Model-based inference of a plant-specific dual role for HOPS in regulating guard cell vacuole fusion.

Stomata are the pores on a leaf surface that regulate gas exchange. Each stoma consists of two guard cells whose movements regulate pore opening and thereby control CO2 fixation and water loss. Guard cell movements depend in part on the remodeling of vacuoles, which have been observed to change from a highly fragmented state to a fused morphology during stomata opening. This change in morphology requires a membrane fusion mechanism that responds rapidly to environmental signals, allowing plants to respond to diurnal and stress cues. With guard cell vacuoles being both large and responsive to external signals, stomata represent a unique system in which to delineate mechanisms of membrane fusion. Fusion of vacuole membranes is a highly conserved process in eukaryotes, with key roles played by two multi-subunit complexes: HOPS (homotypic fusion and vacuolar protein sorting) and SNARE (soluble NSF attachment protein receptor). HOPS is a vacuole tethering factor that is thought to chaperone SNAREs from apposing vacuole membranes into a fusion-competent complex capable of rearranging membranes. To resolve a counter-intuitive observation regarding the role of HOPS in regulating plant vacuole morphology, we derived a quantitative model of vacuole fusion dynamics and used it to generate testable predictions about HOPS-SNARE interactions. We derived our model by applying simulation-based inference to integrate prior knowledge about molecular interactions with limited, qualitative observations of emergent vacuole phenotypes. By constraining the model parameters to yield the emergent outcomes observed for stoma opening - as induced by two distinct chemical treatments - we predicted a dual role for HOPS and identified a stalled form of the SNARE complex that differs from phenomena reported in yeast. We predict that HOPS has contradictory actions at different points in the fusion signaling pathway, promoting the formation of SNARE complexes, but limiting their activity.

Adaptive language model training for molecular design.

The vast size of chemical space necessitates computational approaches to automate and accelerate the design of molecular sequences to guide experimental efforts for drug discovery. Genetic algorithms provide a useful framework to incrementally generate molecules by applying mutations to known chemical structures. Recently, masked language models have been applied to automate the mutation process by leveraging large compound libraries to learn commonly occurring chemical sequences (i.e., using tokenization) and predict rearrangements (i.e., using mask prediction). Here, we consider how language models can be adapted to improve molecule generation for different optimization tasks. We use two different generation strategies for comparison, fixed and adaptive. The fixed strategy uses a pre-trained model to generate mutations; the adaptive strategy trains the language model on each new generation of molecules selected for target properties during optimization. Our results show that the adaptive strategy allows the language model to more closely fit the distribution of molecules in the population. Therefore, for enhanced fitness optimization, we suggest the use of the fixed strategy during an initial phase followed by the use of the adaptive strategy. We demonstrate the impact of adaptive training by searching for molecules that optimize both heuristic metrics, drug-likeness and synthesizability, as well as predicted protein binding affinity from a surrogate model. Our results show that the adaptive strategy provides a significant improvement in fitness optimization compared to the fixed pre-trained model, empowering the application of language models to molecular design tasks.

Cholesterol-induced suppression of Kir2 channels is mediated by decoupling at the inter-subunit interfaces.

Cholesterol is a major regulator of multiple types of ion channels. Although there is increasing information about cholesterol binding sites, the molecular mechanisms through which cholesterol binding alters channel function are virtually unknown. In this study, we used a combination of Martini coarse-grained simulations, a network theory-based analysis, and electrophysiology to determine the effect of cholesterol on the dynamic structure of the Kir2.2 channel. We found that increasing membrane cholesterol reduced the likelihood of contact between specific regions of the cytoplasmic and transmembrane domains of the channel, most prominently at the subunit-subunit interfaces of the cytosolic domains. This decrease in contact was mediated by pairwise interactions of specific residues and correlated to the stoichiometry of cholesterol binding events. The predictions of the model were tested by site-directed mutagenesis of two identified residues-V265 and H222-and high throughput electrophysiology.

Solving the puzzle of Fe homeostasis by integrating molecular, mathematical, and societal models.

