Search

The inner mitochondrial membrane (IMM) is the site of bulk ATP generation in cells and has a broadly conserved lipid composition enriched in unsaturated phospholipids and cardiolipin (CL). While proteins that shape the IMM and its characteristic cristae membranes (CM) have been defined, specific mechanisms by which mitochondrial lipids dictate its structure and function have yet to be elucidated. Here we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions shape CM morphology and ATP generation. When modulating fatty acid unsaturation in engineered yeast strains, we observed that loss of di-unsaturated phospholipids (PLs) led to a breakpoint in IMM topology and respiratory capacity. We found that PL unsaturation modulates the organization of ATP synthases that shape cristae ridges. Based on molecular modeling of mitochondrial-specific membrane adaptations, we hypothesized that conical lipids like CL buffer against the effects of saturation on the IMM. In cells, we discovered that loss of CL collapses the IMM at intermediate levels of PL saturation, an effect that is independent of ATP synthase oligomerization. To explain this interaction, we employed a continuum modeling approach, finding that lipid and protein-mediated curvatures are predicted to act in concert to form curved membranes in the IMM. The model highlighted a snapthrough instability in cristae tubule formation, which could drive IMM collapse upon small changes in composition. The interaction between CL and di-unsaturated PLs suggests that growth conditions that alter the fatty acid pool, such as oxygen availability, could define CL function. While loss of CL only has a minimal phenotype under standard laboratory conditions, we show that its synthesis is essential under microaerobic conditions that better mimic natural yeast fermentation. Lipid and protein-mediated mechanisms of curvature generation can thus act together to support mitochondrial architecture under changing environments.

Membrane curvature is essential to diverse cellular functions. While classically attributed to structured domains, recent work illustrates that intrinsically disordered proteins are also potent drivers of membrane bending. Specifically, repulsive interactions among disordered domains drive convex bending, while attractive interactions, which lead to liquid-like condensates, drive concave bending. How might disordered domains that contain both repulsive and attractive domains impact curvature? Here we examine chimeras that combine attractive and repulsive interactions. When the attractive domain was closer to the membrane, its condensation amplified steric pressure among repulsive domains, leading to convex curvature. In contrast, when the repulsive domain was closer to the membrane, attractive interactions dominated, resulting in concave curvature. Further, a transition from convex to concave curvature occurred with increasing ionic strength, which reduced repulsion while enhancing condensation. In agreement with a simple mechanical model, these results illustrate a set of design rules for membrane bending by disordered proteins.

In the highly dynamic metabolic landscape of a neuron, mitochondrial membrane architectures can provide critical insight into the unique energy balance of the cell. Current theoretical calculations of functional outputs like ATP and heat often represent mitochondria as idealized geometries and therefore can miscalculate the metabolic fluxes. To analyze mitochondrial morphology in neurons of mouse cerebellum neuropil, 3D tracings of complete synaptic and axonal mitochondria were constructed using a database of serial TEM tomography images and converted to watertight meshes with minimal distortion of the original microscopy volumes with a granularity of 1.6 nanometer isotropic voxels. The resulting in silico representations were subsequently quantified by differential geometry methods in terms of the mean and Gaussian curvatures, surface areas, volumes, and membrane motifs, all of which can alter the metabolic output of the organelle. Finally, we identify structural motifs that are present across this population of mitochondria; observations which may contribute to future modeling studies of mitochondrial physiology and metabolism in neurons.

Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared to approximation-based methods (e.g., finite element method), the class of discrete mesh models offers greater flexibility to simulate complex physics and shapes in three dimensions; its formulation produces an efficient algorithm while maintaining coordinate-free geometric descriptions. However, ambiguities in geometric definitions in the discrete context have led to a lack of consensus on which discrete mesh model is theoretically and numerically optimal; a bijective relationship between the terms contributing to both the energy and forces from the discrete and smooth geometric theories remains to be established. We address this and present an extensible framework, Mem3DG, for modeling 3D mechanochemical dynamics of membranes based on Discrete Differential Geometry (DDG) on triangulated meshes. The formalism of DDG resolves the inconsistency and provides a unifying perspective on how to relate the smooth and discrete energy and forces. To demonstrate, Mem3DG is used to model a sequence of examples with increasing mechanochemical complexity: recovering classical shape transformations such as 1) biconcave disk, dumb-bell, and unduloid and 2) spherical bud on spherical, flat-patch membrane; investigating how the coupling of membrane mechanics with protein mobility jointly affects phase and shape transformation. As high-resolution 3D imaging of membrane ultrastructure becomes more readily available, we envision Mem3DG to be applied as an end-to-end tool to simulate realistic cell geometry under user-specified mechanochemical conditions.Why it mattersCellular membranes have shapes and shape changes which characterize cells/organelles, and support nutrient trafficking among other critical processes. Modeling membrane shape changes using mechanical principles can provide insight into how cells robustly bend membranes to support life. Mathematical and computational strategies to solve the equations describing membrane shape evolution can be complex and challenging without simplifying assumptions. Here, we present a new, general, numerical approach to model arbitrary 3D membrane shapes in response to interaction with curvature sensing and generating membrane proteins. The accompanying implementation, Mem3DG, is a software tool to make computational membrane mechanics accessible to the general researcher.HighlightsIntroduces a discrete theory for membrane mechanics which connects with smooth theoryDiscrete energy/force are functions of basic geometric quantitiesRecipes for extending the discrete framework with additional physics are providedDescribes a user-friendly software implementation called Mem3DGMem3DG is designed to facilitate modeling in tandem with experimental studiesSignificance and noveltyHelfrich Hamiltonian is widely used to model biomembranes. Many numerical methods have been developed to solve the geometric PDE. Compared to approximation-based methods, discrete-mesh-based models have many advantages when incorporating multiphysics in 3D due to their flexibility, efficiency, and straightforward implementation. However, there is no consensus on which mesh-based model is optimal, and a connection between the discrete and smooth geometric theory remains obscure. In this work, we provide a unifying perspective by identifying fundamental geometric invariants of the discrete force derived from a discrete energy. As a demonstration of generality of the framework to various physics, we follow a formulaic procedure to derive additional physics such as interfacial line tension, surface-bulk adsorption, protein lateral diffusion, and curvature-dependent protein aggregation.

Biological aerosols, typically identified through their fluorescence properties, strongly influence clouds and climate. Sea spray aerosol (SSA) particles are a major source of biological aerosols, but detection in the atmosphere is challenging due to potential interference from other sources. Here, the fluorescence signature of isolated SSA, produced using laboratory-based aerosol generation methods, was analyzed and compared with two commonly used fluorescence techniques: excitation-emission matrix spectroscopy (EEMS) and the wideband integrated bioaerosol sensor (WIBS). A range of dynamic biological ocean scenarios were tested to compare EEMS and WIBS analyses of SSA. Both techniques revealed similar trends in SSA fluorescence intensity in response to changes in ocean microbiology, demonstrating the potential to use the WIBS to measure fluorescent aerosols alongside EEMS bulk solution measurements. Together, these instruments revealed a unique fluorescence signature of isolated, nascent SSA and, for the first time, a size-segregated emission of fluorescent species in SSA. Additionally, the fluorescence signature of aerosolized marine bacterial isolates was characterized and showed similar fluorescence peaks to those of SSA, suggesting that bacteria are a contributor to SSA fluorescence. Through investigation of isolated SSA, this study provides a reference for future identification of marine biological aerosols in a complex atmosphere.

The protein, azurin, has enabled the study of the tryptophan radical. Upon UV excitation of tyrosine-deficient apoazurin and in the presence of a Co(III) electron acceptor, the neutral radical (W48•) is formed. The lifetime of W48• in apoazurin is 41 s, which is shorter than the lifetime of several hours in Zn-substituted azurin. Molecular dynamics simulations revealed enhanced fluctuations of apoazurin which likely destabilize W48•. The photophysics of W48 was investigated to probe the precursor state for ET. The phosphorescence intensity was eliminated in the presence of an electron acceptor while the fluorescence was unchanged; this quenching of the phosphorescence is attributed to ET. The kinetics associated with W48• were examined with a model that incorporates intersystem crossing, ET, deprotonation, and decay of the cation radical. The estimated rate constants for ET (6 × 106 s-1) and deprotonation (3 × 105 s-1) are in agreement with a photoinduced mechanism where W48• is derived from the triplet state. The triplet as the precursor state for ET was supported by photolysis of apoazurin with 280 nm in the absence and presence of triplet-absorbing 405 nm light. Absorption bands from the neutral radical were observed only in the presence of blue light.

