Biology subjects

Williams, E. P.

Publications and source records attributed to Williams, E. P..

7 recordsLinked to original sources

bioRxiv2026

High latitude, high tolerance: Northern juvenile Chinook salmon exhibit substantial thermal plasticity and acute heat tolerance

In a rapidly warming North, Chinook salmon are facing rising river temperatures, increasing frequencies of heat waves, and greater annual thermal variation. These factors have putatively contributed to substantial declines in Alaska Chinook salmon abundance; understanding the thermal sensitivity and acclimation capacity of Chinook salmon at the northern extents of their range is therefore imperative. To this end, we acclimated juvenile Yukon River Chinook to five ecologically relevant summer temperatures (12.5, 15, 17.5, 20, and 22.5{degrees}C) under two feeding treatments of 100% or 40% satiation. We then assessed whole organism heat tolerance at rest and while swimming, along with the thermal sensitivity of heart rate and cardiac electrical activity. Yukon River Chinook substantially increased whole organism heat tolerance at rest and under exercise with warm acclimation. Cardiac heat tolerance also increased, and fish showed marked thermal compensation of maximum heart rate, resetting it to lower levels with warm acclimation. Feed treatment had a limited effect outside of peak heart rate and the transition temperatures of Q10. Warm acclimation was also associated with a shortening of the PR and QRS intervals and a lengthening of the QT interval. Across all acclimation groups, the PR interval plateaued to an extent far greater than heart rate itself, suggesting that limitations to AV conduction may limit cardiac function at high acute temperatures. Altogether, high latitude juvenile Chinook display remarkable heat tolerance and thermal plasticity, which may be preserved in association with the large seasonal, weather dependent, and spatial thermal variation Yukon River Chinook face during freshwater rearing and along with their extensive seaward and return migrations. The acute heat tolerance of Yukon River Chinook, which is comparable to or outperforming lower latitude Chinook and other salmonids, emphasizes the need for population-specific work for informed conservation efforts.

physiology↗

bioRxiv2026

Discovery of a molecular glue inhibitor that stabilises a non-productive Kalirin-Rac1 complex

Rho guanosine triphosphatases (GTPases) are molecular-switches implicated in neurodegenerative diseases, yet targeting them through competitive inhibition remains a challenge due to their high affinity for guanine nucleotides. Guanine nucleotide exchange factors (GEFs) catalyse GDP-to-GTP nucleotide exchange to activate GTPases, providing an alternative opportunity for GTPase modulation. Herein, we describe a complex-targeted strategy to inhibit nucleotide exchange with covalent molecular glues that engage the Kalirin-Rac1 GEF-GTPase complex at the nucleotide binding site are sequester the GEF Kalirin. Fragment hits were identified through XChem and in silico screening, and a fragment merging approach resulted in the generation of covalent inhibitors RS-009 and MC-278. Multiple analyses demonstrate our compounds inhibit nucleotide exchange both through competition with the nucleotides and by stabilising a ternary inhibitor-Rac1-Kalirin complex, thereby trapping Kalirin in a non-productive state and reducing GEF turnover. Biochemical selectivity screening and cellular activity-based protein profiling (ABPP) show that selectivity can be achieved across distinct GEF-GTPase complexes, which may result in improved spatiotemporal control over targeting the GTPase alone. This work provides evidence for targeting GTPase signalling via stabilization of the GEF-GTPase complex in a unique covalent molecular glue mechanism and provides the basis of a chemical probe or therapeutic.

biochemistry↗

bioRxiv2026

Metabolic plasticity facilitates a high-latitude life of feast and famine in Arctic char