To ensure optimal utilization and bioavailability, iron uptake, transport, subcellular localization, and assimilation are tightly regulated in plants. Herein, we examine recent advances in our understanding of cellular responses to Fe deficiency. We then use intracellular mechanisms of Fe homeostasis to discuss how formalizing cell biology knowledge via a mathematical model can advance discovery even when quantitative data is limited. Using simulation-based inference to identify plausible systems mechanisms that conform to known emergent phenotypes can yield novel, testable hypotheses to guide targeted experiments. However, this approach relies on the accurate encoding of domain-expert knowledge in exploratory mathematical models. We argue that this would be facilitated by fostering more "systems thinking" life scientists and that diversifying your research team may be a practical path to achieve that goal.

Predicting Inter-individual Variability During Lipid Resuscitation of Bupivacaine Cardiotoxicity in Rats: A Virtual Population Modeling Study.

INTRODUCTION: Intravenous lipid emulsions (ILE) have been credited for successful resuscitation in drug intoxication cases where other cardiac life-support methods have failed. However, inter-individual variability can function as a confounder that challenges our ability to define the scope of efficacy for lipid interventions, particularly as relevant data are scarce. To address this challenge, we developed a quantitative systems pharmacology model to predict outcome variability and shed light on causal mechanisms in a virtual population of rats subjected to bupivacaine toxicity and ILE intervention. MATERIALS AND METHODS: We combined a physiologically based pharmacokinetic-pharmacodynamic model with data from a small study in Sprague-Dawley rats to characterize individual-specific cardiac responses to lipid infusion. We used the resulting individual parameter estimates to posit a population distribution of responses to lipid infusion. On that basis, we constructed a large virtual population of rats (N = 10,000) undergoing lipid therapy following bupivacaine cardiotoxicity. RESULTS: Using unsupervised clustering to assign resuscitation endpoints, our simulations predicted that treatment with a 30% lipid emulsion increases bupivacaine median lethal dose (LD50) by 46% when compared with a simulated control fluid. Prior experimental findings indicated an LD50 increase of 48%. Causal analysis of the population data suggested that muscle accumulation rather than liver accumulation of bupivacaine drives survival outcomes. CONCLUSION: Our results represent a successful prediction of complex, dynamic physiological outcomes over a virtual population. Despite being informed by very limited data, our mechanistic model predicted a plausible range of treatment outcomes that accurately predicts changes in LD50 when extrapolated to putatively toxic doses of bupivacaine. Furthermore, causal analysis of the predicted survival outcomes indicated a critical synergy between scavenging and direct cardiotonic mechanisms of ILE action.

Molecular Dynamics Simulations of Kir2.2 Interactions with an Ensemble of Cholesterol Molecules.

Cholesterol is a major regulator of multiple types of ion channels, but the specific mechanisms and the dynamics of its interactions with the channels are not well understood. Kir2 channels were shown to be sensitive to cholesterol through direct interactions with "cholesterol-sensitive" regions on the channel protein. In this work, we used Martini coarse-grained simulations to analyze the long (µs) timescale dynamics of cholesterol with Kir2.2 channels embedded into a model membrane containing POPC phospholipid with 30 mol% cholesterol. This approach allows us to simulate the dynamic, unbiased migration of cholesterol molecules from the lipid membrane environment to the protein surface of Kir2.2 and explore the favorability of cholesterol interactions at both surface sites and recessed pockets of the channel. We found that the cholesterol environment surrounding Kir channels forms a complex milieu of different short- and long-term interactions, with multiple cholesterol molecules concurrently interacting with the channel. Furthermore, utilizing principles from network theory, we identified four discrete cholesterol-binding sites within the previously identified cholesterol-sensitive region that exist depending on the conformational state of the channel-open or closed. We also discovered that a twofold decrease in the cholesterol level of the membrane, which we found earlier to increase Kir2 activity, results in a site-specific decrease of cholesterol occupancy at these sites in both the open and closed states: cholesterol molecules at the deepest of these discrete sites shows no change in occupancy at different cholesterol levels, whereas the remaining sites showed a marked decrease in occupancy.

Oxygen and Hydrogen Isotopes in Human Hair and Tap Water: Modeling Relationships in a Modern Mexican Population.

