Tropospheric carbonyl sulfide mass balance based on direct measurements of sulfur isotopes

Robust estimates for the rates and trends in terrestrial gross primary production (GPP; plant CO₂ uptake) are needed. Carbonyl sulfide (COS) is the major long-lived sulfur-bearing gas in the atmosphere and a promising proxy for GPP. Large uncertainties in estimating the relative magnitude of the COS sources and sinks limit this approach. Sulfur isotope measurements (³⁴S/³²S; δ³⁴S) have been suggested as a useful tool to constrain COS sources. Yet such measurements are currently scarce for the atmosphere and absent for the marine source and the plant sink, which are two main fluxes. Here we present sulfur isotopes measurements of marine and atmospheric COS, and of plant-uptake fractionation experiments. These measurements resulted in a complete data-based tropospheric COS isotopic mass balance, which allows improved partition of the sources. We found an isotopic (δ³⁴S ± SE) value of 13.9 ± 0.1‰ for the troposphere, with an isotopic seasonal cycle driven by plant uptake. This seasonality agrees with a fractionation of −1.9 ± 0.3‰ which we measured in plant-chamber experiments. Air samples with strong anthropogenic influence indicated an anthropogenic COS isotopic value of 8 ± 1‰. Samples of seawater-equilibrated-air indicate that the marine COS source has an isotopic value of 14.7 ± 1‰. Using our data-based mass balance, we constrained the relative contribution of the two main tropospheric COS sources resulting in 40 ± 17% for the anthropogenic source and 60 ± 20% for the oceanic source. This constraint is important for a better understanding of the global COS budget and its improved use for GPP determination.

The Earth system is going through rapid changes as the climate warms and CO₂ level rises. This rise in CO₂ is mitigated by plant uptake; hence, it is important to estimate global and regional photosynthesis rates and trends (1). Yet, robust tools for investigating these processes at a large scale are scarce (2). Recent studies suggest that carbonyl sulfide (COS) could provide an improved constraint on terrestrial photosynthesis (gross primary production, GPP) (2–12). COS is the major long-lived sulfur-bearing gas in the atmosphere and the main supplier of sulfur to the stratospheric sulfate aerosol layer (13), which exerts a cooling effect on the Earth’s surface and regulates stratospheric ozone chemistry (14).During terrestrial photosynthesis, COS diffuses into leaf stomata and is consumed by photosynthetic enzymes in a similar manner to CO₂ (3–5). Contrary to CO₂, COS undergoes rapid and irreversible hydrolysis mainly by the enzyme carbonic-anhydrase (6, 7). Thus, COS can be used as a proxy for the one-way flux of CO₂ removal from the atmosphere by terrestrial photosynthesis (2, 8–11). However, the large uncertainties in estimating the COS sources weaken this approach (10–12, 15). Tropospheric COS has two main sources: the oceans and anthropogenic emissions, and one main sink–terrestrial plant uptake (8, 10–13). Smaller sources include biomass burning, soil emissions, wetlands, volcanoes, and smaller sinks include OH destruction, stratospheric destruction, and soil uptake (12). The largest source of COS to the atmosphere is the ocean, both as direct COS emission, and as indirect carbon disulfide (CS₂) and dimethylsulfide (DMS) emissions that are rapidly oxidized to COS (10, 16–20). Recent studies suggest oceanic COS emissions are in the range of 200–4,000 GgS/y (19–22). The second major COS source is the anthropogenic source, which is dominated by indirect emissions derived from CS₂ oxidation, mainly from the use of CS₂ as an industrial solvent. Direct emissions of COS are mainly derived from coal and fuel combustion (17, 23, 24). Recent studies suggest that anthropogenic emissions are in the range of 150–585 GgS/y (23, 24). The terrestrial plant uptake is estimated to be in the range of 400–1,360 GgS/y (11). Measurements of sulfur isotope ratios (δ³⁴S) in COS may be used to track COS sources and thus reduce the uncertainties in their flux estimations (15, 25–27). However, the isotopic mass balance approach works best if the COS end members are directly measured and have a significantly different isotopic signature. Previous δ³⁴S measurements of atmospheric COS are scarce and there have been no direct measurements of two important components: the δ³⁴S of oceanic COS emissions, and the isotopic fractionation of COS during plant uptake (15, 25–27). In contrast to previous studies that used assessments for these isotopic values, our aim was to directly measure the isotopic values of these missing components, and to determine the tropospheric COS δ³⁴S variability over space and time.     

Cellular pathways of calcium transport and concentration toward mineral formation in sea urchin larvae

Sea urchin larvae have an endoskeleton consisting of two calcitic spicules. The primary mesenchyme cells (PMCs) are the cells that are responsible for spicule formation. PMCs endocytose sea water from the larval internal body cavity into a network of vacuoles and vesicles, where calcium ions are concentrated until they precipitate in the form of amorphous calcium carbonate (ACC). The mineral is subsequently transferred to the syncytium, where the spicule forms. Using cryo-soft X-ray microscopy we imaged intracellular calcium-containing particles in the PMCs and acquired Ca-L_2,3 X-ray absorption near-edge spectra of these Ca-rich particles. Using the prepeak/main peak (L₂′/ L₂) intensity ratio, which reflects the atomic order in the first Ca coordination shell, we determined the state of the calcium ions in each particle. The concentration of Ca in each of the particles was also determined by the integrated area in the main Ca absorption peak. We observed about 700 Ca-rich particles with order parameters, L₂′/ L₂, ranging from solution to hydrated and anhydrous ACC, and with concentrations ranging between 1 and 15 M. We conclude that in each cell the calcium ions exist in a continuum of states. This implies that most, but not all, water is expelled from the particles. This cellular process of calcium concentration may represent a widespread pathway in mineralizing organisms.

