Biology subjects

Layton, A.

Publications and source records attributed to Layton, A..

At least 19 recordsLinked to original sources

bioRxiv2026

A Type VII-secreted toxin enables inter-mycobacterial competition

Summary ParagraphMost bacteria live in complex environments where resources are scarce and competition is fierce. These organisms have evolved mechanisms to compete with other bacteria, often through the specialised secretion of proteinaceous toxins. Mycobacteria have not previously been reported to engage in this form of competition. The thick and unusual cell wall of mycobacteria, comprised of peptidoglycan, arabinogalactan and mycolic acids, is generally thought to be highly protective to these bacteria. Many enzymes have evolved to maintain this structure, including the GH183 family, which cleaves arabinogalactan. Here, we establish for the first time that some mycobacteria have weaponised a subset of these endo-D-arabinanases to enable inter-bacterial competition. We show that mycobacteria secrete an endo-D-arabinanase effector via the type VII secretion system that specifically targets the arabinogalactan layer of the Mycobacteriales cell envelope. Using structural biology and biochemistry, we identify the molecular basis for this activity and reveal a new protein family that protects the bacterium from the activity of this toxin. Finally, our data uncover widespread T7-secreted toxins in the Mycobacteriales, pointing to extensive inter-mycobacterial competition.

microbiology↗

bioRxiv2025

Unraveling the Mechanistic Links Between Blood Pressure Regulation and Calcium-Magnesium Homeostasis: Insights into Hypertension, Hyperparathyroidism, and Mineral Disorders

The systems regulating blood pressure and calcium-magnesium (Ca2+-Mg2+) homeostasis are increasingly recognized to have significant, clinically relevant interactions, where alterations in one can lead to significant changes in the other. In this study, we developed a computational model integrating blood pressure regulation and Ca2{square}-Mg2{square} homeostasis in a male rat. We simulated various conditions, including hypertension, Ca2{square}, Mg2{square}, and vitamin D3 deficiencies, and primary hyperparathyroidism. Simulations of hypertension, induced by various stimuli like increased renin or aldosterone secretion, demonstrated significant effects on parathyroid hormone (PTH), calcitriol, renal Ca2{square}/Mg2{square} handling, and bone resorption. Dietary Ca2{square}, Mg2{square}, and vitamin D3 deficiencies elevated mean arterial pressure, with Mg2{square} deficiency having a stronger effect. Furthermore, the model predicted that primary hyperparathyroidism elevates PTH, Ca2{square}, and calcitriol, leading to increased mean arterial pressure and bone loss. Overall, this model provides valuable insights into the mechanistic links between blood pressure regulation and Ca2{square}-Mg2{square} homeostasis, offering insights into clinical conditions like hypertension and hyperparathyroidism.

systems biology↗

bioRxiv2025

Non-canonical inflammasome drives intrinsic anti-microbial responses in human Natural Killer (NK) cells.

Inflammasome pathways are critical for detecting pathogens and initiating inflammatory responses, yet how individual cell types configure these signalling platforms remains poorly understood. Here, we demonstrate that human Natural Killer cells possess distinct inflammasome machinery, lacking canonical components and innate sensors (NLRP3, NLRC4, TLR4) but harbour a functional non-canonical inflammasome (NCI). Using Salmonella enterica Typhimurium infection of primary human NK cells, we show that cytosolic bacterial access triggers caspase-4-dependent pyroptosis and IL-18 secretion, without canonical inflammasome activation or IL-1{beta} production. Strikingly, murine NK cells express inflammasome transcripts but lack functional caspase-11 protein and do not undergo pyroptosis upon infection, revealing species-specific post-transcriptional regulation. We further identify IL-12, but not IFN{gamma}, as a priming signal for NCI components in human NK cells, a functional distinction from macrophages and epithelial cells. Together, these findings reveal that human NK cells have evolved a specialised inflammasome with unique regulatory inputs, establishing these cells as autonomous sensors of intracellular Gram-negative infection.

immunology↗

bioRxiv2024

Predicted Effect of Circadian Regulation of Renal Transporters in a Hypertensive Rat