This study investigated the relationship between 18O and 2H isotopes in samples of Mexican hair and drinking water. The purpose of this study was twofold: to quantify the relationship between isotopes in Mexican hair and tap water, in order to understand the impact of water stress and differing socioeconomic status on accurate predictions of drinking water; and to determine whether currently existing semimechanistic models can accurately represent the relationship between hair and tap water. This study used a subset of paired samples of human hair (n = 62) and tap water (n = 76). Isotope values in tap water ranged from -11.4‰ to -4.3‰ and -79.1‰ to -22.5‰, and in hair from +9.5‰ to +16.1‰ and -90.8‰ to -53.7‰, for δ18O and δ2H, respectively. The most depleted δ18O and δ2H hair values came from individuals in the state of Morelos. For modern Mexican populations, positive correlations between isotopes in hair and water were not significant, with correlation coefficients r = 0.61 (p = 0.05) and r = 0.60 (p = 0.06) for 18O and 2H, respectively. Error-in-variables regression yielded linear fits that were somewhat better for 2H relative to 18O: δ18Oh = 0.183 [±0.132] δ18Otw + 15.7 [±0.9]‰ (r2 = 0.23); δ2Hh = 0.181 [±0.076] δ2Htw - 64.0 [±3.0]‰ (r2 = 0.34). In short, data from this Mexican population did not exhibit the strong relationships between isotope values of 18O and 2H in tap water and hair that have been characteristic of other populations studied to date. Given the economic stratification of this region and the poor correlation between hair and water samples, the authors considered the possibility that l, the fraction of the diet derived from local sources, and fs, the fraction of nonexchangeable H in keratin that was fixed in vivo, are local rather than global parameters for this population. The authors estimated different values of l and fs for each location. Given the anticipated importance of the nonlocal dietary contribution, they treated the isotopic content of nonlocal food and the offset parameters for predicting isotopes in locally derived food as tuning parameters and compared the results with parameters based on the American supermarket diet. They found that, although O and H isotopes in water and hair maintained similar geographic distributions, O and H isotopes in tap water explained only a small part of the variation observed in hair samples. Compared to the standard American supermarket diet, the Mexican estimates for nonlocal diet and local diet offsets predicted regional distributions of l and fs that cleanly segregated urban areas from rural towns.

Differential Effects of Sterols on Ion Channels: Stereospecific Binding vs Stereospecific Response.

Numerous ion channels have been shown to be regulated by the level of membrane cholesterol, but the mechanisms responsible for these effects are still not well understood. The key question in the field is how to discriminate between the contributions of the two central mechanisms that might be responsible for the sensitivity of ion channels to cholesterol: specific sterol-protein interactions or regulation of channels by the bilayer physical properties. Comparative analysis of cholesterol and its isomers on the function of an ion channel is a powerful tool to achieve this goal. An increasing number of studies show that cholesterol regulates several types of ion channels in a stereospecific manner, suggesting an involvement of specific sterol-protein interactions. However in this chapter, we present evidence that the stereospecificity of cholesterol-ion channel interactions may be mediated, not by a lack of binding, as has been generally assumed, but by the specificity of the interaction, which results in a functional effect, in the case of native cholesterol, and a lack of functional effect, in the case of a cholesterol isomer. In other words, accumulating evidence suggests that the structural requirements of ion channel cholesterol-binding sites are lax, allowing chiral isomers of cholesterol to bind to the same site in a nonstereospecific way, but the ability of a sterol to confer a functional effect on the channel activity can still be stereospecific. This is an important distinction both conceptually and methodologically. Indeed, our analysis shows that the orientations of cholesterol and its chiral isomer ent-cholesterol within a hydrophobic binding pocket of Kir2.2 are significantly different, and we propose that this difference may underlie distinct functional outcomes.

Molecular-Scale Biophysical Modulation of an Endothelial Membrane by Oxidized Phospholipids.