Dendritic spines act as biochemical computational units and must adapt their responses according to their activation history. Calcium influx acts as the first signaling step during postsynaptic activation and is a determinant of synaptic weight change. Dendritic spines also come in a variety of sizes and shapes. To probe the relationship between calcium dynamics and spine morphology, we used a stochastic reaction-diffusion model of calcium dynamics in idealized and realistic geometries. We show that despite the stochastic nature of the various calcium channels, receptors, and pumps, spine size and shape can modulate calcium dynamics and subsequently synaptic weight updates in a deterministic manner. Through a series of exhaustive simulations and analyses, we found that the calcium dynamics and synaptic weight change depend on the volume-to-surface area of the spine. The relationships between calcium dynamics and spine morphology identified in idealized geometries also hold in realistic geometries, suggesting that there are geometrically determined deterministic relationships that may modulate synaptic weight change.

Background: Marathon participation is becoming increasingly popular among individuals ≥40 years of age. Little is known about the prevalence of subclinical coronary artery disease (CAD) and corresponding ischemia in this patient population. The study objectives are: (1) to characterize the prevalence of silent CAD in marathoners ≥ 40 years old using cardiac computed tomography angiography (CCT); and (2) if subclinical CAD was detected, to determine the functional significance of occult lesions by stress echocardiography (SE). Methods: Marathoners aged ≥ 40 years who completed a full marathon between 2018 and 2019 were recruited to undergo a prospective CCT. Coronary artery stenosis was graded as zero, mild (1%-49%), moderate (50%-69%), or severe (> 70%). All study participants diagnosed with mild-to-severe atherosclerotic CAD on CCT further underwent functional imaging with exercise treadmill SE. Results: A total of 65 individuals (53 ± 7 years, 65% males, 24 ± 3 kg/m2) underwent a prospective CCT within 12 months of marathon completion. Of the total study population, 13 participants (20%) were diagnosed with CAD, of whom 10 (77%) had mild disease, 1 (8%) had moderate disease, and 2 (15%) had severe disease by CCT. Despite the identification of subclinical CAD on CCT, none of the 13 patients had any evidence of inducible ischemia on SE. Conclusions: This is the first study to incorporate both CCT and SE in the evaluation of subclinical CAD in marathoners ≥40 years old. Although the overall prevalence of anatomic CAD was 20%, there was no evidence of functional ischemia in this highly competitive cohort. Résumé: Contexte: Les marathons ont gagné en popularité auprès des individus âgés de 40 ans ou plus. On en sait toutefois peu sur la prévalence de la coronaropathie subclinique et de l’ischémie qui lui est associée dans cette population de patients. L’étude visait à 1) caractériser la prévalence de la coronaropathie silencieuse chez les marathoniens âgés de 40 ans ou plus à l’aide d’une angiographie cardiaque par tomodensitométrie (ACTDM) si une coronaropathie subclinique était détectée, à déterminer l’importance fonctionnelle des lésions occultes par une échocardiographie d’effort (EE). Méthodologie: Des marathoniens âgés de 40 ans ou plus ayant réalisé un marathon entre 2018 et 2019 ont été recrutés et soumis à une ACTDM prospective. Les sténoses des artères coronaires étaient classées selon une échelle allant de zéro, légère (1 à 49 %), modérée (50 à 69 %) à sévère (> 70 %). Tous les participants à l’étude ayant reçu un diagnostic de coronaropathie athéroscléreuse légère à sévère à la suite de l’ACTDM ont été soumis à une imagerie fonctionnelle avec EE sur tapis roulant. Résultats: Au total, 65 sujets (53 ± 7 ans, 65 % d’hommes, 24 ± 3 kg/m2) ont été soumis à une ACTDM prospective dans un délai de 12 mois à la suite de leur dernier marathon. Dans l’ensemble de la population à l’étude, 13 participants (20 %) ont reçu un diagnostic de coronaropathie; 10 (77 %) présentaient une maladie bénigne, 1 (8 %) présentait une maladie modérée et 2 (15 %) présentaient une maladie sévère selon l’ACTDM. Même si une coronaropathie subclinique a été diagnostiquée lors de l’ACTDM, aucun des 13 patients ne présentait de signe d’ischémie inductible à l’EE. Conclusions: Il s’agit de la première étude à utiliser l’ACTDM et l’EE pour évaluer la présence d’une coronaropathie chez des marathoniens âgés de 40 ou plus. Même si la prévalence globale de la coronaropathie anatomique était de 20 %, il n’y avait aucun signe d’ischémie fonctionnelle au sein de cette cohorte hautement compétitive.

