Biology subjects

Wilson, R. P.

Publications and source records attributed to Wilson, R. P..

11 recordsLinked to original sources

bioRxiv2026

Hepatocyte growth factor activator inhibitor-2 rapidly inactivates airway-expressed human Type II Transmembrane Serine Proteases

Human Type II Transmembrane Serine Proteases (TTSPs) are essential entry factors for various influenza A and coronaviruses, and drive cancer metastasis when they are overexpressed by tumor cells. However, the natural inhibition mechanisms that regulate these proteases are not well understood. One natural transmembrane protease inhibitor, hepatocyte growth factor activator inhibitor-2 (HAI-2), has been shown to block TMPRSS2 activity and can prevent SARS-CoV-2 infection and reduce TMPRSS2-driven prostate cancer metastasis when overexpressed. In this study, we present biochemical and biophysical evidence showing that HAI-2 effectively inactivates TMPRSS2 and other TTSPs only after they have undergone zymogen activation. Through mutagenesis and ligand binding assays, we demonstrate that Kunitz Domain 1 (KD1) and KD2 can form stable ternary complexes with TMPRSS2 and other TTSPs, but do not employ the typical Laskowski inhibitor mechanism found for other macromolecular serine protease inhibitors. We also show that HAI-2 proteins do not inhibit the coagulation protease thrombin and that multivalent human IgG-tagged HAI-2 proteins are highly potent TMPRSS2 inhibitors. Our findings provide a mechanistic understanding of how TTSP activity is regulated in human airway cells and offer a foundation for developing engineered soluble HAI-2 proteins as anti-TTSP antivirals and anti-cancer therapeutics.

biochemistry↗

bioRxiv2025

Epigenetic lockdown of type I interferon sensing and signalling in human pluripotent cells.

The Human Silencing Hub (HUSH) complex safeguards genome integrity in human somatic cells by repressing transposable elements and regulating type I interferon (IFN-I) induction. In early development, the IFN-I pathway is inactive, yet its underlying regulation is poorly understood. Here, we use depletion of the HUSH complex in human induced pluripotent stem cells (iPSCs) as a tool to investigate epigenetic control of the IFN-I system in early development. We confirmed that human iPSCs display an attenuated IFN-I pathway, whereas iPSC-derived neural progenitor cells (NPCs) respond robustly to IFN-I pathway agonists. We found that, in iPSCs, depletion of MPP8, a core component of all HUSH complexes, was sufficient to induce both expression of young LINE-1 elements and genes linked to the IFN system including double-stranded RNA sensors and interferon-stimulated genes (ISGs). ISG upregulation had little effect on pluripotency markers and occurred without IFN signalling, suggesting that, in contrast to differentiated cells, these ISGs are direct transcriptional targets of the HUSH complex in early development. Chromatin profiling by CUT&Tag confirmed MPP8 enrichment at HUSH-regulated ISGs and revealed a bimodal binding profile of MPP8 to both ISGs and non-ISGs, the latter largely driven by young LINE-1 elements. We propose that shutdown of the IFN-I system in pluripotent stem cells is essential to prevent lethality from unwarranted self-nucleic acid sensing. This shutdown is achieved through a triple-layer of epigenetic lockdown acting on ligands, sensors, and effectors across the IFN-I pathway. Pluripotent cells, therefore, represent a ground state of immune evasion that cancer cells may evolve towards through increasing expression of MPP8.

molecular biology↗

bioRxiv2024

Magellanic penguins balance navigation with foraging opportunities in complex current regimes

Animals navigating in fluid environments often face lateral forces from wind or water currents that challenge travel efficiency and route accuracy. We investigated how 27 Magellanic penguins (Spheniscus magellanicus) adapt their navigation strategies to return to their colony amid regional tidal ocean currents. Using GPS-enhanced dead-reckoning loggers and high-resolution ocean current data, we reconstructed penguin travel vectors during foraging trips to assess their responses to variable currents during their colony-bound movements. By integrating estimates of energy costs and prey pursuits, we found that birds balanced direct navigation with current-driven drift: in calm currents, they maintained precise line-of-sight headings to their colony. In stronger currents, they aligned their return with lateral flows, which increased travel distance, but at minimal energy costs, and provided them with increased foraging opportunities. Since the lateral tidal currents always reversed direction over the course of return paths, the penguins return paths were consistently S-shaped but still resulted in the birds returning efficiently to their colonies. These findings suggest that Magellanic penguins can sense current drift and use it to optimize energy expenditure by maintaining overall directional accuracy while capitalizing on foraging opportunities.