The influence of two bioactive oxidized phospholipids on model bilayer properties, membrane packing, and endothelial cell biomechanics was investigated computationally and experimentally. The truncated tail phospholipids, 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphocholine (POVPC) and 1-palmitoyl-2-glutaroyl-sn-glycero-3-phosphocholine (PGPC), are two major oxidation products of the unsaturated phospholipid 1-palmitoyl-2-arachidonoyl-sn-glycero-phosphocholine. A combination of coarse-grained molecular dynamics simulations, Laurdan multiphoton imaging, and atomic force microscopy microindentation experiments was used to determine the impact of POVPC and PGPC on the structure of a multicomponent phospholipid bilayer and to assess the consequences of their incorporation on membrane packing and endothelial cell stiffness. Molecular simulations predicted differential bilayer perturbation effects of the two oxidized phospholipids based on the chemical identities of their truncated tails, including decreased bilayer packing, decreased bilayer bending modulus, and increased water penetration. Disruption of lipid order was consistent with Laurdan imaging results indicating that POVPC and PGPC decrease the lipid packing of both ordered and disordered membrane domains. Computational predictions of a larger membrane perturbation effect by PGPC correspond to greater stiffness of PGPC-treated endothelial cells observed by measuring cellular elastic moduli using atomic force microscopy. Our results suggest that disruptions in membrane structure by oxidized phospholipids play a role in the regulation of overall endothelial cell stiffness.

The emerging threat of superwarfarins: history, detection, mechanisms, and countermeasures.

Superwarfarins were developed following the emergence of warfarin resistance in rodents. Compared to warfarin, superwarfarins have much longer half-lives and stronger affinity to vitamin K epoxide reductase and therefore can cause death in warfarin-resistant rodents. By the mid-1970s, the superwarfarins brodifacoum and difenacoum were the most widely used rodenticides throughout the world. Unfortunately, increased use was accompanied by a rise in accidental poisonings, reaching >16,000 per year in the United States. Risk of exposure has become a concern since large quantities, up to hundreds of kilograms of rodent bait, are applied by aerial dispersion over regions with rodent infestations. Reports of intentional use of superwarfarins in civilian and military scenarios raise the specter of larger incidents or mass casualties. Unlike warfarin overdose, for which 1-2 days of treatment with vitamin K is effective, treatment of superwarfarin poisoning with vitamin K is limited by extremely high cost and can require daily treatment for a year or longer. Furthermore, superwarfarins have actions that are independent of their anticoagulant effects, including both vitamin K-dependent and -independent effects, which are not mitigated by vitamin K therapy. In this review, we summarize superwarfarin development, biology and pathophysiology, their threat as weapons, and possible therapeutic approaches.

Multi-modal contributions to detoxification of acute pharmacotoxicity by a triglyceride micro-emulsion.

Triglyceride micro-emulsions such as Intralipid® have been used to reverse cardiac toxicity induced by a number of drugs but reservations about their broad-spectrum applicability remain because of the poorly understood mechanism of action. Herein we report an integrated mechanism of reversal of bupivacaine toxicity that includes both transient drug scavenging and a cardiotonic effect that couple to accelerate movement of the toxin away from sites of toxicity. We thus propose a multi-modal therapeutic paradigm for colloidal bio-detoxification whereby a micro-emulsion both improves cardiac output and rapidly ferries the drug away from organs subject to toxicity. In vivo and in silico models of toxicity were combined to test the contribution of individual mechanisms and reveal the multi-modal role played by the cardiotonic and scavenging actions of the triglyceride suspension. These results suggest a method to predict which drug toxicities are most amenable to treatment and inform the design of next-generation therapeutics for drug overdose.

Resuscitation with lipid emulsion: dose-dependent recovery from cardiac pharmacotoxicity requires a cardiotonic effect.

