Biology subjects

Hall, M. D.

Publications and source records attributed to Hall, M. D..

At least 19 recordsLinked to original sources

bioRxiv2026

Monoclonal nephritic factors reveal insights into C3 convertase dynamics and dysregulation

C3- and C5-nephritic factors are potent but poorly understood autoantibodies that dysregulate complement convertases. To date, their underlying mechanisms of action, epitopes, and sequences remain unknown. To address this knowledge gap, we immune profiled B cells from a nephritic factor-positive C3 glomerulopathy patient and identified the first monoclonal C3- and C5-nephritic factors. We present the structure of a C3-nephritic factor bound to a C3 convertase with the convertase protease domain unexpectedly rotated and inhibited. This rotation advances our understanding of complement convertase progression and decay, explains disease-associated convertase variants, and reveals the molecular mechanism by which nephritic factors can either activate or inhibit convertase activity. We also detail heterogeneity within and between C3- and C5-nephritic factors in terms of convertase binding, stabilizing capacity, regulator inhibition, fluid-phase activation, and disease contribution. These findings improve stratification of patients with C3 glomerulopathy, redefine basic C3 convertase dynamics, and provide insights into antibody-mediated modulation of the complement system.

immunology↗

bioRxiv2025

Local adaptation in climate tolerance at a small geographic scale contrasts with broad latitudinal patterns

While climate adaptation is typically quantified across broad gradients, the potential for adaptation to the same environmental variables at small scales is rarely tested. If local-scale environmental heterogeneity can generate patterns of adaptation similar to broad gradients, then we currently underestimate adaptive capacity to global change. We quantified population variation in climate tolerance traits and their plasticity for five populations of Drosophila melanogaster from a 3000-km latitudinal gradient, which we contrasted with eight local populations from an environmentally heterogeneous 600x300km area. Population variation in stress tolerance at the local scale was comparable to that across latitude. Consistent with local adaptation, populations from warmer and drier environments showed greater heat and desiccation tolerance, and populations from more predictable environments showed greater plasticity. Climate adaptation at smaller geographic scales can therefore be comparable to adaptation across broad geographic scales. However, patterns of adaptation often changed across geography, which makes predicting responses to global change challenging.

evolutionary biology↗

bioRxiv2025

Identification of antibody-drug conjugate payloads which are substrates of ATP-binding cassette drug efflux transporters

AimAntibody-drug conjugates (ADCs) feature an antibody recognizing a specific protein joined to a potent toxic payload. Numerous antibody-drug conjugates have received FDA approval; however, clinical resistance arises. Resistance mechanisms include decreased expression or mutation of the antibody target, impaired payload release, or increased expression of ATP-binding cassette (ABC) efflux transporters associated with multidrug resistance. We therefore sought to characterize the interactions of ABC multidrug transporters with ADC payloads. MethodsWe performed a high-throughput screen with 27 common ADC payloads using cells lines expressing ABC transporters P-glycoprotein (P-gp, encoded by ABCB1) or ABCG2 (encoded by ABCG2). Confirmatory assays were also performed using cells transfected to express P-gp, ABCG2, or MRP1 (encoded by ABCC1). ResultsSeveral commonly used ADC payloads were substrates of P-gp, including calicheamicin gamma1, monomethyl auristatin E, DM1, and DM4. All the pyrrolobenzodiazepines tested--SJG136, SGD-1882, SG2057, and SG3199--were substrates of P-gp, ABCG2, and MRP1. The modified anthracyclines nemorubicin and its metabolite PNU-159682 were poorly transported by both ABCB1 and ABCG2 and displayed nanomolar to picomolar toxicity. Further, we found that the efficacy of the FDA-approved ADC mirvetuximab soravtansine, with DM4 as the toxic payload, was decreased in cell lines expressing P-gp. Duocarmycin DM and PNU-159682 were exquisitely toxic to a panel of 99 cancer cell lines of varying origins. ConclusionSeveral commonly used ADC payloads can be transported by ABC transporters, potentially leading to transporter-mediated drug resistance in patients. Future ADCs should be developed using payloads that are not ABC transporter substrates.