animal behavior and cognition↗

bioRxiv2024

Structural basis of TMPRSS11D specificity and autocleavage activation

Transmembrane Protease, Serine-2 (TMPRSS2) and TMPRSS11D are human proteases that enable SARS-CoV-2 and Influenza A/B virus infections, but their biochemical mechanisms for facilitating viral cell entry remain unclear. We demonstrate these proteases can spontaneously and efficiently cleave their own zymogen activation motifs, thereby activating their wider protease activity on other cellular substrates. We determined TMPRSS11D co-crystal structures in complexes with a native TMPRSS11D zymogen activation motif and with an engineered activation motif, providing insights into TMPRSS11D autocleavage activation and revealing unique regions of its substrate binding cleft. We further show that a protease inhibitor that underwent clinical trials for TMPRSS2-targeted COVID-19 therapy, nafamostat mesylate, was rapidly cleaved by TMPRSS11D and converted to low activity derivatives. These insights into human protease viral tropism and into liabilities with existing human serine protease inhibition strategies will guide future drug discovery campaigns for these targets.

biochemistry↗

bioRxiv2023

Validating Dynamic Body Acceleration metrics as a measure of energy expenditure in a Neotropical primate

2AO_SCPLOWBSTRACTC_SCPLOWQuantifying energy expenditure in free-living primates is fundamentally important yet challenging. Acceleration-based metrics such as Dynamic Body Acceleration (DBA), obtained from accelerometers, are potential proxies for energy expenditure, yet have not been previously validated in primates. Here, we validated DBA in black lion tamarins (Leontopithecus chrysopygus) by comparison to doubly labelled water (DLW) in 10 captive tamarins housed at the Rio de Janeiro Primate Centre. Individuals were equipped over 48 hours with a backpack with a tri-axial accelerometer and received an intra-peritoneal DLW injection at the beginning of the experiment, with blood samples taken 1 and 48h later. Daily Energy Expenditure by DLW was 326 (SD=66) kJ/day, close to expected values for primates of their size. The accelerometers recorded at 40 Hz, collecting >6.9 million records per axis for each individual. Individual DBA metrics were calculated and regressed against DLW daily energy measures. From this regression, we found a consistent and significant linear relationship (R2 = 0.46) between DLW and DBA, which could be improved by the incorporation of activity and resting time information (R2 = 0.52). Our results provide the first estimates of total daily energy expenditure for black lion tamarins and a validation of the method for estimating energy expenditure through accelerometers. Given the similar levels of total energy expenditure of captive and wild primates, this method can now be used in the field to estimate the energy cost of black lion tamarin movements in its natural environment. 1 SO_SCPLOWUMMARYC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSTATEMENTC_SCPLOWDynamic body acceleration was validated against doubly labelled water in black lion tamarins, showing it is a useful tool for measuring free-living energy demands.

zoology↗

bioRxiv2022

Wake respirometry may quantify stress and energetics of free-living animals

Quantifying activity-specific energy expenditure in free-living animals is a major challenge as current methods require calibration in the lab and animal capture. We propose "wake respirometry", a new method of quantifying fine-scale changes in CO2 production in unrestrained animals, using a non-dispersive infrared CO2 sensor positioned downwind of the animal i.e. in its wake. We parameterise the dispersion of CO2 in a wake using known CO2 concentrations, flow rates and wind speeds. Tests with three bird species in a wind tunnel demonstrated that the system can resolve breath-by-breath changes in CO2 concentration, with clear exhalation signatures increasing in period and integral with body size. Changes in physiological state were detectable following handling, flight and exposure to a perceived threat. We discuss the potential of wake respirometry to quantify stress and respiratory patterns in wild animals and estimate activity-specific metabolic rates through the full integration of CO2 production across the wake.