BACKGROUND: Recent publications have questioned the validity of the "lipid sink" theory of lipid resuscitation while others have identified sink-independent effects and posed alternative mechanisms such as hemodilution. To address these issues, the authors tested the dose-dependent response to intravenous lipid emulsion during reversal of bupivacaine-induced cardiovascular toxicity in vivo. Subsequently, the authors modeled the relative contribution of volume resuscitation, drug sequestration, inotropy and combined drug sequestration, and inotropy to this response with the use of an in silico model. METHODS: Rats were surgically prepared to monitor cardiovascular metrics and deliver drugs. After catheterization and instrumentation, animals received a nonlethal dose of bupivacaine to produce transient cardiovascular toxicity, then were randomized to receive one of the four treatments: 30% intravenous lipid emulsion, 20% intravenous lipid emulsion, intravenous saline, or no treatment (n = 7 per condition; 28 total animals). Recovery responses were compared with the predictions of a pharmacokinetic-pharmacodynamic model parameterized using previously published laboratory data. RESULTS: Rats treated with lipid emulsions recovered faster than did rats treated with saline or no treatment. Intravenous lipid emulsion of 30% elicited the fastest hemodynamic recovery followed in order by 20% intravenous lipid emulsion, saline, and no treatment. An increase in arterial blood pressure underlay the recovery in both lipid emulsion-treated groups. Heart rates remained depressed in all four groups throughout the observation period. Model predictions mirrored the experimental recovery, and the model that combined volume, sequestration, and inotropy predicted in vivo results most accurately. CONCLUSION: Intravenous lipid emulsion accelerates cardiovascular recovery from bupivacaine toxicity in a dose-dependent manner, which is driven by a cardiotonic response that complements the previously reported sequestration effect.

Validity of the lipid sink as a mechanism for the reversal of local anesthetic systemic toxicity: a physiologically based pharmacokinetic model study.

BACKGROUND: In vitro observations support the lipid sink theory of therapeutic action by confirming the capacity of lipid emulsions to successfully uptake bupivacaine from aqueous media. However, competing hypotheses and some in/ex vivo small animal studies suggest that a metabolic or positive inotropic effect underlies the dramatic effects of lipid therapy. Controlled clinical tests to establish causality and mechanism of action are an impossibility. In an effort to quantitatively probe the merits of a "sink" mechanism, a physiologically based pharmacokinetic model has been developed that considers the binding action of plasma lipid. METHODS: The model includes no fitting parameters and accounts for concentration dependence of plasma protein and lipid:anesthetic binding as well as the metabolism of the lipid scavenger. Predicted pharmacokinetics were validated by comparison with data from healthy volunteers administered a nontoxic dose of bupivacaine. The model was augmented to simulate lipid therapy and extended to the case of accidental IV infusion of bupivacaine at levels known to cause systemic toxicity. RESULTS: The model yielded quantitative agreement with available pharmacokinetic data. Simulated lipid infusion following an IV overdose was predicted to yield (1) an increase in total plasma concentration, (2) a decrease in unbound concentration, and (3) a decrease in tissue content of bupivacaine. CONCLUSIONS: Results suggest that the timescale on which tissue content is reduced varies from organ to organ, with the concentration in the heart falling by 11% within 3 min. This initial study suggests that, in isolation, the lipid sink is insufficient to guarantee a reversal of systemic toxicity.

Fractional Order Analysis of Sephadex Gel Structures: NMR Measurements Reflecting Anomalous Diffusion.

We report the appearance of anomalous water diffusion in hydrophilic Sephadex gels observed using pulse field gradient (PFG) nuclear magnetic resonance (NMR). The NMR diffusion data was collected using a Varian 14.1 Tesla imaging system with a home-built RF saddle coil. A fractional order analysis of the data was used to characterize heterogeneity in the gels for the dynamics of water diffusion in this restricted environment. Several recent studies of anomalous diffusion have used the stretched exponential function to model the decay of the NMR signal, i.e., exp[-(bD)(α)], where D is the apparent diffusion constant, b is determined the experimental conditions (gradient pulse separation, durations and strength), and α is a measure of structural complexity. In this work, we consider a different case where the spatial Laplacian in the Bloch-Torrey equation is generalized to a fractional order model of diffusivity via a complexity parameter, ß, a space constant, µ, and a diffusion coefficient, D. This treatment reverts to the classical result for the integer order case. The fractional order decay model was fit to the diffusion-weighted signal attenuation for a range of b-values (0 < b < 4,000 s-mm(-2)). Throughout this range of b values, the parameters ß, µ and D, were found to correlate with the porosity and tortuosity of the gel structure.

Vesicle formation and endocytosis: function, machinery, mechanisms, and modeling.