Calcium ions play a critical role in many cellular processes. Calcium ions are messengers for a wide range of cellular activities, including fertilization, cell differentiation, secretion, muscle contraction, and programmed cell death (1, 2). Therefore, the concentration of Ca²⁺ in the cytosol is highly regulated at around 100 to 200 nM during resting stages (3–5). Ca²⁺ homeostasis is mediated by Ca-binding proteins and different organelles in the cell, including the endoplasmic reticulum (ER) and the mitochondria that serve as significant Ca²⁺ stores and as signal generators (6–8).Calcium ions are an important component of many biominerals such as bones, teeth, shells, and spines (9). In comparison to Ca²⁺ signaling, which requires small amounts of Ca²⁺, biomineralization processes require massive sequestering and transport of ions from the environment and/or from the food to the site of mineralization. The sequestered ions can reach the mineralization site as solutes but can also concentrate intracellularly inside vesicles, where they precipitate to form highly disordered mineral phases (10–15). In the latter case, specialized cells take up the ions through ion pumps, ion channels, or by endocytosis of extracellular fluid and process the calcium ions until export to the final mineralization location (16–19).In this study, we evaluate the contents of calcium-containing vesicles in primary mesenchyme cells (PMCs), which are involved in the formation of the calcitic skeleton of the sea urchin larvae. In this way, we obtain insights into how calcium ions, extracted from the environment, are concentrated and stored for spicule formation.Paracentrotus lividus sea urchin embryos form an endoskeleton consisting of two calcitic spicules within 72 h after fertilization (20, 21). The source of the calcium ions is the surrounding sea water, whereas the carbonate ions are thought to originate from both sea water and metabolic processes in the embryo (22, 23). Sea water enters the embryonic body cavity (blastocoel) through the permeable ectoderm cell layer of the embryo (24). Endocytosis of sea water and blastocoel fluid into PMCs as well as endothelial and epithelial cells (25, 26) was tracked by labeling sea water with calcein, a fluorescent calcium-binding and membrane-impermeable dye (17, 26–28). The endocytosed fluid in the PMCs was observed to form a network of vacuoles and vesicles (26). Beniash et al. observed electron-dense granules of sizes 0.5 to 1.5 µm in PMCs, which are composed of amorphous calcium carbonate (ACC) (10). Intracellular vesicles of similar size were observed Vidavsky et al., using cryo-scanning electron microscopy (SEM) and air-SEM, containing calcium carbonate deposits composed of nanoparticles 20 to 30 nm in size (25). Ca deposits within the same range of sizes were also observed in the rough ER of PMCs (29).The intracellularly produced ACC is subsequently exported to the growing spicule, where it partially transforms into calcite through secondary nucleation (30–33). The location and distribution of ACC and calcite in the spicule were studied by using extended X-ray absorption fine structure, X-ray absorption near-edge spectroscopy (XANES), and photoelectron emission microscopy (PEEM) (30, 34, 35). Three distinct mineral phases were identified in the spicule: hydrated ACC (ACC*H₂O), anhydrous ACC, and crystalline calcite (34). According to theoretical simulations of Rez and Blackwell (36), the two different amorphous phases arise from different levels of ordering of the oxygen coordination polyhedron around calcium. The coordination polyhedron becomes more ordered as the transformation to the crystalline phase progresses. The phase information contained in the XANES spectra is exploited here to characterize the mineral phases in the intracellular vesicles.Cryo-soft X-ray transmission microscopy (cryo-SXM) is an attractive technique for tomography and spectromicroscopy of biological samples in the hydrated state (37–39). Imaging is performed in the “water window” interval of X-ray energies, namely between the carbon (C) K-edge (284 eV) and the oxygen (O) K-edge (543 eV). As a result, in the “water window” C is highly absorbing, whereas O, and thus H₂O, is almost transparent. Subsequently, carbon-rich moieties such as lipid bodies, proteins, and membranes appear dark in transmission, whereas the water rich cytosol appears lighter (40). The Ca L_2,3-absorption edge between ∼346 and 356 eV also resides in the “water window” (41). Therefore, imaging across this absorption edge enables the characterization of Ca-rich moieties in whole, hydrated cells. Each pixel of the same field of view, imaged as the energy is varied across the Ca L_2,3-edge, can be assigned an individual Ca L_2,3-edge XANES spectrum. This technique was applied to the calcifying coccolithophorid alga (42, 43). In this study, we use cryo-SXM and XANES to locate and characterize both the phases and the concentrations of Ca-rich bodies in sea urchin larval cells.     

Cholinergic suppression of hippocampal sharp-wave ripples impairs working memory

Learning and memory are assumed to be supported by mechanisms that involve cholinergic transmission and hippocampal theta. Using G protein–coupled receptor-activation–based acetylcholine sensor (GRAB_ACh3.0) with a fiber-photometric fluorescence readout in mice, we found that cholinergic signaling in the hippocampus increased in parallel with theta/gamma power during walking and REM sleep, while ACh3.0 signal reached a minimum during hippocampal sharp-wave ripples (SPW-R). Unexpectedly, memory performance was impaired in a hippocampus-dependent spontaneous alternation task by selective optogenetic stimulation of medial septal cholinergic neurons when the stimulation was applied in the delay area but not in the central (choice) arm of the maze. Parallel with the decreased performance, optogenetic stimulation decreased the incidence of SPW-Rs. These findings suggest that septo–hippocampal interactions play a task-phase–dependent dual role in the maintenance of memory performance, including not only theta mechanisms but also SPW-Rs.