ecology↗

bioRxiv2021

Ecological inference using data from accelerometers needs careful protocols

O_LIAccelerometers in animal-attached tags have proven to be powerful tools in behavioural ecology, being used to determine behaviour and provide proxies for movement-based energy expenditure. Researchers are collecting and archiving data across systems, seasons and device types. However, in order to use data repositories to draw ecological inference, we need to establish the error introduced according to sensor type and position on the study animal and establish protocols for error assessment and minimization. C_LIO_LIUsing laboratory trials, we examine the absolute accuracy of tri-axial accelerometers and determine how inaccuracies impact measurements of dynamic body acceleration (DBA), as the main acceleration-based proxy for energy expenditure. We then examine how tag type and placement affect the acceleration signal in birds using (i) pigeons Columba livia flying in a wind tunnel, with tags mounted simultaneously in two positions, (ii) back- and tail-mounted tags deployed on wild kittiwakes Rissa tridactyla. Finally, we (iii) present a case study where two generations of tag were deployed using different attachment procedures on red-tailed tropicbirds Phaethon rubricauda foraging in different seasons. C_LIO_LIBench tests showed that individual acceleration axes required a two-level correction (representing up to 4.3% of the total value) to eliminate measurement error. This resulted in DBA differences of up to 5% between calibrated and uncalibrated tags for humans walking at different speeds. Device position was associated with greater variation in DBA, with upper- and lower back-mounted tags in pigeons varying by 9%, and tail- and back-mounted tags varying by 13% in kittiwakes. Finally, DBA varied by 25% in tropicbirds between seasons, which may be attributable to tag attachment procedures. C_LIO_LIAccelerometer accuracy, tag placement, and attachment details critically affect the signal amplitude and thereby the ability of the system to detect biologically meaningful phenomena. We propose a simple method to calibrate accelerometers that should be used prior to deployments and archived with resulting data, suggest a way that researchers can assess accuracy in previously collected data, and caution that variable tag placement and attachment can increase sensor noise and even generate trends that have no biological meaning. C_LI

animal behavior and cognition↗

bioRxiv2021

Structure, activity and inhibition of human TMPRSS2, a protease implicated in SARS-CoV-2 activation

Transmembrane protease, serine 2 (TMPRSS2) has been identified as key host cell factor for viral entry and pathogenesis of SARS-coronavirus-2 (SARS-CoV-2). Specifically, TMPRSS2 proteolytically processes the SARS-CoV-2 Spike (S) Protein, enabling virus-host membrane fusion and infection of the lungs. We present here an efficient recombinant production strategy for enzymatically active TMPRSS2 ectodomain enabling enzymatic characterization, and the 1.95 [A] X-ray crystal structure. To stabilize the enzyme for co-crystallization, we pre-treated TMPRSS2 with the synthetic protease inhibitor nafamosat to form a stable but slowly reversible (15 hour half-life) phenylguanidino acyl-enzyme complex. Our study provides a structural basis for the potent but non-specific inhibition by nafamostat and identifies distinguishing features of the TMPRSS2 substrate binding pocket that will guide future generations of inhibitors to improve selectivity. TMPRSS2 cleaved recombinant SARS-CoV-2 S protein ectodomain at the canonical S1/S2 cleavage site and at least two additional minor sites previously uncharacterized. We established enzymatic activity and inhibition assays that enabled ranking of clinical protease inhibitors with half-maximal inhibitory concentrations ranging from 1.7 nM to 120 M and determination of inhibitor mechanisms of action. These results provide a body of data and reagents to support future drug development efforts to selectively inhibit TMPRSS2 and other type 2 transmembrane serine proteases involved in viral glycoprotein processing, in order to combat current and future viral threats. SUMMARY PARAGRAPHViruses hijack the biochemical activity of host proteins for viral invasion and replication. Transmembrane protease, serine-2 (TMPRSS2) is a surface-expressed protease implicated in the activation of influenza A, influenza B, and coronaviruses, including SARS-CoV-2, to drive efficient infection of the lungs1-5. TMPRSS2 is an attractive target for antiviral therapies, as inhibiting its proteolytic activity blocks efficient viral entry5,6. However, a structural and biochemical understanding of the protease has remained elusive and no selective inhibitors are available. We engineered on-demand activatable TMPRSS2 ectodomain and determined the 1.95 [A] X-ray crystal structure of the stabilized acyl-enzyme after treatment with nafamostat, a protease inhibitor under investigation as a COVID-19 therapeutic. The structure reveals unique features of the TMPRSS2 substrate recognition pocket and domain architecture, and explains the potent, but nonselective inhibition by nafamostat. TMPRSS2 efficiently cleaved the SARS-CoV-2 S protein at the canonical S1/S2 site as well as two minor sites previously uncharacterized. We further established a robust enzymatic assay system and characterized inhibition by two additional clinical protease inhibitors under study for COVID-19, camostat and bromhexine. Our results provide a body of data and reagents to enable ongoing drug development efforts to selectively inhibit TMPRSS2 and other TTSPs involved in viral glycoprotein processing, in order to combat current and future viral threats.