pharmacology and toxicology↗

bioRxiv2025

Variation in temperature but not diet determines the stability of latitudinal clines in tolerance traits and their plasticity

Latitudinal clines are routinely used as evidence of adaptation across broad climatic gradients. However, if environmental variation influences the strength of latitudinal clines, then clinal patterns will be unstable, and using patterns of adaptation to predict population responses to global change will be difficult. To test whether environmental variation influences latitudinal clines, we sampled five populations of Drosophila melanogaster spanning 3000-km of east coast Australia, and measured stress tolerance (heat, cold and desiccation) and body size on flies that developed in six combinations of temperature (13{degrees}C, 25{degrees}C and 29{degrees}C) and diet (standard and low-calorie) treatments. We found latitudinal clines where populations further from the equator had larger wings, higher cold tolerance and lower heat tolerance. For all traits, temperature determined the strength of latitudinal clines, whereas diet had little influence. Steeper clines often emerged in warmer treatments, created by latitudinal clines in plasticity. In the warmest temperature, higher latitude populations showed larger increases in heat tolerance, larger reductions in desiccation tolerance but smaller decreases in cold tolerance. Heat tolerance was the only trait that supported the climate variability hypothesis and a trade-off between plasticity and tolerance. Environment-dependent latitudinal clines are therefore likely to determine variation in population responses to global change.

evolutionary biology↗

bioRxiv2024

Discovery of Novel and Selective GPR17 Antagonists as Pharmacological Tools for Developing New Therapeutic Strategies in Diabetes and Obesity

G protein coupled receptors (GPCRs) are promising targets for diabetes and obesity therapy due to their roles in metabolism and excellent potential for pharmacological manipulation. We previously reported that Gpr17 ablation in the brain-gut axis leads to improved metabolic homeostasis, suggesting GPR17 antagonism could be developed for diabetes and obesity treatment. Here, we performed high throughput screening (HTS) and identified two new GPR17 antagonists (compound 978 and 527). Both compounds antagonized downstream Gi/o, Gq and {beta}-arrestin signaling with high selectivity for GPR17, but not the closely related purinergic and cysteinyl leukotriene receptors. The molecular mechanisms of antagonism were revealed through Schild analysis, structure-activity relationship (SAR) studies and homology modelling. Compound 978 and its analog (793) attenuated GPR17 signaling and promoted glucagon-like peptide-1 (GLP-1) secretion in enteroendocrine cells. In summary, we identified selective GPR17 antagonists through HTS, which represent promising pharmacological tools for developing new therapeutic strategies in diabetes and obesity. SignificanceOur work highlights the therapeutic potential of GPR17 antagonism in the treatment of diabetes and obesity by leveraging its role in metabolic regulation. In previous studies, we have shown that Gpr17 ablation improves metabolic homeostasis, and here we expanded our research by identifying two novel small molecule antagonists of GPR17 through high-throughput screening. The compounds inhibited multiple downstream signaling pathways of GPR17 with high selectivity over other closely related receptors. Of particular significance, compound 978 and its analogs not only attenuated GPR17 signaling but also increased glucagon-like peptide-1 (GLP-1) secretion, a critical hormone for glucose homeostasis and appetite regulation. These findings shed new light into the molecular mechanisms of GPR17 antagonism and introduce valuable pharmacological tools for further exploration of therapeutic strategies in diabetes and obesity.

pharmacology and toxicology↗

bioRxiv2024

The sicker sex is plastic: Thermal plasticity determines sex biases in pathogen transmission