The kidney regulates extracellular fluid and electrolyte homeostasis. Its function is modulated by the renin-angiotensin-aldosterone system (RAAS). Overactivation of the RAAS, such as in chronic Ang II infusion, promotes vasoconstriction, anti-natriuresis, and hypertension. Kidney function is also modulated by circadian clocks. Indeed, glomerular filtration rate, filtered electrolyte loads, urine volume, and urinary excretion all exhibit notable diurnal rhythms, which reflect, in part, the regulation of renal transporter proteins by circadian clock genes. Key renal transporters that are regulated by clock gene proteins include sodium-hydrogen exchanger 3 (NHE3), sodium-glucose cotransporter 1 (SGLT1), Na+-K+-2Cl- cotransporter (NKCC2), Na+-Cl- cotransporter (NCC), and epithelial sodium channel (ENaC), which are targeted by diuretics used to treat hypertension. The objective of the present study was to assess the effect of administration time on the natriuretic and diuretic effects of loop, thiazide, and K+-sparing diuretics, which are common treatments for hypertension, and how those effects differ between a normotensive and hypertensive kidney. Loop diuretics inhibit NKCC2 on the apical membrane of the thick ascending limb; notably, In Ang II-induced hypertension, NKCC2 is differentially regulated along the medullary versus cortical thick ascending limb. Thiazide diuretics inhibit NCC on the distal convoluted tubule, and K+-sparing diuretics inhibit ENaC on the connecting tubule and collecting duct. We simulated Na+ transporter inhibition using computational models of kidney function at different times of day. The simulation results predicted qualitatively similar diurnal oscillations in segmental transport in the normotensive and hypertensive kidneys, and highlighted significant time-of-day differences in the natriuresis, diuresis, and kaliuresis responses. NEW & NOTEWORTHYChronic infusion of angiotensin II promotes vasoconstriction, salt retention, and hypertension. Blood pressure and kidney function exhibit circadian rhythms. Given the diurnal variations in the expression levels of key renal electrolyte transporters, how do the natriuretic and diuretic effects of diuretics, a common treatment for hypertension that targets renal transporters, vary during the day? To answer this question, we simulated Na+ transporter inhibition using computational models of kidney function at different times of day.

physiology↗

bioRxiv2023

Modeling Sex Differences in the Effects of Diuretics in Renal Epithelial Transport during Angiotensin II-induced Hypertension

Chronic angiotensin II (AngII) infusion is an experimental model that induces hypertension in rodents. The natriuresis, diuresis, and blood pressure responses differ between males and females, perhaps unexpectedly, given the rodent kidney, which plays a key role in blood pressure regulation, exhibit marked sex differences. Those sex differences include morphology, hemodynamics, and, under healthy (undrugged) conditions, solute and electrolyte transporter abundance. Notably, compared to the male rat nephron, the female rat nephron exhibits lower Na+/H+ exchanger 3 (NHE3) activity along the proximal tubule, but higher Na+ transporter activities along the distal segments. AngII infusion-induced hypertension induces a pressure natriuretic response that reduces NHE3 activity and shifts Na+ transport capacity downstream, to different extents in the two sexes. The goals of this study are (i) to understand how the sexually dimorphic responses differentially impact segmental electrolyte transport following a 14- day AngII infusion, and (ii) to identify and explain any sex differences in the effects of loop diuretics, thiazide diuretics, and K+-sparing diuretics. To achieve those goals, we developed sex-specific computational models of renal epithelial transport of electrolytes and water. Model simulations suggest that the NHE3 downregulation in the proximal tubule is a major contributor to natriuresis and diuresis in hypertension, with a stronger effect in males. Due to the downstream shift of Na+ transport load in hypertension, all three diuretic classes are predicted to induce stronger natriuretic and diuretic effects under hypertension compared to normotension, especially in females. New and NoteworthySex differences in the prevalence of hypertension are found in humans and animal models. The kidney, which plays an important role in blood pressure regulation, exhibits sex differences in morphology, hemodynamics, and membrane transporter distributions. This computational modeling study provides insights into how the sexually dimorphic responses to a 14-day angiotensin II infusion differentially impact segmental electrolyte transport. Simulations results also explain sex differences in the effects of loop diuretics, thiazide diuretics, and K+-sparing diuretics.