biochemistry↗

bioRxiv2021

Fine-scale changes in speed and altitude suggest protean movements in homing pigeon flights

The flight speeds that animals should adopt to minimise energy expenditure in different scenarios can be predicted by the curve of power against speed. However, relatively few studies have examined how animals respond to the landscape below them, which could affect speed through modifications in climb rate and perceived predation risk. We equipped homing pigeons (Columba livia) with high frequency loggers to examine how flight speed varies in relation to topography and land cover, predicting that these parameters may have a substantial impact on flight speed and hence cost. Pigeons showed mixed evidence for an energy saving strategy, as they minimised climb rates by starting their ascent ahead of hills, but selected rapid speeds in their ascents. Birds did not modify their speed substantially in relation to land cover, but higher speeds were observed during descending flight, highlighting the importance to consider the rate of change in altitude before estimating power use from speed. Finally, we document an unexpected variability in speed and altitude over fine scales; a source of substantial inefficiency. We suggest this may a form of protean behaviour adopted to reduce predation risk when flocking is not an option, and that such a strategy could be widespread.

animal behavior and cognition↗

bioRxiv2020

Forces experienced by instrumented animals depend on lifestyle

Animal-attached devices have transformed our understanding of vertebrate ecology. However, to be acceptable, researchers must minimize tag-related harm. The long-standing recommendation that tag masses should not exceed 3% of the animals body mass ignores tag forces generated by movement. We used collar-attached accelerometers on four free-ranging carnivores, spanning two orders of magnitude in mass, to reveal that during movement, forces exerted by 3% tags were generally equivalent to 4-19% of the animals masses, with a record of 54% in a hunting cheetah. Controlled studies on domestic dogs revealed how the tag forces are dictated by animal gait and speed but appear largely invariant of body mass. This fundamentally changes how acceptable tag mass limits should be determined, requiring cognizance of animal athleticism. One Sentence SummaryThere can be no universal rule for collar-tag masses as a percentage of carrier mass since tag forces depend on lifestyle.

ecology↗

bioRxiv2020

Why did the animal turn? Time-varying step selection analysis for inference between observed turning points in high frequency data

O_LIStep selection analysis (SSA) is a fundamental technique for uncovering the drivers of animal movement decisions. Its typical use has been to view an animal as "selecting" each measured location, given its current (and possibly previous) locations. Although an animal is unlikely to make decisions precisely at the times its locations are measured, if data are gathered at a relatively low frequency (every few minutes or hours) this is often the best that can be done. Nowadays, though, tracking data is increasingly gathered at very high frequencies, often [≥]1Hz, so it may be possible to exploit these data to perform more behaviourally-meaningful step selection analysis. C_LIO_LIHere, we present a technique to do this. We first use an existing algorithm to determine the turning-points in an animals movement path. We define a "step" to be a straight-line movement between successive turning-points. We then construct a generalised version of integrated SSA (iSSA), called time-varying iSSA (tiSSA), which deals with the fact that turning-points are usually irregularly spaced in time. We demonstrate the efficacy of tiSSA by application to data on both simulated animals and free-ranging goats (Capra aegagrus hircus), comparing our results to those of regular iSSA with locations that are separated by a constant time-interval. C_LIO_LIUsing (regular) iSSA with constant time-steps can give results that are misleading compared to using tiSSA with the actual turns made by the animals. Furthermore, tiSSA can be used to infer covariates that are dependent on the time between turns, which is not possible with regular iSSA. As an example, we show that our study animals tend to spend less time between successive turns when the ground is rockier and/or the temperature is hotter. C_LIO_LIBy constructing a step selection technique that works between observed turning-points of animals, we enable step selection to be used on high-frequency movement data, which are becoming increasingly prevalent in modern biologging studies. Furthermore, since turning-points can be viewed as decisions, our method places step selection analysis on a more behaviourally-meaningful footing compared to previous techniques. C_LI

ecology↗