Sex differences are predicted to play an important role in the spread and evolution of pathogens. However, attempts to generalize the sicker sex have been challenged by intraspecific variability of sex-biases across the infection process. Sex specific plasticity provides a framework to resolve this by elucidating how infection is shaped at the sex-pathogen-environment interface. Using the Daphnia magna and Pasteuria ramosa system, we measure infection outcomes for males and females across three temperatures and seven pathogen densities to quantify how sex specific plasticity shapes susceptibility, pathogen loads, and ultimately transmission. We find unique forms of plasticity at each stage of infection - including equivalent, sex-specific, and divergent plasticity. Integrating these into a single estimate of transmission reveals a clear pattern - male-biased transmission at cold temperatures, and female-biased transmission at warm temperatures. Sex specific thermal plasticity thus determines the sicker sex, with implications for pathogen spread and evolution in a warming world.

ecology↗

bioRxiv2024

Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity

A standard method in phylogenetic reconstruction for representing variation in substitution rates between sites in the genome is the discrete Gamma model (DGM). Relative rates are assumed to be distributed according to a discretised Gamma distribution, where the probabilities that a site is included in each class are equal. Here, we identify a serious bias in the branch lengths of reconstructed phylogenies when the DGM is used, with the magnitude of the effect varying with the number of sequences in the alignment. We demonstrate the existence of the bias in both simulated dataset and using real HIV-1 sequences; in both cases branch lengths are overestimated. We show that the alternative "FreeRate" model, which assumes no parametric distribution and allows the class probabilities to vary, is not subject to the issue. We further establish that the reason for the behaviour is the equal class probabilities, not the discretisation itself. We explore the mathematics of for the phenomenon, showing how maximum likelihood branch lengths under the DGM may differ from the true ones used to generate the tree, and that branch lengths will be overestimated where there is a long-tail of fast-evolving sites in the true rate distribution, which is the usual situation in real datasets. We recommend that the DGM be retired from general use. While FreeRate is an immediately available replacement, it is known to be difficult to fit, and thus there is scope for innovation in rate heterogeneity models.

evolutionary biology↗

bioRxiv2024

Taking a BREATH (Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories) to simultaneously infer phylogenetic and transmission trees for partially sampled outbreaks

We introduce and apply Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories (BREATH), a method to simultaneously construct phylogenetic trees and transmission trees using sequence data for a host-to-host outbreak. BREATHs transmission process that accounts for a flexible natural history of infection (including a latent period if desired) and a separate process for sampling. It allows for unsampled individuals and within-host evolution. It also accounts for the fact that an outbreak may still be ongoing at the time of analysis, using right truncation adjustment. We perform a simulation study to verify our implementation and explore sensitivity to unknown or misspecified parameters. We then apply BREATH to a previously-described 13-year outbreak of tuberculosis. We find that using a transmission process to inform the phylogenetic reconstruction results in better resolution of the phylogeny (in topology, branch length and tree height) and a more precise estimate of the time of origin of the outbreak. Considerable uncertainty remains about transmission events in the outbreak, but our reconstructed transmission network resolves two major waves of transmission consistent with the previously-described epidemiology, estimates the numbers of unsampled individuals, and describes some high-probability transmission pairs. An open source implementation of BREATH is available from https://github.com/rbouckaert/BREATH as the BREATH package to BEAST 2.

evolutionary biology↗

bioRxiv2024

A comprehensive collection of pain and addiction targets and compounds library for high throughput screening and AI-driven drug discovery

As part of the NIH Helping to End Addiction Long-term (HEAL) Initiative, the National Center for Advancing Translational Sciences (NCATS) is dedicated to the development of new pharmacological tools and investigational drugs for managing and treating pain, as well as the prevention and treatment of opioid misuse and addiction. In line with these objectives, we created a comprehensive, annotated small molecule library including drugs, probes, and tool compounds that act on published pain and addiction-relevant targets. Nearly 3,000 small molecules associated with approximately 200 known and hypothesized HEAL targets have been assembled, curated, and annotated in one collection. Physical samples of the library compounds have been acquired and plated in 1536-well format, enabling rapid and efficient high throughput screen (HTS) against a wide range of assays. The creation of the HEAL Targets and Compounds Library, coupled with an integrated computational platform for AI-driven machine learning (ML), structural modeling, and virtual screening (VS), provides a valuable source for strategic drug repurposing, innovative profiling, and hypothesis testing of novel targets related to pain and opioid use disorder (OUD). The library is available to investigators for screening pain and OUD-relevant phenotypes.