physiology↗

bioRxiv2023

Modeling magnesium and calcium transport along male rat kidney and the effects of diuretics

Calcium (Ca2+) and magnesium (Mg2+) are essential for cellular function. The kidneys play an important role in maintaining the homeostasis of these cations. Their reabsorption along the nephron is dependent on distinct trans- and paracellular pathways, and is coupled to the transport of other electrolytes. Notably, sodium (Na+) transport establishes an electrochemical gradient to drive Ca2+ reabsorption. Consequently, alterations in renal Na+ handling, under pathophysiological conditions or pharmacological manipulations, can have major effects on Ca2+ transport. One such condition is the administration of diuretics, which are used to treat a large range of clinical conditions, but most commonly for the management of blood pressure and fluid balance. While the pharmacological targets of diuretics typically directly mediate Na+ transport, they also indirectly affect renal Ca2+ and Mg2+ handling, i.e., by establishing a prerequisite electrochemical gradient. Thus, substantial alterations in divalent cation handling can be expected following diuretic treatment. To investigate renal Ca2+ and Mg2 handling, and how those processes are affected by diuretics treatment, we have developed sex-specific computational models of electrolyte transport along the nephrons. Model simulations indicate that along the proximal tubule and thick ascending limb, the transport of Ca2+ and Mg2+ occusr in parallel with Na+, but those processes are dissociated along the distal convoluted tubule. We also simulated the effects of acute administration of loop, thiazide, and K-sparing diuretics. The model predicted significantly increased Mg2+ excretion, no significant alteration in Mg2+ excretion, and significantly decreased Mg2+ excretion on treatment with loop, thiazide, and K-sparing diuretics, respectively, in agreement with experimental studies. The present models can be used to conduct in silico studies on how the kidney adapts to alterations in Ca2+ and Mg2+ homeostasis during various physiological and pathophysiological conditions, such as pregnancy, diabetes, and chronic kidney disease.

physiology↗

bioRxiv2023

Impact of angiotensin-receptor blockers on intrarenal renin-angiotensin system activity in hypertension: A PK/PD modelling study

The renin-angiotensin system (RAS) is a primary regulator of volume homeostasis and blood pressure, whose over-activation is commonly associated with hypertension. Indeed, medications that target the RAS are generally effective in reducing blood pressure. However, more can be learned about how these medications influence the intrarenal RAS. Angiotensin-receptor blockers (ARBs) in particular have been shown to exert different effects on the intrarenal and systemic RASs in various experimental models of hypertension. In rats chronically infused with angiotensin II (Ang II), ARBs consistently prevent intrarenal, but not systemic Ang II levels from rising. The former effect is sufficient in preventing the development of hypertension. The regulation of intrarenal RAS, independently of the systemic RAS, by ARBs has been hypothesized to be mediated by the inhibition of all positive feedback loops inherent to the intrarenal RAS, also known as the "key point breakdown effect." To investigate the validity of this hypothesis, we developed a PK/PD model of the ARB Losartan that considers the kidney, and applied the model to study how this class of medication influences intrarenal RAS activity and consequently blood pressure regulation in male rats. Simulations indicate that ARBs more effectively inhibit the activation of the intrarenal RAS because, unlike in the plasma, this process relies on the accumulation of cell-associated Ang II. We hypothesize that it is by blocking this intracellular uptake pathway, and restricting Ang II to extracellular regions of the kidney where the peptide cannot initiate downstream signalling, that Losartan normalizes blood pressure. While the key point break down effect assists in this response, it alone is not sufficient. Our results highlight the intrarenal RAS as the key pharmacological target of ARB treatment and emphasize the importance of this local tissue RAS in the development of hypertension.