O_LIHigh northern latitudes experience extreme winters and pronounced environmental variation. Arctic animals possess remarkable and diverse physiological mechanisms to thrive under this variation, but such mechanisms are poorly studied, particularly in the aquatic realm. C_LIO_LIWe combined Arctic field and laboratory experiments to reveal how one of Earths most northerly distributed fish species, the Arctic char, seasonally adjusts its metabolism to conserve energy over winter while not feeding and to capitalize on more optimal growth conditions in summer. C_LIO_LILaboratory reared Arctic char were fed or food deprived at common summer (8{degrees}C) and winter (2{degrees}C) temperatures for >120 days. Oxygen consumption rates were assessed as a proxy for rate of aerobic metabolic energy expenditure. Cooling from 8 to 2{degrees}C reduced resting aerobic energy expenditure by 35%, while food deprivation independently drove a reduction of 46-50%. Combined, resting energy expenditure was 197% higher under simulated summer (fed at 8{degrees}C) than winter conditions (food deprived at 2{degrees}C). C_LIO_LIReductions in resting energy expenditure with food deprivation were driven, at least in part, by marked tissue-specific decreases in organ size and protein synthesis rates in tissues with central roles in growth and digestion. C_LIO_LIWild adult anadromous Arctic char exhibited, seasonal plasticity consistent with our laboratory experiments. Resting energy expenditure at 10{degrees}C was 27% higher after summer feeding than in the spring after winter fasting, while liver and digestive organ masses were also markedly reduced overwinter. C_LIO_LIIn contrast, peak aerobic metabolic performance and relative heart mass were largely maintained during food deprivation indicating a protection of systems that support aerobic metabolic capacity. C_LIO_LIDespite recruiting strategies for substantial energy savings, wild and laboratory reared Arctic char still largely depleted their on-board fat stores with food-deprivation, underscoring that these strategies are essential when food is limited. Given that the Arctic is among the most rapidly changing regions on Earth, temperatures, productivity, and the timing of key seasonal event are all shifting with implications for the efficacy of such strategies for high-latitude animals. C_LI

zoology↗

bioRxiv2024

Crystallographic fragment screen of Enterovirus D68 3C protease and iterative design of lead-like compounds using structure-guided expansions

The development of effective broad-spectrum antivirals forms an important part of preparing for future pandemics. One cause for concern is the currently emerging pathogen Enterovirus D68 (EV-D68) which primarily spreads through respiratory routes causing mostly mild to severe respiratory illness but, in severe cases, acute flaccid myelitis. The 3C protease of EV-D68 (3Cpro) is a potential target for the development of antiviral drugs due to its essential role in the viral life cycle and high sequence conservation amongst family members. In this study, we describe the identification of fragments which bind to3Cpro using crystallographic screening and the expansion of these into more lead-like compounds. The hits revealed interesting directions for hit-to-lead progression, specifically the importance of the pocket occupied by the conserved glutamine sidechain of the substrates and the interactions formed. Additionally, two pockets could be joined by not following the backbone of the native substrates, thus circumventing the screening issues arising from the flexibility of the catalytic triad. These observations of the novel binding modes of the chemical matter found by this screen can help shape future drug design campaigns against 3C proteases.

biochemistry↗

bioRxiv2024

Crystallographic Fragment Screen of Coxsackievirus A16 2A Protease identifies new opportunities for the development of broad-spectrum anti-enterovirals

Enteroviruses are the causative agents of paediatric hand-foot-and-mouth disease, and a target for pandemic preparedness due to the risk of higher order complications in a large-scale outbreak. The 2A protease of these viruses is responsible for the self-cleavage of the poly protein, allowing for correct folding and assembly of capsid proteins in the final stages of viral replication. These 2A proteases are highly conserved between Enterovirus species, such as Enterovirus A71 and Coxsackievirus A16. Inhibition of the 2A protease deranges capsid folding and assembly, preventing formation of mature virions in host cells and making the protease a valuable target for antiviral activity. Herein, we describe a crystallographic fragment screening campaign that identified 75 fragments which bind to the 2A protease including 38 unique compounds shown to bind within the active site. These fragments reveal a path for the development of non-peptidomimetic inhibitors of the 2A protease with broad-spectrum anti-enteroviral activity.

biochemistry↗

bioRxiv2024

Regulated mRNA recruitment in dinoflagellates is reflected in hyper-variable mRNA spliced leaders and novel eIF4Es