Sea spray aerosols (SSA) play an important role in radiative forcing by directly scattering solar radiation and indirectly by acting as cloud condensation or ice nuclei. These climate-relevant aero...

Sea spray aerosols (SSAs) affect the Earth’s climate directly by scattering solar radiation and indirectly by acting as ice and cloud condensation nuclei. The relative magnitude of these effects remains uncertain, in part, from substantial compositional and morphological variability between individual particles. Here, the evolving heterogeneity within populations of primary SSAs produced from wave breaking of natural seawater within a wave flume is investigated. Over the course of the study, two successive phytoplankton blooms were induced in the seawater. The morphology, organic volume fraction, hygroscopicity, phase state, and surface tension of individual SSAs collected via deposition on a substrate were characterized using atomic force microscopy. Particles between ca. 0.3 and 1 μm in volume equivalent diameter displayed a distinctive morphology revealing an inorganic core coated with an organic shell. The inferred organic volume fraction was the largest at the peak of the first bloom. The corresponding shell thicknesses ranged from 21 to 40 nm at 20% relative humidity (RH). The organic shell phase state of the majority of the particles during both blooms was semisolid at 20% and 60% RH. At 20% RH, a minor fraction of the organic shells behaved as a solid, while at 60% RH some behaved as liquids during the first bloom. Similar results were evident at 20% RH for the second bloom but with no observed liquid particles at 60% RH. The thick, semisolid organic coatings could potentially reduce atmospheric water and gas uptake efficiencies onto SSAs at lower RH, along with the potential for ice nucleating activity. However, at 80% RH, the SSAs deliquesced and exhibited liquid-like behavior with surface tension values measured over individual particles of 41–87 mN m–1, demonstrating high particle-to-particle variability. The suppressed surface tension at 80% RH relative to pure water is attributed to the high concentrations of surface-active organic compounds, potentially further limiting the diffusion rate of gas molecules through the interface.

The modification of neural circuits depends on the strengthening and weakening of synaptic connections. Synaptic strength is often correlated to the density of the ionotropic, glutamatergic receptors, AMPARs, (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors) at the postsynaptic density (PSD). While AMPAR density is known to change based on complex biological signalling cascades, the effect of geometric factors such as dendritic spine shape, size and curvature remain poorly understood. In this work, we developed a deterministic, spatiotemporal model to study the dynamics of AMPARs during long-term potentiation (LTP). This model includes a minimal set of biochemical events that represent the upstream signalling events, trafficking of AMPARs to and from the PSD, lateral diffusion in the plane of the spine membrane, and the presence of an extrasynaptic AMPAR pool. Using idealized and realistic spine geometries, we show that the dynamics and increase of bound AMPARs at the PSD depends on a combination of endo- and exocytosis, membrane diffusion, the availability of free AMPARs and intracellular signalling interactions. We also found non-monotonic relationships between spine volume and the change in AMPARs at the PSD, suggesting that spines restrict changes in AMPARs to optimize resources and prevent runaway potentiation. KEY POINTS: Synaptic plasticity involves dynamic biochemical and physical remodelling of small protrusions called dendritic spines along the dendrites of neurons. Proper synaptic functionality within these spines requires changes in receptor number at the synapse, which has implications for downstream neural functions, such as learning and memory formation. In addition to being signalling subcompartments, spines also have unique morphological features that can play a role in regulating receptor dynamics on the synaptic surface. We have developed a spatiotemporal model that couples biochemical signalling and receptor trafficking modalities in idealized and realistic spine geometries to investigate the role of biochemical and biophysical factors in synaptic plasticity. Using this model, we highlight the importance of spine size and shape in regulating bound AMPA receptor dynamics that govern synaptic plasticity, and predict how spine shape might act to reset synaptic plasticity as a built-in resource optimization and regulation tool.