physiology↗

bioRxiv2023

Coupling of renal sodium and calcium transport: A modeling analysis

Calcium (Ca2+) transport along the nephron occurs via specific transcellular and paracellular pathways, and is coupled to the transport of other electrolytes. Notably sodium (Na+) transport establishes an electrochemical gradient to drive Ca2+ reabsorption. Hence, alterations in renal Na+ handling, under pathophysiological conditions or pharmacological manipulations, can have major effects on Ca2+ transport. An important class of pharmacological agent is diuretics, which are commonly prescribed for the management of blood pressure and fluid balance. The pharmacological targets of diuretics generally directly facilitate Na+ transport, but also indirectly affect renal Ca2+ handling. To better understand the underlying mechanisms, we have developed a computational model of electrolyte transport along the superficial nephron in the kidney of a male and female rat. Sex differences in renal Ca2+ handling are represented. Model simulations predict in the female rat nephron lower Ca2+ reabsorption in the proximal tubule and thick ascending limb, but higher reabsorption in the late distal convoluted tubule and connecting tubule, compared to the male nephron. The male rat kidney model yields a higher urinary calcium excretion than female, consistent with animal experiments. Additionally, we conducted simulations of inhibition of channels and transporters that play a major role in Na+ and Ca2+ transport. Model results indicate that along the proximal tubule and ascending thick ascending limb, Ca2+ and Na+ transport occurs in parallel, but those processes are dissociated in the distal convoluted tubule. Simulations also reveal sex-specific responses to different pharmacological manipulations.

physiology↗

bioRxiv2023

Adversarial training improves model interpretability in single-cell RNA-seq analysis

For predictive computational models to be considered reliable in crucial areas such as biology and medicine, it is essential for them to be accurate, robust, and interpretable. A sufficiently robust model should not have its output affected significantly by a slight change in the input. Also, these models should be able to explain how a decision is made. Efforts have been made to improve the robustness and interpretability of these models as independent challenges, however, the effect of robustness and interpretability on each other is poorly understood. Here, we show that predicting cell type based on single-cell RNA-seq data is more robust by adversarially training a deep learning model. Surprisingly, we find this also leads to improved model interpretability, as measured by identifying genes important for classification. We believe that adversarial training will be generally useful to improve deep learning robustness and interpretability, thereby facilitating biological discovery.

bioinformatics↗

bioRxiv2023

Sex and time-of-day differences in kidney oxygen consumption

Renal hemodynamics, renal transporter expression levels, and urine excretion all exhibit circadian variations. Disturbance of these diurnal patterns is associated with hypertension and chronic kidney disease. Renal hemodynamics determines oxygen delivery, whereas renal transport and metabolism determines oxygen consumption. The balance between oxygen delivery and consumption then yields renal oxygenation. We hypothesized that kidney oxygenation also demonstrates 24-h periodicity. Another notable modulator of kidney function is sex, which has impacts on renal hemodynamics and transport function that are regulated by as well as independent of the circadian clock. The goal of this study was to investigate the diurnal and sexual variations in renal oxygen consumption and oxygenation. For this purpose, we developed computational models of rat kidney function that represent sexual dimorphism and circadian variation in renal hemodynamics and transporter activities. Model simulations predicted substantial differences in tubular Na+ transport and oxygen consumption among different nephron segments. We also simulated the effect of loop diuretics, which are used in the treatment of renal hypoxia, on the outer medullary oxygen tension. Our model predicted a significantly higher effect of loop diuretics on renal oxygenation in female rats compared to male rats. In addition, loop diuretics were more effective when administered during the active phase.

physiology↗

bioRxiv2023

The Power of Two: integrating deep diffusion models and variational autoencoders for single-cell transcriptomics analysis

Discovering a lower-dimensional embedding of single-cell data can greatly improve downstream analysis. The embedding should encapsulate both the high-level semantics and low-level variations in order to be meaningful and interpretable. Although current generative models have been used to learn such a low-dimensional representation, they have several limitations. Here, we introduce scVAEDer, a scalable deep-learning model that combines the power of variational autoencoders and deep diffusion models to learn a meaningful representation which can capture both global semantics and local variations in the data. By using the learned embedding, we show that scVAEDer can generate novel scRNA-seq data, predict the effect of the perturbation on various cell types, identify changes in gene expression during dedifferentiation, and detect master regulators in a biological process.

bioinformatics↗

bioRxiv2022

Fatecode: Cell fate regulator prediction using classification autoencoder perturbation