The neurotransmitter acetylcholine is thought to be critical for hippocampus-dependent declarative memories (1, 2). Reduction in cholinergic neurotransmission, either in Alzheimer’s disease or in experiments with cholinergic antagonists, such as scopolamine, impairs memory function (3–8). Acetylcholine may bring about its beneficial effects on memory encoding by enhancing theta rhythm oscillations, decreasing recurrent excitation, and increasing synaptic plasticity (9–11). Conversely, drugs which activate cholinergic receptors enhance learning and, therefore, are a neuropharmacological target for the treatment of memory deficits in Alzheimer’s disease (5, 12, 13).The contribution of cholinergic mechanisms in the acquisition of long-term memories and the role of the hippocampal–entorhinal–cortical interactions are well supported by experimental data (5, 12, 13). In addition, working memory or “short-term” memory is also supported by the hippocampal–entorhinal–prefrontal cortex (14–16). Working memory in humans is postulated to be a conscious process to “keep things in mind” transiently (16). In rodents, matching to sample task, spontaneous alternation between reward locations, and the radial maze task have been suggested to function as a homolog of working memory [“working memory like” (17)].Cholinergic activity is a critical requirement for working memory (18, 19) and for sustaining theta oscillations (10, 20–22). In support of this contention, theta–gamma coupling and gamma power are significantly higher in the choice arm of the maze, compared with those in the side arms where working memory is no longer needed for correct performance (23–26). It has long been hypothesized that working memory is maintained by persistent firing of neurons, which keep the presented items in a transient store in the prefrontal cortex and hippocampal–entorhinal system (27–31), although the exact mechanisms are debated (32–37). An alternative hypothesis holds that items of working memory are stored in theta-nested gamma cycles (38). Common in these models of working memory is the need for an active, cholinergic system–dependent mechanism (39–41). However, in spontaneous alternation tasks, the animals are not moving continuously during the delay, and theta oscillations are not sustained either. During the immobility epochs, theta is replaced by intermittent sharp-wave ripples (SPW-R), yet memory performance does not deteriorate. On the contrary, artificial blockade of SPW-Rs can impair memory performance (42, 43), and prolongation of SPW-Rs improves performance (44). Under the cholinergic hypothesis of working memory, such a result is unexpected.To address the relationship between cholinergic/theta versus SPW-R mechanism in spontaneous alternation, we used a G protein–coupled receptor-activation–based acetylcholine sensor (GRAB_ACh3.0) (45) to monitor acetylcholine (ACh) activity during memory performance in mice. In addition, we optogenetically enhanced cholinergic tone, which suppresses SPW-Rs by a different mechanism than electrically or optogenetically induced silencing of neurons in the hippocampus (43, 44). We show that cholinergic signaling in the hippocampus increases in parallel with theta power/score during walking and rapid eye movement (REM) sleep and reaches a transient minimum during SPW-Rs. Selective optogenetic stimulation of medial septal cholinergic neurons decreased the incidence of SPW-Rs during non-REM sleep (46–48), as well as during the delay epoch of a working memory task and impaired memory performance. These findings demonstrate that memory performance is supported by complementary theta and SPW-R mechanisms.     

From the Cover: Solar anti-icing surface with enhanced condensate self-removing at extreme environmental conditions

The inhibition of condensation freezing under extreme conditions (i.e., ultra-low temperature and high humidity) remains a daunting challenge in the field of anti-icing. As water vapor easily condensates or desublimates and melted water refreezes instantly, these cause significant performance decrease of most anti-icing surfaces at such extreme conditions. Herein, inspired by wheat leaves, an effective condensate self-removing solar anti-icing/frosting surface (CR-SAS) is fabricated using ultrafast pulsed laser deposition technology, which exhibits synergistic effects of enhanced condensate self-removal and efficient solar anti-icing. The superblack CR-SAS displays superior anti-reflection and photothermal conversion performance, benefiting from the light trapping effect in the micro/nano hierarchical structures and the thermoplasmonic effect of the iron oxide nanoparticles. Meanwhile, the CR-SAS displays superhydrophobicity to condensed water, which can be instantly shed off from the surface before freezing through self-propelled droplet jumping, thus leading to a continuously refreshed dry area available for sunlight absorption and photothermal conversion. Under one-sun illumination, the CR-SAS can be maintained ice free even under an ambient environment of −50 °C ultra-low temperature and extremely high humidity (ice supersaturation degree of ∼260). The excellent environmental versatility, mechanical durability, and material adaptability make CR-SAS a promising anti-icing candidate for broad practical applications even in harsh environments.