Timely access to emergency funding has been identified as a bottleneck for outbreak response in Nigeria. In February 2019, a new revolving outbreak investigation fund (ROIF) was established by the Nigeria Centre for Disease Control (NCDC). We abstracted the date of NCDC notification, date of verification, and date of response for 25 events that occurred prior to establishing the fund (April 2017 to August 2019) and for 8 events that occurred after establishing the fund (February to October 2019). The median time to notification (1 day) and to verification (0 days) did not change after establishing the ROIF, but the median time to response significantly decreased, from 6 days to 2 days (

Across the world, the level of pandemic preparedness varies and no country is fully prepared to respond to all public health events. The International Health Regulations 2005 require state parties to develop core capacities to prevent, detect, and respond to public health events of international concern. In addition to annual self-assessment, these capacities are peer reviewed once every 5 years through the voluntary Joint External Evaluation (JEE). In this article, we share Nigeria's experience of conducting a country-led midterm self-assessment using a slightly modified application of the second edition of the World Health Organization (WHO) JEE and the new WHO benchmarks tool. Despite more stringent scoring criteria in the revised JEE tool, average scoring showed modest capacity improvements in 2019 compared with 2017. Of the 19 technical areas assessed, 11 improved, 5 did not change, and 3 had lower scores. No technical area attained the highest-level scoring of 5. Understanding the level of, and gaps in, pandemic preparedness enables state parties to develop plans to improve health security; the outcome of the assessment included the development of a 12-month operational plan. Countries need to intentionally invest in preparedness by using existing frameworks (eg, JEE) to better understand the status of their preparedness. This will ensure ownership of developed plans with shared responsibilities by all key stakeholders across all levels of government.

Organic emissions from coastal waters play an important but poorly understood role in atmospheric chemistry in coastal regions. A mesocosm experiment focusing on facilitated biological blooms in coastal seawater, SeaSCAPE (Sea Spray Chemistry and Particle Evolution), was performed to study emission of volatile gases, primary sea spray aerosol, and formation of secondary marine aerosol as a function of ocean biological and chemical processes. Here, we report observations of aerosol-phase benzothiazoles in a marine atmospheric context with complementary measurements of dissolved-phase benzothiazoles. Though previously reported dissolved in polluted coastal waters, we report the first direct evidence of the transfer of these molecules from seawater into the atmosphere. We also report the first gas-phase observations of benzothiazole in the environment absent a direct industrial, urban, or rubber-based source. From the identities and temporal dynamics of the dissolved and aerosol species, we conclude that the presence of benzothiazoles in the coastal water (and thereby their emissions into the atmosphere) is primarily attributable to anthropogenic sources. Oxidation experiments to explore the atmospheric fate of gas-phase benzothiazole show that it produces secondary aerosol and gas-phase SO2, making it a potential contributor to secondary marine aerosol formation in coastal regions and a participant in atmospheric sulfur chemistry.