bioinformatics↗

bioRxiv2023

Pharmaceutical pollution alters the cost of bacterial infection and its relationship to pathogen load

The relationship between pathogen proliferation and the cost of infection experienced by a host drives the ecology and evolution of host-pathogen dynamics. While environmental factors can shape this relationship, there is currently limited knowledge on the consequences of emerging contaminants, such as pharmaceutical pollutants, for the commonly observed trade-off between a pathogens growth within the host and the damage it causes, termed its virulence. Here, we investigated how exposure to fluoxetine (Prozac), a commonly detected psychoactive pollutant, could alter this key relationship using the water flea Daphnia magna and its bacterial pathogen Pasteuria ramosa as a model system. Across a variety of fluoxetine concentrations, we found that fluoxetine shaped the damage a pathogen caused, such as the reduction in fecundity or intrinsic growth experienced by infected individuals, but with minimal change in average pathogen spore loads. Instead, fluoxetine modified the relationship between the degree of pathogen proliferation and its virulence, with both the strength of this trade-off and the component of host fitness most affected varying by fluoxetine concentration and host genotype. Our study underscores the potential for pharmaceutical pollution to modify the virulence of an invading pathogen, as well as the fundamental trade-off between host and pathogen fitness, even at the trace amounts increasingly found in natural waterways.

ecology↗

bioRxiv2023

Conditional lethality profiling reveals anticancer mechanisms of action and drug-nutrient interactions

Chemical screening studies have identified drug sensitivities across hundreds of cancer cell lines but most putative therapeutics fail to translate. Discovery and development of drug candidates in models that more accurately reflect nutrient availability in human biofluids may help in addressing this major challenge. Here we performed high-throughput screens in conventional versus Human Plasma-Like Medium (HPLM). Sets of conditional anticancer compounds span phases of clinical development and include non-oncology drugs. Among these, we characterize a unique dual-mechanism of action for brivudine, an agent otherwise approved for antiviral treatment. Using an integrative approach, we find that brivudine affects two independent targets in folate metabolism. We also traced conditional phenotypes for several drugs to the availability of nucleotide salvage pathway substrates and verified others for compounds that seemingly elicit off-target anticancer effects. Our findings establish generalizable strategies for exploiting conditional lethality in HPLM to reveal therapeutic candidates and mechanisms of action.

cancer biology↗

bioRxiv2023

Is there a sicker sex? Dose relationships modify male-female differences in infection prevalence

Throughout the animal kingdom there are striking differences in the propensity of one sex or the other to become infected. However, attempts to generalise when we should expect males or females to emerge as the sicker sex have proven challenging. We argue that this is because our current understanding of sex differences in susceptibility is inherently limited, as most inferences have come from field studies (where exposure dose is difficult to quantify), or by measuring infection rates in vitro at a limited range of pathogen doses. Without considering how susceptibility changes across a range of pathogen doses (i.e., the dose-susceptibility relationship), we have likely underestimated the scope in which sex differences can arise, reducing our capacity to accurately characterise the sicker sex. Here, to expand our scope, we use the Daphnia magnia and Pasteuria ramosa system to measure infection prevalence across a fifteen thousandfold change in pathogen dose and quantify male and female differences through formal models of environmental transmission. Through this, we reveal that the expression of sex differences in susceptibility is entirely dose-dependent, with males more susceptible at low doses, and females more susceptible at high doses. The scope for male-female differences to emerge is therefore much greater than previously expected - extending to differences in absolute resistance, per-propagule infectivity risks, and the dose-specific behaviour of pathogens. Crucially, none of these components in isolation could define the sicker sex. If we wish to understand the broader patterns underlying whether males or females are the sicker sex, there is a need to apply this expanded scope across the animal kingdom. This will help us understand when and why a sicker sex emerges, and the implications for diseases in nature - where sex ratios and pathogen densities vary drastically.