Dinoflagellates are eukaryotic algae with large genomes that rely heavily on post-transcriptional control for the regulation of gene expression. Dinoflagellate mRNAs are trans-spliced with a conserved 22 base spliced leader sequence (SL) that includes the 5-cap to which the translation initiation factor 4E (eIF4E) binds to facilitate ribosomal recruitment. The binding of an eIF4E to a specific mRNA SL is a potential regulatory point in controlling dinoflagellate gene expression. Here we show that m7G is the 5-cap base of the 65 bp SL RNA with additional methylations throughout the SL to give a mixture of novel multi-methylated sequences in Amphidinium carterae (CCMP1314). There is also sequence variability in all four bases seen at the first position followed by a variety of polymorphisms. Three novel clades of eIF4E have been shown in dinoflagellates that are distinct from the three metazoan classes of eIF4E. Members of each clade differ significantly from each other, but all bear the distinctive features of a cap-binding protein. Here we show large differences in expression and activity in six of the eight eIF4E family members from A. carterae. Transcripts of each are expressed throughout the diel cycle, but only eIF4E-1 family members and eIF4E-2a show discernable expression at the level of protein. Recombinant eIF4E-1 family members and eIF4E-3a, but not eIF4E-2a, are able to bind to m7GTP substrates in vitro. Overall, eIF4E-1a emerges with characteristics consistent with the role of a prototypical initiation factor; eIF4E-1a is the most conserved and highly expressed eIF4E family member, has the highest affinity for m7GpppG and m7GpppC by surface plasmon resonance, and is able to complement a yeast strain conditionally deficient in eIF4E. The large number of eIF4E family members along with the sequence and methylation state variability in the mRNA SLs underscore the unique nature of the translational machinery in the dinoflagellate lineage and suggest a wide range of possibilities for differential recruitment of mRNAs to the translation machinery. Impact StatementIn the dinoflagellate, A. carterae, hyper-variable mRNA spliced leaders and novel eIF4Es reflect the reliance of dinoflagellates on variable mRNA recruitment for the regulation of gene expression.

molecular biology↗

bioRxiv2020

COVID-19 cytokines and the hyperactive immune response: Synergism of TNF-α and IFN-γ in triggering inflammation, tissue damage, and death

The COVID-19 pandemic has caused significant morbidity and mortality. Currently, there is a critical shortage of proven treatment options and an urgent need to understand the pathogenesis of multi-organ failure and lung damage. Cytokine storm is associated with severe inflammation and organ damage during COVID-19. However, a detailed molecular pathway defining this cytokine storm is lacking, and gaining mechanistic understanding of how SARS-CoV-2 elicits a hyperactive inflammatory response is critical to develop effective therapeutics. Of the multiple inflammatory cytokines produced by innate immune cells during SARS-CoV-2 infection, we found that the combined production of TNF- and IFN-{gamma} specifically induced inflammatory cell death, PANoptosis, characterized by gasdermin-mediated pyroptosis, caspase-8-mediated apoptosis, and MLKL-mediated necroptosis. Deletion of pyroptosis, apoptosis, or necroptosis mediators individually was not sufficient to protect against cell death. However, cells deficient in both RIPK3 and caspase-8 or RIPK3 and FADD were resistant to this cell death. Mechanistically, the JAK/STAT1/IRF1 axis activated by TNF- and IFN-{gamma} co-treatment induced iNOS for the production of nitric oxide. Pharmacological and genetic deletion of this pathway inhibited pyroptosis, apoptosis, and necroptosis in macrophages. Moreover, inhibition of PANoptosis protected mice from TNF- and IFN-{gamma}-induced lethal cytokine shock that mirrors the pathological symptoms of COVID-19. In vivo neutralization of both TNF- and IFN-{gamma} in multiple disease models associated with cytokine storm showed that this treatment provided substantial protection against not only SARS-CoV-2 infection, but also sepsis, hemophagocytic lymphohistiocytosis, and cytokine shock models, demonstrating the broad physiological relevance of this mechanism. Collectively, our findings suggest that blocking the cytokine-mediated inflammatory cell death signaling pathway identified here may benefit patients with COVID-19 or other cytokine storm-driven syndromes by limiting inflammation and tissue damage. The findings also provide a molecular and mechanistic description for the term cytokine storm. Additionally, these results open new avenues for the treatment of other infectious and autoinflammatory diseases and cancers where TNF- and IFN-{gamma} synergism play key pathological roles.

immunology↗