Condensation freezing/frosting on solid surfaces causes severe economic and safety issues. Thus, highly efficient anti-icing/frosting approaches are vital in many engineering applications, ranging from air conditioners to power transmission systems (1–4). Tremendous efforts have been invested into designing active and passive anti-icing surfaces. Active anti-icing strategies including mechanical, chemical, and thermal methods often consume high amounts of energy and require specific facilities for deicing, which limit their practical applications (5, 6). Passive anti-icing surfaces involve strategies to delay and inhibit ice formation, such as hydrated surfaces, lubricant-infused surfaces, bioinspired anti-freezing surfaces, and superhydrophobic surfaces (SHSs) (3, 7–13). Although these passive icephobic materials offer numerous advantages to prevent ice accretion, each comes with its own limitations (14).At extreme environmental conditions where condensation and desublimation are strongly promoted, an optimal passive anti-icing surface should immediately remove condensed water droplets and leave no water for freezing. To prepare such a kind of surface, lots of efforts have been made to study the abilities of SHSs for removing condensed water. However, regular SHSs are incapable of removing microscale condensed water droplets under humid conditions due to the wetting of surface micronanostructures, which leads to the formation of highly pinned Wenzel droplets and the loss of superhydrophobicity (15–17). Tremendous investigations have shown that SHSs with specially designed structures can retain superhydrophobicity to condensed water droplets, and coalesced droplets can be spontaneously removed from the surface via self-propelled jumping (18–20). The self-propelled jumping of condensed droplets is driven by the released surface energy during droplet coalescence after overcoming solid–liquid adhesion (21–25). However, these surfaces inevitably lose their water repellency at low temperatures (i.e., < −15 °C) because of freezing (9, 21, 26). Thus, it is highly desirable to design new anti-icing surfaces that can maintain capability for removing the condensed water at extreme environmental conditions, which is highly important for anti-icing applications in many scenarios (i.e., aircrafts flying through clouds, wind turbines operating in winter, and power transmission facilities working in extremely cold and humid regions) (27).Recently, intensive research efforts have been dedicated to solar anti-icing/frosting surfaces (SASs), which can absorb sunlight efficiently and convert solar energy to heat, thereby delaying or preventing ice formation (28–30). Because of its effective utilization of clean and renewable solar energy, SASs are environmentally friendly and energy efficient. Notably, a number of photothermal conversion materials including carbon materials, conjugated polymers, two-dimensional nanostructural materials, and metallic particles have also been applied as SASs (28, 31–34). Although remarkable improvements have been made, some challenges have yet to be tackled. For instance, most of the reported SASs cannot remove the condensed water effectively, particularly in cold and humid conditions (35, 36). The accumulation of the condensed water would significantly enhance reflectance leading to reduced photothermal efficiency (37) and decreased temperature. As a result, frost formation through the freezing of condensed water (condensation frosting) will prevent sunlight from reaching the SAS, resulting in the complete loss of its photothermal capability: as light harvesting becomes less efficient, the temperature of the SAS decreases, resulting in a vicious compounding cycle of condensation freezing. Moreover, the contaminants on the SAS can also inhibit sunlight absorption (38). Therefore, it is desirable to develop highly photothermal–efficient SASs with the abilities of removing condensed water to maintain high temperature and self-cleaning for avoiding blockage of sunlight by contaminants.Herein, we present a proof-of-concept SAS with synergistically binary effects of enhanced condensate self-removing and efficient solar anti-icing. We fabricated hierarchically structured materials using ultrafast pulsed laser deposition (PLD) technology. Low-effective refractive index and multilayered iron oxide structures endow the material with broadband ultralow reflectance and high solar-to-heat conversation efficiency. The hierarchically structured SHS demonstrated the capability of removing condensates before freezing via self-propelled droplet jumping induced by droplet coalescence and evaporation flux under heating. The sustained shedding of condensed water droplets resulted in a continuously refreshed, dry and clean area available for efficient sunlight absorption and photothermal conversion; the temperature of the condensate self-removing solar anti-icing/frosting surface (CR-SAS) could be constantly maintained above the freezing temperature, which in turn ensured high-performance water repellency. With such synergistic mutual-benefitting effects of condensate self-removal and photothermal heating, under one-sun illumination, the CR-SAS remained ice-free even at an ambient temperature (T_a) of −50 °C and ultra-high humidity with a supersaturation degree (SSD) of ∼260, demonstrating superior anti-icing performances under extremely harsh operating conditions.     

Identifying hydrophobic protein patches to inform protein interaction interfaces

Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.

Protein–protein interactions play a crucial role in numerous biological processes, ranging from signal transduction and immune response to protein aggregation and phase behavior (1–3). Consequently, being able to understand, predict, and modulate protein interactions has important implications for understanding cellular processes and mitigating the progression of disease (4, 5). A necessary first step toward this ambitious goal is uncovering the interfaces through which proteins interact (6–8). In principle, identifying hydrophobic protein regions, which interact weakly with water, should be a promising strategy for uncovering protein interaction interfaces (9, 10). Indeed, the release of weakly interacting hydration waters from hydrophobic regions can drive protein interactions, as well as other aqueous assemblies (11–13). However, even when the structure of a protein is available at atomistic resolution, it is challenging to identify its hydrophobic patches because they are not uniformly nonpolar, but display variations in polarity and charge at the nanoscale. Moreover, the emergent hydrophobicity of a protein patch stems from the collective response of protein hydration waters to the nanoscale chemical and topographical patterns displayed by the patch (14–20) and cannot be captured by simply counting the number of nonpolar groups in the patch, or even through more involved additive approaches, such as hydropathy scales or surface-area models (21–28).To address this challenge, we build upon seminal theoretical advances and molecular simulation studies, which have shown that near a hydrophobic surface, it is easier to disrupt surface–water interactions and form interfacial cavities (29–34). To uncover protein regions that have the weakest interactions with water, here, we employ specialized molecular simulations, wherein protein–water interactions are disrupted by systematically displacing water molecules from the protein hydration shell (35–37). By identifying the protein patches that nucleate cavities most readily in our simulations, we are then able to uncover the most hydrophobic protein regions. Interestingly, we find that both hydrophobic and hydrophilic protein patches are highly heterogeneous and contain comparable numbers of nonpolar and polar atoms. Our results thus highlight the nontrivial relationship between the chemical composition of protein patches and their emergent hydrophobicity (24–26), and further emphasize the importance of accounting for the collective solvent response in characterizing protein hydrophobicity (16). We then interrogate whether the most hydrophobic protein patches, which nucleate cavities readily, are also likely to mediate protein interactions. Across five proteins that participate in either homodimer or heterodimer formation, we find that roughly 60 to 70% of interfacial contacts and only about 10 to 20% of noncontacts nucleate cavities. Our work thus provides a versatile computational framework for characterizing hydrophobicity and uncovering interaction interfaces of not just proteins, but also of other complex amphiphilic solutes, such as cavitands, dendrimers, and patchy nanoparticles (38–41).     