evolutionary biology↗

bioRxiv2023

Contrasting the form and strength of pre- and postcopulatory sexual selection in a transparent worm with fluorescent sperm

Sexual traits may be selected during multiple consecutive episodes of selection, occurring before, during, or after copulation. The overall strength and shape of selection acting on sexually selected traits may thus be determined by how selection (co-)varies along different episodes. However, it is challenging to measure pre- and postcopulatory phenotypic traits alongside variation in fitness components at each different episode. Here, we used a transgenic line of the transparent flatworm Macrostomum lignano expressing green fluorescent protein (GFP) in all cell types, including sperm cells, enabling in vivo sperm tracking. We exposed GFP(+) focal worms to three groups in which we assessed their mating success, sperm-transfer efficiency, and sperm fertilising efficiency. Moreover, we measured 13 morphological traits on the focal worms to study the fitness landscape in multivariate trait space. We found linear selection on sperm production rate arising from pre- and postcopulatory components, and on copulatory organ shape arising from sperm fertilising efficiency. We further found nonlinear (mostly concave) selection on combinations of copulatory organ and sperm morphology traits arising mostly from sperm-transfer efficiency and sperm fertilising efficiency. Our study shows that contrasting patterns of phenotypic selection are observed by measuring how sexual selection builds-up over consecutive episodes of selection.

evolutionary biology↗

bioRxiv2023

Anticipating change: the impact of simulated seasonal heterogeneity on heat tolerances along a latitudinal cline.

An understanding of thermal limits and variation across geographic regions is central to predicting how any population may respond to scenarios of global change. Latitudinal clines, in particular, have been used in demonstrating that populations can be locally adapted to their own thermal environment and, as a result, not all populations will be equally impacted by an increase in temperature. But how robust are these signals of thermal adaptation to the other ecological challenges that animals commonly face in the wild? Seasonal changes in population density, food availability, or photoperiod are common ecological challenges that could disrupt patterns of thermal tolerance along a cline if each population differentially used these signals to anticipate future temperatures and adjust their thermal tolerances accordingly. In this study, we aimed to test the robustness of a cline in thermal tolerance to simulated signals of seasonal heterogeneity. Experimental animals were derived from clones of the Australian water flea, Daphnia carinata, sampled from nine populations along a latitudinal transect in eastern Australia. We then factorially combined summer (18h light, 6h dark) and winter (6h light, 18h dark) photoperiods with high (5 million algal cells individual-1 day-1) and low (1 million algal cells individual-1 day-1) food availabilities, before performing static heat shock assays and recording knockdown times as a measure of thermal tolerance. In general, higher food availably led to an increase in thermal tolerances, with the magnitude of increase varying by clone. In contrast, summer photoperiods led to rank order changes in thermal tolerances, with heat resistance increasing for some clones, and other decreasing for others. Heat resistance, however, still declined along the latitudinal cline, irrespective of the manipulation of seasonal signals, with northern clones always showing greater thermal resistance, and that this was most likely driven by adaptation to winter thermal conditions. While photoperiod and food availability can clearly shape thermal tolerances for specific clones or populations, they are unlikely to be used to anticipate future temperatures, and thus observed clines in heat resistance will remained robust to these forms of seasonal heterogeneity.

evolutionary biology↗

bioRxiv2022

Viral burdens are associated with age and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection related sampling bias.