Cell reprogramming, which guides the conversion between cell states, is a promising technology for tissue repair and regeneration. Typically, a group of key genes, or master regulators, are manipulated to control cell fate, with the ultimate goal of accelerating recovery from diseases or injuries. Of importance is the ability to correctly identify the master regulators from single-cell transcriptomics datasets. To accomplish that goal, we propose Fatecode, a computational method that combines in silico perturbation experiments with cell trajectory modeling using deep learning to predict master regulators and key pathways controlling cell fate. Fatecode uses only scRNA-seq data from wild-type samples to learn and predict how cell type distribution changes following a perturbation. We assessed Fatecodes performance using simulations from a mechanistic gene regulatory network model and diverse gene expression profiles covering blood and brain development. Our results suggest that Fatecode can detect known master regulators of cell fate from single-cell transcriptomics datasets. That capability points to Fatecodes potential in accelerating the discovery of cell fate regulators that can be used to engineer and grow cells for therapeutic use in regenerative medicine applications.

systems biology↗

bioRxiv2022

Determinants of natriuretic, diuretic, and kaliuretic effects of diuretics: Sex and administration time

Sex differences in renal function and blood pressure have been widely described across many species. Blood pressure dips during sleep and peaks in the early morning. Similarly, glomerular filtration rate, filtered electrolyte loads, urine volume, and urinary excretion all exhibit notable diurnal rhythms, which reflect, in part, the regulation of renal transporter proteins by circadian clock genes. That regulation is sexually dimorphic; as such, sex and time-of-day are not two independent regulators of kidney function and blood pressure. The objective of this study is to assess the effect of sex and administration time on the natriuretic and diuretic effects of loop, thiazide, and K+-sparing diuretics, which are common treatment for hypertension. Loop diuretics inhibit NKCC2 on the apical membrane of the thick ascending limb, thiazide diuretics inhibit NCC on the distal convoluted tubule, and K+-sparing diuretics inhibit ENaC on the connecting tubule and collecting duct. We simulate Na+ transporter inhibition using our sex- and time-of-day-specific computational models of mouse kidney function. Simulations results highlight significant sex and time-of day differences in drug response. Loop diuretics induce larger natriuretic and diuretic effects during the active phase. The natriuretic and diuretic effects of thiazide diuretics exhibit sex and time-of-day differences, whereas these effects of K+-sparing diuretics exhibit significant time-of-day difference in females only. Kaliuretic effect depends on the type of diuretics and time of administration. The present computational models can be a useful tool in chronotherapy, to tailor drug administration time to match the bodys diurnal rhythms to optimize the drug effect.

physiology↗

bioRxiv2022

A Complete Set of Equations for a Computational Model of Electrolyte and Water Transport along the Nephrons in a Mammalian Kidney

To investigate kidney under different physiological and pharmacological conditions, we have developed and applied computational models of electrolyte and water transport along nephrons in a kidney. The models predict spredict luminal fluid flow, hydrostatic pressure, membrane potential, luminal and cytosolic solute concentrations, and transcellular and paracellular fluxes through transporters and channels. The complete set of model equations are presented here.

physiology↗

bioRxiv2022

Modelling Sex Differences in Circadian Regulation of Kidney Function of the Mouse

Kidney function is regulated by the circadian clock. Not only do glomerular filtration rate (GFR) and urinary excretion oscillate during the day, the expressions of several renal transporter proteins also exhibit circadian rhythms. Interestingly, the circadian regulation of these transporters may be sexually dimorphic. Thus, the goal of this study is to investigate the mechanisms by which kidney function of the mouse is modulated by sex and time of day. To accomplish this, we have developed the first computational models of epithelial water and solute transport along the mouse nephrons that represent the effects of sex and circadian clock on renal hemodynamics and transporter activity. We conduct simulations to study how the circadian control of renal transport genes affects overall kidney function, and how that process differs between male and female mice. Simulation results predict that tubular transport differs substantially among segments, with relative variations in water and Na+ reabsorption along the proximal tubules and thick ascending limb tracking that of GFR. In contrast, relative variations in distal segment transport are much larger, with Na+ reabsorption almost doubling during the active phase. Oscillations in Na+ transport drive K+ transport variations in the opposite direction. Model simulations of BMAL1 knockout mice predict a significant reduction in net Na+ reabsorption along the distal segments in both sexes, but more so in males than females. This can be attributed to the reduction of mean ENaC activity in males only, a sex-specific effect that may lead to a reduction in blood pressure in males.