Impaired TRPV4-eNOS signaling in trabecular meshwork elevates intraocular pressure in glaucoma

Primary Open Angle Glaucoma (POAG) is the most common form of glaucoma that leads to irreversible vision loss. Dysfunction of trabecular meshwork (TM) tissue, a major regulator of aqueous humor (AH) outflow resistance, is associated with intraocular pressure (IOP) elevation in POAG. However, the underlying pathological mechanisms of TM dysfunction in POAG remain elusive. In this regard, transient receptor potential vanilloid 4 (TRPV4) cation channels are known to be important Ca²⁺ entry pathways in multiple cell types. Here, we provide direct evidence supporting Ca²⁺ entry through TRPV4 channels in human TM cells and show that TRPV4 channels in TM cells can be activated by increased fluid flow/shear stress. TM-specific TRPV4 channel knockout in mice elevated IOP, supporting a crucial role for TRPV4 channels in IOP regulation. Pharmacological activation of TRPV4 channels in mouse eyes also improved AH outflow facility and lowered IOP. Importantly, TRPV4 channels activated endothelial nitric oxide synthase (eNOS) in TM cells, and loss of eNOS abrogated TRPV4-induced lowering of IOP. Remarkably, TRPV4-eNOS signaling was significantly more pronounced in TM cells compared to Schlemm’s canal cells. Furthermore, glaucomatous human TM cells show impaired activity of TRPV4 channels and disrupted TRPV4-eNOS signaling. Flow/shear stress activation of TRPV4 channels and subsequent NO release were also impaired in glaucomatous primary human TM cells. Together, our studies demonstrate a central role for TRPV4-eNOS signaling in IOP regulation. Our results also provide evidence that impaired TRPV4 channel activity in TM cells contributes to TM dysfunction and elevated IOP in glaucoma.

Glaucoma is a heterogenic group of multifactorial neurodegenerative diseases characterized by progressive optic neuropathy. It is the leading cause of irreversible vision loss with more than 70 million people affected worldwide (1), and the prevalence is estimated to increase to 111.6 million by the year 2040 (2). Primary open angle glaucoma (POAG) is the most common form of glaucoma, accounting for ∼70% of all cases (1). POAG is characterized by progressive loss of retinal ganglion cell axons that leads to an irreversible loss of vision (1, 3). Elevated intraocular pressure (IOP) is a major, and the only treatable, risk factor associated with POAG (4). The trabecular meshwork (TM), a molecular sieve-like structure, maintains homeostatic control over IOP by constantly adjusting the resistance to aqueous humor (AH) outflow. In POAG, there is increased resistance to AH outflow, elevating IOP (5). This increase in AH outflow resistance is associated with dysfunction of the TM (6–8).The TM has an intrinsic ability to sense the AH flow and regulate outflow facility to maintain IOP homeostasis (6), although the precise flow-sensing mechanisms in TM cells are unclear. In this regard, transient receptor potential vanilloid 4 (TRPV4) cation channels have emerged as a major flow-activated Ca²⁺ entry pathway in multiple cell types (9–12). Upon activation, TRPV4 channels allow localized Ca²⁺ influx (termed as TRPV4 sparklets), which influences a variety of cellular homeostatic processes (13, 14). TRPV4 sparklets are spatially restricted signals with a spatial spread (maximum width at half maximal amplitude) of ∼11 microns (13). Treatment with a selective TRPV4 channel activator GSK1016790A (GSK101) lowered IOP in rats and mice (15). Furthermore, baseline IOP was higher in global TRPV4^−/− mice compared to their wild-type (WT) littermates (15). However, the exact cell type responsible for these IOP-lowering effects is not known. Previous studies have shown that TRPV4 channel protein is expressed in TM cells and tissues (15, 16). The physiological roles of TRPV4 channels in TM cells (TRPV4_TM) and downstream signaling mechanisms remain unknown. TM constitutively expresses Ca²⁺-sensitive endothelial nitric oxide synthase (eNOS) (17), a known regulator of outflow facility and IOP (18–22). In vascular endothelial cells, TRPV4 channels are important regulators of eNOS activity (23–26). We, therefore, hypothesized that TRPV4_TM-eNOS signaling promotes outflow facility and reduces IOP.Glaucoma-associated pathological changes are known to impair physiological function of TM (8). One of the hallmarks of the glaucomatous TM is its inability to maintain normal IOP and AH outflow resistance (6). Here, we postulated that impaired TRPV4_TM-eNOS signaling contributes to TM dysfunction and elevated IOP in glaucoma. In this report, our studies in human TM cells and TM tissue showed shear stress–mediated activation of TRPV4-eNOS signaling. Moreover, reduced AH outflow and elevated IOPs were observed in TM-specific TRPV4^−/− (TRPV4_TM^−/−) mice and eNOS^−/− mice. Importantly, TRPV4_TM activity and shear stress–mediated activation of TRPV4_TM-eNOS signaling are compromised in human glaucomatous TM cells. Our results provide direct evidence for a physiological role of TRPV4_TM-eNOS signaling and indicate that impaired TRPV4_TM-eNOS signaling may underlie TM dysfunction and IOP dysregulation in glaucoma.     

Replisome bypass of a protein-based R-loop block by Pif1

Efficient and faithful replication of the genome is essential to maintain genome stability. Replication is carried out by a multiprotein complex called the replisome, which encounters numerous obstacles to its progression. Failure to bypass these obstacles results in genome instability and may facilitate errors leading to disease. Cells use accessory helicases that help the replisome bypass difficult barriers. All eukaryotes contain the accessory helicase Pif1, which tracks in a 5′–3′ direction on single-stranded DNA and plays a role in genome maintenance processes. Here, we reveal a previously unknown role for Pif1 in replication barrier bypass. We use an in vitro reconstituted Saccharomyces cerevisiae replisome to demonstrate that Pif1 enables the replisome to bypass an inactive (i.e., dead) Cas9 (dCas9) R-loop barrier. Interestingly, dCas9 R-loops targeted to either strand are bypassed with similar efficiency. Furthermore, we employed a single-molecule fluorescence visualization technique to show that Pif1 facilitates this bypass by enabling the simultaneous removal of the dCas9 protein and the R-loop. We propose that Pif1 is a general displacement helicase for replication bypass of both R-loops and protein blocks.