Background: The global spread of the SARS-CoV-2 virus highlights both the importance of frontline healthcare workers (HCW) in pandemic response and their heightened vulnerability during infectious disease outbreaks. Adequate preparation, including the development of human resources for health (HRH) is essential to an effective response. ICAP at Columbia University (ICAP) partnered with Resolve to Save Lives and MOHs to design an emergency training initiative for frontline HCW in 11 African countries, using a competency-based backward-design approach and tailoring training delivery and health facility selection based on country context, location and known COVID-19 community transmission. Methods: Pre and Post-test assessments were conducted on participants completing the COVID-19 training. Parametric and non-parametric methods were used to examine average individual-level changes from pre- to post-test, and compare performance between countries, cadres, sex and facility types. A post evaluation online training survey using Qualtrics was distributed to assess participants’ satisfaction and explore training relevance and impact on their ability to address COVID-19 in their facilities and communities. Results: A total of 8,797 HCW at 945 health facilities were trained between June 2020 and October 2020. Training duration ranged from 1 to 8 days (median: 3days) and consisted of in person, virtual or self guided training. Of the 8,105 (92%) HCW working at health facilities, the majority (62%) worked at secondary level facilities as these were the HF targeted for COVID-19 patients. Paired pre- and post-test results were available for 2,370 (25%) trainees, and 1,768 (18%) participants completed the post-evaluation training survey. On average, participants increased their pre- to post-test scores by 15 percentage points (95% CI: 0.14, 0.15). While confidence in their ability to manage COVID-19 was high following the training, respondents reported that lack of access to testing kits (55%) and PPE (50%), limited space in the facility to isolate patients (45%), and understaffing (39%) were major barriers. Conclusion: Ongoing investment in health systems and focused attention to health workforce capacity building is critical to outbreak response. The success of our short-term IPC training initiative was due both to the speed, rigor and flexibility of its design and delivery, and to the pre-existing systems, resources, and partnerships that enabled its rapid implementation

Background Health workers (HWs) in Africa face challenges accessing and learning from existing online training opportunities. To address these challenges, we developed a modular, self-paced, mobile-ready and work-relevant online course covering foundational infection prevention and control (IPC) concepts. Here, we evaluate the first pilot of this course, conducted with HWs in Nigeria. Methods We used a learner-centered design and prototyping process to create a new approach to delivering online training for HWs. The resulting course comprised 10 self-paced modules optimized for use on mobile devices. Modules presented IPC vignettes in which learning was driven by short assessment questions with feedback. Learners were recruited by distributing a link to the training through Nigeria-based email lists, WhatsApp groups and similar networks of HWs, managers and allied professionals. The course was open to learners for 8 weeks. We tracked question responses and time on task with platform analytics and assessed learning gains with pre- and post-testing. Significance was evaluated with the Wilcoxon signed-rank test, and effect size was calculated using Cohen’s d. Results Three hundred seventy-two learners, with roles across the health system, enrolled in the training; 59% completed all 10 modules and earned a certificate. Baseline knowledge of foundational IPC concepts was low, as measured by pre-test scores (29%). Post-test scores were significantly higher at 54% (effect size 1.22, 95% confidence interval 1.00-1.44). Learning gains were significant both among learners with low pre-test scores and among those who scored higher on the pre-test. We used the Net Promoter Score (NPS), a common user experience metric, to evaluate the training. The NPS was + 62, which is slightly higher than published scores of other self-paced online learning experiences. Conclusions High completion rates, significant learning gains and positive feedback indicate that self-paced, mobile-ready training that emphasizes short, low-stakes assessment questions can be an effective, scalable way to train HWs who choose to enroll. Low pre-test scores suggest that there are gaps in IPC knowledge among this learner population.

The nuclear protein DEK is an endogenous DNA-binding chromatin factor regulating hematopoiesis. DEK is one of only 2 known secreted nuclear chromatin factors, but whether and how extracellular DEK regulates hematopoiesis is not known. We demonstrated that extracellular DEK greatly enhanced ex vivo expansion of cytokine-stimulated human and mouse hematopoietic stem cells (HSCs) and regulated HSC and hematopoietic progenitor cell (HPC) numbers in vivo and in vitro as determined both phenotypically (by flow cytometry) and functionally (through transplantation and colony formation assays). Recombinant DEK increased long-term HSC numbers and decreased HPC numbers through a mechanism mediated by the CXC chemokine receptor CXCR2 and heparan sulfate proteoglycans (HSPGs) (as determined utilizing Cxcr2-/- mice, blocking CXCR2 antibodies, and 3 different HSPG inhibitors) that was associated with enhanced phosphorylation of ERK1/2, AKT, and p38 MAPK. To determine whether extracellular DEK required nuclear function to regulate hematopoiesis, we utilized 2 mutant forms of DEK: one that lacked its nuclear translocation signal and one that lacked DNA-binding ability. Both altered HSC and HPC numbers in vivo or in vitro, suggesting the nuclear function of DEK is not required. Thus, DEK acts as a hematopoietic cytokine, with the potential for clinical applicability.