Vesicle formation provides a means of cellular entry for extracellular substances and for recycling of membrane constituents. Mechanisms governing the two primary endocytic pathways (i.e., caveolae- and clathrin-mediated endocytosis, as well as newly emerging vesicular pathways) have become the focus of intense investigation to improve our understanding of nutrient, hormone, and drug delivery, as well as opportunistic invasion of pathogens. In this review of endocytosis, we broadly discuss the structural and signaling proteins that compose the molecular machinery governing endocytic vesicle formation (budding, invagination, and fission from the membrane), with some regard for the specificity observed in certain cell types and species. Important biochemical functions of endocytosis and diseases caused by their disruption also are discussed, along with the structures of key components of endocytic pathways and their known mechanistic contributions. The mechanisms by which principal components of the endocytic machinery are recruited to the plasma membrane, where they interact to induce vesicle formation, are discussed, together with computational approaches used to simulate simplified versions of endocytosis with the hope of clarifying aspects of vesicle formation that may be difficult to determine experimentally. Finally, we pose several unanswered questions intended to stimulate further research interest in the cell biology and modeling of endocytosis.

Study of miscible and immiscible flows in a microchannel using magnetic resonance imaging.

Magnetic resonance imaging (MRI) is a noninvasive technique that can be used to visualize mixing processes in optically opaque systems in up to three dimensions. Here, MRI has been used for the first time to obtain both cross-sectional velocity and concentration maps of flow through an optically opaque Y-shaped microfluidic sensor. Images of 23 micromx23 microm resolution were obtained for a channel of rectangular cross section (250 micromx500 microm) fed by two square inlets (250 micromx250 microm). Both miscible and immiscible liquid systems have been studied. These include a system in which the coupling of flow and mass transfer has been observed, as the diffusion of the analyte perturbs local hydrodynamics. MRI has been shown to be a versatile tool for the study of mixing processes in a microfluidic system via the multidimensional spatial resolution of flow and mass transfer.

Enhanced (13)C PFG NMR for the study of hydrodynamic dispersion in porous media.

PFG NMR methods are frequently used as a means of probing both coherent and incoherent molecular motions of fluids contained within heterogeneous porous media. The time scale over which molecular displacements can be probed in a conventional PFG NMR experiment is limited by the relaxation characteristics of (1)H - the nucleus that is typically observed. In multiphase systems, due to its sensitivity to susceptibility gradients and interactions with surfaces,(1)H signal is frequently characterized by rapid T(1) and T(2) relaxation. In this work, a heteronuclear approach to PFG NMR is demonstrated which allows the study of molecular displacement over extended time scales (and, consequently, length scales) by exploiting the longer relaxation time of (13)C. The method presented employs the DEPT technique of polarization transfer in order to enhance both the sensitivity and efficiency of (13)C detection. This hybrid coherence transfer PFG technique has been used to acquire displacement propagators for flow through a bead pack with an observation time of up to 35 s.

Distribution of surfactants in latex films: a Rutherford Backscattering study.

Uneven distribution of surfactant in dried latex films can affect the final film properties such as its water-resistance, gloss, and adhesiveness. Therefore, it is important to understand the driving force for surfactant transport during drying. In this paper, the accumulation of surfactant on the surface of poly(styrene-co-butyl acrylate) latex is studied using Rutherford Backscattering (RBS) and compared with results from a model that is based on the diffusive transport of particles and surfactant. Experimentally, a 30-50 nm thick surface layer, rich in surfactant, is seen and the concentration in the bulk of the film, obtained from RBS, agrees, at least qualitatively, with the model predictions for two of the surfactants tested.

In situ 13C DEPT-MRI as a tool to spatially resolve chemical conversion and selectivity of a heterogeneous catalytic reaction occurring in a fixed-bed reactor.

The distortionless enhancement by polarisation transfer (DEPT) nuclear magnetic resonance (NMR) technique, combined with magnetic resonance imaging (MRI), has been used to provide the first in situ spatially-resolved and quantitative measurement of chemical conversion and selectivity within a fixed-bed reactor using natural abundance 13C NMR.