Efficient and faithful replication of the genome is essential to maintain genome stability and is carried out by a multiprotein complex called the replisome (1–4). There are numerous obstacles to progression of the replisome during the process of chromosome duplication. These obstacles include RNA-DNA hybrids (R-loops), DNA secondary structures, transcribing RNA polymerases, and other tightly bound proteins (5–9). Failure to bypass these barriers may result in genome instability, which can lead to cellular abnormalities and genetic disease. Cells contain various accessory helicases that help the replisome bypass these difficult barriers (10–20). A subset of these helicases act on the opposite strand of the replicative helicase (1, 2, 14, 19).All eukaryotes contain an accessory helicase, Pif1, which tracks in a 5′–3′ direction on single-stranded DNA (ssDNA) (11–16). Pif1 is important in pathways such as Okazaki-fragment processing and break-induced repair that require the removal of DNA-binding proteins as well as potential displacement of R-loops (11–13, 21, 15–18, 22–25). Genetic studies and immunoprecipitation pull-down assays indicate that Pif1 interacts with PCNA (the DNA sliding clamp), Pol ε (the leading-strand polymerase), the MCMs (the motor subunits of the replicative helicase CMG), and RPA (the single-stranded DNA-binding protein) (15, 26, 27). Pif1 activity in break-induced repair strongly depends on its interaction with PCNA (26). These interactions with replisomal components suggest that Pif1 could interact with the replisome during replication. In Escherichia coli, the replicative helicase is the DnaB homohexamer that encircles the lagging strand and moves in a 5′–3′ direction (20). E. coli accessory helicases include the monomeric UvrD (helicase II) and Rep, which move in the 3′–5′ direction and operate on the opposite strand from the DnaB hexamer. It is known that these monomeric helicases promote the bypass of barriers during replication such as stalled RNA polymerases (5). The eukaryotic replicative helicase is the 11-subunit CMG (Cdc45, Mcm2–7, GINS) and tracks in the 3′–5′ direction, opposite to the direction of Pif1 (25, 28). Once activated by Mcm10, the MCM motor domains of CMG encircle the leading strand (29–32). We hypothesized that, similar to UvrD and Rep in E. coli, Pif1 interacts with the replisome tracking in the opposite direction to enable bypass of replication obstacles.In this report, we use an in vitro reconstituted Saccharomyces cerevisiae replisome to study the role of Pif1 in bypass of a “dead” Cas9 (dCas9), which is a Cas9 protein that is deactivated in DNA cleavage but otherwise fully functional in DNA binding. As with Cas9, dCas9 is a single-turnover enzyme that can be programmed with a guide RNA (gRNA) to target either strand. The dCas9–gRNA complex forms a roadblock consisting of an R-loop and a tightly bound protein (dCas9), a construct that is similar to a stalled RNA polymerase. This roadblock (hereafter dCas9 R-loop) arrests replisomes independent of whether the dCas9 R-loop is targeted to the leading or lagging strand (30). Besides its utility due to its programmable nature (33), the use of the dCas9 R-loop allows us to answer several mechanistic questions. For example, the ability to program the dCas9 R-loop block to any specific sequence enables us to observe whether block removal is different depending on whether the block is on the leading or lagging strand. Furthermore, the inner diameter of CMG can accommodate double-stranded DNA (dsDNA) and possibly an R-loop, but not a dCas9 protein. Using the dCas9 R-loop block allows us to determine the fate of each of its components.Here, we report that Pif1 enables the bypass of the dCas9 R-loop by the replisome. Interestingly, dCas9 R-loops targeted to either the leading or lagging strand are bypassed with similar efficiency. In addition, the PCNA clamp is not required for bypass of the block, indicating that Pif1 does not need to interact with PCNA during bypass of the block. We used a single-molecule fluorescence imaging to show that both the dCas9 and the R-loop are displaced as an intact nucleoprotein complex. We propose that Pif1 is a general displacement helicase for replication bypass of both R-loops and protein blocks.     

Wild-type α-synuclein inherits the structure and exacerbated neuropathology of E46K mutant fibril strain by cross-seeding

Heterozygous point mutations of α-synuclein (α-syn) have been linked to the early onset and rapid progression of familial Parkinson’s diseases (fPD). However, the interplay between hereditary mutant and wild-type (WT) α-syn and its role in the exacerbated pathology of α-syn in fPD progression are poorly understood. Here, we find that WT mice inoculated with the human E46K mutant α-syn fibril (hE46K) strain develop early-onset motor deficit and morphologically different α-syn aggregation compared with those inoculated with the human WT fibril (hWT) strain. By using cryo-electron microscopy, we reveal at the near-atomic level that the hE46K strain induces both human and mouse WT α-syn monomers to form the fibril structure of the hE46K strain. Moreover, the induced hWT strain inherits most of the pathological traits of the hE46K strain as well. Our work suggests that the structural and pathological features of mutant strains could be propagated by the WT α-syn in such a way that the mutant pathology would be amplified in fPD.