To advance the mission of in silico cell biology, modeling the interactions of large and complex biological systems becomes increasingly relevant. The combination of molecular dynamics (MD) simulations and Markov state models (MSMs) has enabled the construction of simplified models of molecular kinetics on long timescales. Despite its success, this approach is inherently limited by the size of the molecular system. With increasing size of macromolecular complexes, the number of independent or weakly coupled subsystems increases, and the number of global system states increases exponentially, making the sampling of all distinct global states unfeasible. In this work, we present a technique called independent Markov decomposition (IMD) that leverages weak coupling between subsystems to compute a global kinetic model without requiring the sampling of all combinatorial states of subsystems. We give a theoretical basis for IMD and propose an approach for finding and validating such a decomposition. Using empirical few-state MSMs of ion channel models that are well established in electrophysiology, we demonstrate that IMD models can reproduce experimental conductance measurements with a major reduction in sampling compared with a standard MSM approach. We further show how to find the optimal partition of all-atom protein simulations into weakly coupled subunits.

Each year, over one hundred million people become ill and tens of thousands die from exposure to viruses and bacteria from sewage transported to the ocean by rivers, estuaries, stormwater, and other coastal discharges. Water activities and seafood consumption have been emphasized as the major exposure pathways to coastal water pollution. In contrast, relatively little is known about the potential for airborne exposure to pollutants and pathogens from contaminated seawater. The Cross Surfzone/Inner-shelf Dye Exchange (CSIDE) study was a large-scale experiment designed to investigate the transport pathways of water pollution along the coast by releasing dye into the surfzone in Imperial Beach, CA. Additionally, we leveraged this ocean-focused study to investigate potential airborne transmission of coastal water pollution by collecting complementary air samples along the coast and inland. Aerial measurements tracked sea surface dye concentrations along 5+ km of coast at 2 m × 2 m resolution. Dye was detected in the air over land for the first 2 days during two of the three dye releases, as far as 668 m inland and 720 m downwind of the ocean. These coordinated water/air measurements, comparing dye concentrations in the air and upwind source waters, provide insights into the factors that lead to the water-to-air transfer of pollutants. These findings show that coastal water pollution can reach people through an airborne pathway and this needs to be taken into account when assessing the full impact of coastal ocean pollution on public health. This study sets the stage for further studies to determine the details and importance of airborne exposure to sewage-based pathogens and toxins in order to fully assess the impact of coastal pollution on public health.

Lipopolysaccharides (LPS) in sea spray aerosol (SSA) particles have recently been shown to undergo heterogeneous reactions with HNO3 in the atmosphere. Here, we integrate theory and experiment to further investigate how the most abundant sea salt cations, Na+, Mg2+, and Ca2+, impact HNO3 reactions with LPS-containing SSA particles. Aerosol reaction flow tube studies show that heterogeneous reactions of SSA particles with divalent cation (Mg2+ and Ca2+) and LPS signatures were less reactive with HNO3 than those dominated by monovalent cations (Na+). All-atom molecular dynamics simulations of model LPS aggregates suggest that divalent cations cross-link the oligosaccharide chains to increase molecular aggregation and rigidity, which changes the particle phase and morphology, decreases water diffusion, and consequently decreases the reactive uptake of HNO3. This study provides new insight into how complex chemical interactions between ocean-derived salts and biogenic organic species can impact the heterogeneous reactivity of SSA particles.

Dendritic spines act as biochemical computational units and must adapt their responses according to their activation history. Calcium influx acts as the first signaling step during post-synaptic activation and is a determinant of synaptic weight change. Dendritic spines also come in a variety of sizes and shapes. To probe the relationship between calcium dynamics and spine morphology, we used a stochastic reaction-diffusion model of calcium dynamics in idealized and realistic geometries. We show that despite the stochastic nature of the various calcium channels, receptors, and pumps, spine size and shape can modulate calcium dynamics and subsequently synaptic weight updates in a deterministic manner. Through a series of exhaustive simulations, we find that the calcium dynamics and synaptic weight change depend on the volume-to-surface area of the spine. The relationships between calcium dynamics and spine morphology identified in idealized geometries also hold in realistic geometries suggesting that there are geometrically determined deterministic relationships that may modulate synaptic weight change.