proximity-inducing small molecules

Molecular glues and bifunctional compounds that induce protein-protein associations provide a powerful and general mechanism to modulate cell circuitry. We sought to develop a platform for the direct discovery of compounds able to induce association of any two pre-selected proteins, using the first bromodomain of BRD4 and the VHL-elongin C-elongin B (VCB) complex as a test system. Leveraging the screening power of DNA-encoded libraries (DELs), we synthesized [~]one million DNA-encoded compounds that possess a VHL-targeting fragment, a variety of connectors, and a diversity element generated by split- and-pool combinatorial chemistry. By screening our DEL against BRD4BD1 in the presence and absence of VCB, we could identify VHL-bound molecules that simultaneously bind BRD4. For highly barcode-enriched library members, ternary complex formation leading to BRD4 degradation was confirmed in cells. Furthermore, a ternary complex crystal structure was obtained for the most enriched library member. Our work provides a foundation for adapting DEL screening to the discovery of proximity-inducing small molecules. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/512184v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@43f3c9org.highwire.dtl.DTLVardef@13a1f9eorg.highwire.dtl.DTLVardef@f1d751org.highwire.dtl.DTLVardef@16f3789_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2022

Diversity-oriented synthesis encoded by deoxyoligonucleotides

Diversity-oriented synthesis (DOS)is a powerful strategy to prepare molecules with underrepresented features in commercial screening collections, resulting in the elucidation of novel biological mechanisms. In parallel to the development of DOS, DNA-encoded libraries (DELs) have emerged as an effective, efficient screening strategy to identify protein binders. Despite recent advancements in this field, most DEL syntheses are limited by the presence of sensitive DNA-based constructs. Here, we describe the design, synthesis, and validation experiments performed for a 3.7 million-member DEL, generated using diverse skeleton architectures with varying exit vectors, derived from DOS, to achieve structural diversity beyond what is possible by varying appendages alone. We will make this DEL available to the academic scientific community to increase access to novel structural features and accelerate early-phase drug discovery.

biochemistry↗

bioRxiv2020

Improved neurocognitive performance in FIV infected cats following treatment with the p75 neurotrophin receptor ligand LM11A-31

HIV rapidly infects the central nervous system (CNS) and establishes a persistent viral reservoir within microglia, perivascular macrophages and astrocytes. Inefficient control of CNS viral replication by antiretroviral therapy results in chronic inflammation and progressive cognitive decline in up to 50% of infected individuals with no effective treatment options. Neurotrophin based therapies have excellent potential to stabilize and repair the nervous system. A novel non-peptide ligand, LM11A-31, that targets the p75 neurotrophin receptor (p75NTR) has been identified as a small bioavailable molecule capable of strong neuroprotection with minimal side effects. To evaluate the neuroprotective effects of LM11A-31 in a natural infection model, we treated cats chronically infected with feline immunodeficiency virus (FIV) with 13 mg/kg LM11A-31 twice daily over a period of 10 weeks and assessed effects on cognitive functions, open field behaviors, activity, sensory thresholds, plasma FIV, cerebrospinal fluid (CSF) FIV, peripheral blood mononuclear cell provirus, CD4 and CD8 cell counts and general physiology. Between 12 and 18 months post-inoculation, cats began to show signs of neural dysfunction in T maze testing and novel object recognition, which were prevented by LM11A-31 treatment. Anxiety-like behavior was reduced in the open field and no changes were seen in sensory thresholds. Systemic FIV titers were unaffected but treated cats exhibited a log drop in CSF FIV titers. No significant adverse effects were observed under all conditions. The data indicate that LM11A-31 is likely to be a potent adjunctive treatment for the control of neurodegeneration in HIV infected individuals. Author SummaryThere are no effective treatments to halt the progression of most neurodegenerative diseases including HIV-associated neurodegeneration. Neurotrophins have the potential to provide strong neuroprotection but it has been difficult to develop usable interventions. A new drug, LM11A-31, that targets the p75 neurotrophin receptor has been developed that provides potent neuroprotection, is orally bioavailable and has the potential to prevent disease progression. The current studies were designed to evaluate the effects of the compound in an animal model of active HIV infection in preparation for a human clinical trial. Treatment of chronically infected animals with LM11A-31 normalized deficits in T maze performance, novel object recognition and open field behavior with no measurable adverse effects. Potential adverse effects associated with natural neurotrophins such as changes in sensory perception and increased systemic viral burden were not observed. A decrease in CSF FIV titers and a slight improvement in the CD4:CD8 ratio suggested that LM11A-31 may have beneficial effects beyond the anticipated neuroprotective effects. These findings are similar to beneficial effects seen in other animal models of neurodegeneration and CNS injury and support the use of LM11A-31 as an adjunctive neuroprotective agent for the treatment of HIV infected individuals.

neuroscience↗