α-Synuclein (α-Syn) is the main component of Lewy bodies, which serve as the common histological hallmark of Parkinson’s disease (PD) and other synucleinopathies (1, 2). α-Syn fibrillation and cell-to-cell transmission in the brain play essential roles in disease progression (3–5). Interestingly, WT α-syn could form fibrils with distinct polymorphs, which exhibit disparate seeding capability in vitro and induce distinct neuropathologies in mouse models (6–10). Therefore, it is proposed that α-syn fibril polymorphism may underlie clinicopathological variability of synucleinopathies (6, 9). In fPD, several single-point mutations of SNCA have been identified, which are linked to early-onset, severe, and highly heterogeneous clinical symptoms (11–13). These mutations have been reported to influence either the physiological or pathological function of α-syn (14). For instance, A30P weakens while E46K strengthens α-syn membrane binding affinity that may affect its function in synaptic vesicle trafficking (14, 15). E46K, A53T, G51D, and H50Q have been found to alter the aggregation kinetics of α-syn in different manners (15–17). Recently, several cryogenic electron microscopy (cryo-EM) studies revealed that α-syn with these mutations forms diverse fibril structures that are distinct from the WT α-syn fibrils (18–26). Whether and how hereditary mutations induced fibril polymorphism contributes to the early-onset and exacerbated pathology in fPD remains to be elucidated. More importantly, most fPD patients are heterozygous for SNCA mutations (12, 13, 27, 28), which leads to another critical question: could mutant fibrils cross-seed WT α-syn to orchestrate neuropathology in fPD patients?E46K mutation is one of the eight disease-causing mutations on SNCA originally identified from a Spanish family with autosomal-dominant PD (11). E46K-associated fPD features early-onset motor symptoms and rapid progression of dementia with Lewy bodies (11). Studies have shown that E46K mutant has higher neurotoxicity than WT α-syn in neurons and mouse models overexpressing α-syn (29–32). The underlying mechanism is debatable. Some reported that E46K promotes the formation of soluble species of α-syn without affecting the insoluble fraction (29, 30), while others suggested that E46K mutation may destabilize α-syn tetramer and induce aggregation (31, 32). Our previous study showed that E46K mutation disrupts the salt bridge between E46 and K80 in the WT fibril strain and rearranges α-syn into a different polymorph (33). Compared with the WT strain, the E46K fibril strain is prone to be fragmented due to its smaller and less stable fibril core (33). Intriguingly, the E46K strain exhibits higher seeding ability in vitro, suggesting that it might induce neuropathology different from the WT strain in vivo (33).In this study, we found that human E46K and WT fibril strains (referred to as hE46K and hWT strains) induced α-syn aggregates with distinct morphologies in mice. Mice injected with the hE46K strain developed more α-syn aggregation and early-onset motor deficits compared with the mice injected with the hWT strain. Notably, the hE46K strain was capable of cross-seeding both human and mouse WT (mWT) α-syn to form fibrils (named as hWT_cs and mWT_cs). The cross-seeded fibrils replicated the structure and seeding capability of the hE46K template both in vitro and in vivo. Our results suggest that the hE46K strain could propagate its structure as well as the seeding properties to the WT monomer so as to amplify the α-syn pathology in fPD.     

Coal fly ash is a major carbon flux in the Chang Jiang (Yangtze River) basin

Fly ash—the residuum of coal burning—contains a considerable amount of fossilized particulate organic carbon (FOC_ash) that remains after high-temperature combustion. Fly ash leaks into natural environments and participates in the contemporary carbon cycle, but its reactivity and flux remained poorly understood. We characterized FOC_ash in the Chang Jiang (Yangtze River) basin, China, and quantified the riverine FOC_ash fluxes. Using Raman spectral analysis, ramped pyrolysis oxidation, and chemical oxidation, we found that FOC_ash is highly recalcitrant and unreactive, whereas shale-derived FOC (FOC_rock) was much more labile and easily oxidized. By combining mass balance calculations and other estimates of fly ash input to rivers, we estimated that the flux of FOC_ash carried by the Chang Jiang was 0.21 to 0.42 Mt C⋅y⁻¹ in 2007 to 2008—an amount equivalent to 37 to 72% of the total riverine FOC export. We attributed such high flux to the combination of increasing coal combustion that enhances FOC_ash production and the massive construction of dams in the basin that reduces the flux of FOC_rock eroded from upstream mountainous areas. Using global ash data, a first-order estimate suggests that FOC_ash makes up to 16% of the present-day global riverine FOC flux to the oceans. This reflects a substantial impact of anthropogenic activities on the fluxes and burial of fossil organic carbon that has been made less reactive than the rocks from which it was derived.