physiology↗

bioRxiv2022

A Comparative Study of Epithelial Transport in the Rat and Mouse Kidneys: Modelling and Analysis

The goal of the present study was to investigate the functional implications of sex and species differences in the pattern of transporters along nephrons in the rat and mouse kidney, as reported by Veiras et al. (J Am Soc Nephrol 28: 3504-3517, 2017). To do so, we developed the first sex-specific computational models of epithelial water and solute transport along the nephrons from male and female mouse kidneys, and conducted simulations along with our published rat models. These models account for the sex differences in the abundance of apical and basolateral transporters, glomerular filtration rate, and tubular dimensions. Model simulations predict that 73% and 57% of filtered Na+ is reabsorbed by the proximal tubules of male and female rat kidneys, respectively. Due to their smaller transport area and lower NHE3 activity, the proximal tubules in the mouse kidney reabsorb a significantly smaller fraction of the filtered Na+, at 53% in male and only 34% in female. The lower proximal fractional Na+ reabsorption in female kidneys of both rat and mouse is due primarily to their smaller transport area, lower Na+/H+ exchanger activity, and lower claudin-2 abundance, culminating in significantly larger fractional delivery of water and Na+ to the downstream nephron segments in female kidneys. Conversely, the female distal nephron exhibits a higher abundance of key Na+ transporters, including Na+-Cl- cotransporters in both species, epithelial Na+ channels for the female rat, and Na+-K+-Cl-cotransporters for the female mouse. The higher abundance of transporters accounts for the enhanced water and Na+ transport along the female rat and mouse distal nephrons, relative to the respective male, resulting in similar urine excretion between the sexes. Model simulations indicate that the sex and species differences in renal transporter patterns may partially explain the experimental observation that, in response to a saline load, the diuretic and natriuretic responses were more rapid in female rats than males, but no significant sex difference was found in mice. These computational models can serve as a valuable tool for analyzing findings from experimental studies conducted in rats and mice, especially those involving genetic modifications.

physiology↗

bioRxiv2022

A Complete Set of Equations and Parameters for the Computational Model of Mitochondrial Function for the Proximal Convoluted Tubule and Medullary Thick Ascending Limb Cells in the Rat Kidney

To investigate mitochondrial function of renal epithelial cells under different tissue oxygenation levels, we have developed and applied computational models of mitochondrial function of the proximal convoluted tubule and medullary thick ascending limb cells. The models predict several key cellular quantities, including ATP generation, P/O (phosphate/oxygen) ratio, proton motive force, electrical potential gradient, oxygen consumption, the redox state of important electron carriers, and ATP consumption. The complete set of model equations and parameters are presented here, together with local and global sensitivity analysis results.

cell biology↗

bioRxiv2021

A Mathematical Model of Mitochondria in Proximal Tubule and Thick Ascending Limb Cells

Mitochondria are a key player in several kinds of tissue injury, and are even the ultimate cause of certain diseases. In this work we introduce new models of mitochondrial ATP generation in multiple tissues, including liver hepatocytes and the medullary thick ascending limb in the kidney. Using this model, we predict these tissues responses to hypoxia, uncoupling, ischemia-reperfusion, and oxidative phosphorylation dysfunction. Our results suggest mechanisms explaining differences in robustness of mitochondrial function across tissues.The medullary thick ascending limb and proximal tubule in the kidney both experience a high metabolic demand, while having lower baseline activity of oxidative phosphorylation relative to the liver. These factors make these tissues susceptible to dysfunction of ComplexIII. A lower baseline oxygen tension observed in the thick ascending limb makes it susceptible to Complex IV. On the other hand, since the liver lacks these risk factors, and has higher baseline rates of glycolysis, it is less susceptible to all kinds of oxidative phosphorylation dysfunction.

physiology↗