In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burdens, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. Analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior infection, the average Ct value was 0.94 lower among Alpha variant infections, compared those with the predecessor strain, B.1.177. However, among vaccinated individuals, it was 0.34 lower among Delta variant infections, compared to those with the Alpha variant. In addition, the average Ct value decreased by 0.20 for every 10 year age increment of the infected individual. In summary, within-host viral burdens are associated with age, in addition to the interplay of vaccination status and viral variant.

genetics↗

bioRxiv2022

Thermal acclimation to warmer temperatures can protect host populations from both further heat stress and the potential invasion of pathogens

Phenotypic plasticity in response to shifts in temperature, known as thermal acclimation, is an essential component of the ability of a species to cope with environmental change. Not only does this process potentially improve an individuals thermal tolerance, it will also act simultaneously on various fitness related traits that determine whether a population increases or decreases in size. In light of global change, thermal acclimation therefore has consequences for population persistence that extend beyond simply coping with heat stress. This particularly important when we consider the additional threat of parasitism associated with global change, as the ability of a pathogen to invade a host population depends on both its capacity to proliferate within a host and spread between hosts, and thus the supply of new susceptible hosts in a population. Here, we use the host Daphnia magna and its bacterial pathogen Pasteuria ramosa to investigate how thermal acclimation may impact various aspects of host and pathogen performance at the scale of both an individual and the population. We independently test the effect of maternal thermal acclimation and direct thermal acclimation on host thermal tolerance, measured as knockdown times, as well as host fecundity and lifespan, and pathogen infection success and spore production. We find that direct thermal acclimation enhances host thermal tolerance and intrinsic rates of population growth, despite a decline observed for host fecundity and lifespan. Pathogens, on the other hand, faired consistently worse at warmer temperatures at the within-host scale, and also in their potential to invade a host population. Our results suggest that hosts could benefit more from warming than their pathogens, but highlight that considering both within- and between-host thermal performance, including thermal tolerance and fitness traits, is needed to fully appreciate how increasing thermal variability will impact host and pathogen populations.

ecology↗

bioRxiv2022

A Suite of TMPRSS2 Assays for Screening Drug Repurposing Candidates as Potential Treatments of COVID-19

SARS-CoV-2 is the causative viral pathogen driving the COVID-19 pandemic that prompted an immediate global response to the development of vaccines and antiviral therapeutics. For antiviral therapeutics, drug repurposing allowed for rapid movement of existing clinical candidates and therapies into human clinical trials to be tested as COVID-19 therapies. One effective antiviral treatment strategy used early in symptom onset is to prevent viral entry. SARS-CoV-2 enters ACE2-expressing cells when the receptor-binding domain of the spike protein on the surface of SARS-CoV-2 binds to ACE2 followed by cleavage at two cut sites on the spike protein. TMPRSS2 has a protease domain capable of cleaving the two cut sites; therefore, a molecule capable of inhibiting the protease activity of TMPRSS2 could be a valuable antiviral therapy. Initially, we used a fluorogenic high-throughput screening assay for the biochemical screening of 6030 compounds in NCATS annotated libraries. Then, we developed an orthogonal biochemical assay that uses mass spectrometry detection of product formation to ensure that hits from the primary screen are not assay artifacts from the fluorescent detection of product formation. Finally, we assessed the hits from the biochemical screening in a cell-based SARS-CoV-2 pseudotyped particle entry assay. Of the six molecules advanced for further studies, two are approved drugs in Japan (camostat and nafamostat), two have entered clinical trials (PCI-27483 and otamixaban), while the other two molecules are peptidomimetic inhibitors of TMPRSS2 taken from the literature that have not advanced into clinical trials (compounds 92 and 114). This work demonstrates a suite of assays for the discovery and development of new inhibitors of TMPRSS2.

biochemistry↗

bioRxiv2021

The humanized nanobody RBD-1-2G tolerates the spike N501Y mutation to neutralize SARS-CoV-2

Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants.

synthetic biology↗