Fossil particulate organic carbon (FOC) is a geologically stable form of carbon that was produced by the ancient biosphere and then buried and stored in the lithosphere; it is a key player in the geological carbon cycle (1–7). Uplift and erosion liberate FOC from bedrock, delivering it to the surficial carbon cycle. Some is oxidized in sediment routing systems, but a portion escapes and can be transported by rivers to the oceans (5, 8–10). Oxidation of FOC represents a long-term atmospheric carbon source and O₂ sink, whereas the reburial of FOC in sedimentary basins has no long-term net effect on atmospheric CO₂ and O₂ (1, 9, 11). Exhumation and erosion of bedrock provide a natural source of FOC (2, 8), which we refer to as FOC_rock. Human activities have introduced another form of FOC from the mining and combustion of coal. Burning coal emits CO₂ to the atmosphere but also leaves behind solid waste that contains substantial amounts of organic carbon (OC) that survives high-temperature combustion (12–14). This fossil-fuel-sourced carbon represents a poorly understood anthropogenic flux in the global carbon cycle; it also provides a major source of black carbon, which is a severe pollutant and climate-forcing agent (12–15).Previous studies sought to quantify black carbon in different terrestrial and marine environments and to distinguish fossil fuel versus forest fire sources (14–18). In this study, we focused on fly ash—the material left from incomplete coal combustion. As a major fossil fuel, coal supplies around 30% of global primary energy consumption (19, 20). Despite efforts to capture and utilize fly ash, a fraction enters soils and rivers; the resulting fossil OC from fly ash (FOC_ash) has become a measurable part of the contemporary carbon cycle (14). FOC_ash is also referred to as “unburned carbon” in fly ash (21–25); it provides a useful measure of combustion efficiency and the quality of fly ash as a building material (e.g., in concrete) (23–26). Industrial standards of FOC_ash content in fly ash have been established for material quality assurance (23, 24, 26, 27). However, the characteristics and fluxes of FOC_ash released to the environment, and how these compare to FOC_rock from bedrock erosion, remain less well understood.To fill this knowledge gap, we examined the Chang Jiang (Yangtze River) basin in China—a system that allowed us to evaluate the influence of FOC_ash on the carbon cycle at continental scales. In the 2000s, China became the largest coal-consuming country in the world, with an annual coal consumption of over 2,500 Mt, equating to ∼50% of worldwide consumption (19, 20, 28). Coal contributed over 60% of China’s national primary energy consumption through the 2000s. A significant portion of this coal (approximately one-third) was consumed in the Chang Jiang (CJ) basin, where China’s most populated and economically developed areas are located (29). Significant amounts of fly ash and FOC_ash continue to be produced and consumed in the CJ basin. To determine the human-induced FOC_ash flux, we investigated the FOC_ash cycle in the CJ basin. We characterized OC in a series of samples including fly ash, bedrock sedimentary shale, and river sediment through multiple geochemical analyses. We then estimated the CJ-exported FOC_ash flux and evaluated how human activities modulated FOC transfer at basin scales. We found that in the CJ basin, coal combustion and dam construction have conspired to boost the FOC_ash flux and reduce the FOC_rock flux carried by the CJ; as a result, these two fluxes converged over an interval of 60 y.     

ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating

Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to activated particles that contain pores in the capsid, lack minor capsid protein VP4, and have an altered genome organization. The binding of rhinoviruses to ICAM-1 promotes virus activation; however, the molecular details of the process remain unknown. Here, we present the structures of virion of rhinovirus 14 and its complex with ICAM-1 determined to resolutions of 2.6 and 2.4 Å, respectively. The cryo-electron microscopy reconstruction of rhinovirus 14 virions contains the resolved density of octanucleotide segments from the RNA genome that interact with VP2 subunits. We show that the binding of ICAM-1 to rhinovirus 14 is required to prime the virus for activation and genome release at acidic pH. Formation of the rhinovirus 14–ICAM-1 complex induces conformational changes to the rhinovirus 14 capsid, including translocation of the C termini of VP4 subunits, which become poised for release through pores that open in the capsids of activated particles. VP4 subunits with altered conformation block the RNA–VP2 interactions and expose patches of positively charged residues. The conformational changes to the capsid induce the redistribution of the virus genome by altering the capsid–RNA interactions. The restructuring of the rhinovirus 14 capsid and genome prepares the virions for conversion to activated particles. The high-resolution structure of rhinovirus 14 in complex with ICAM-1 explains how the binding of uncoating receptors enables enterovirus genome release.

Human rhinoviruses are the cause of more than half of common colds (1). Medical visits and missed days of school and work cost tens of billions of US dollars annually (2, 3). There is currently no cure for rhinovirus infections, and the available treatments are only symptomatic. Rhinoviruses belong to the family Picornaviridae, genus Enterovirus, and are classified into species A, B, and C (4). Rhinoviruses A and B can belong to either “major” or “minor” groups, based on their utilization of intercellular adhesion molecule-1 (ICAM-1) or low-density lipoprotein receptor for cell entry (5–7). Type C rhinoviruses use CDHR3 as a receptor (8). Rhinovirus 14 belongs to the species rhinovirus B and uses ICAM-1 as a receptor. Receptors recognized by rhinoviruses and other enteroviruses can be divided into two groups based on their function in the infection process (9). Attachment receptors such as DAF, PSGL1, KREMEN1, CDHR3, and sialic acid enable the binding and endocytosis of virus particles into cells (10–13). In contrast, uncoating receptors including ICAM-1, CD155, CAR, and SCARB2 enable virus cell entry but also promote genome release from virus particles (5, 14–16).Virions of rhinoviruses are nonenveloped and have icosahedral capsids (17). Genomes of rhinoviruses are 7,000 to 9,000 nucleotide-long single-stranded positive-sense RNA molecules (1, 17). The rhinovirus genome encodes a single polyprotein that is co- and posttranslationally cleaved into functional protein subunits. Capsid proteins VP1, VP3, and VP0, originating from one polyprotein, form a protomer, 60 of which assemble into a pseudo-T = 3 icosahedral capsid. To render the virions mature and infectious, VP0 subunits are cleaved into VP2 and VP4 (18, 19). VP1 subunits form pentamers around fivefold symmetry axes, whereas subunits VP2 and VP3 form heterohexamers centered on threefold symmetry axes. The major capsid proteins VP1 through 3 have a jelly roll β-sandwich fold formed by two β-sheets, each containing four antiparallel β-strands, which are conventionally named B to I (20–22). The two β-sheets contain the strands BIDG and CHEF, respectively. The C termini of the capsid proteins are located at the virion surface, whereas the N termini mediate interactions between the capsid proteins and the RNA genome on the inner surface of the capsid. VP4 subunits are attached to the inner face of the capsid formed by the major capsid proteins. The surfaces of rhinovirus virions are characterized by circular depressions called canyons, which are centered around fivefold symmetry axes of the capsids (21).The VP1 subunits of most rhinoviruses, but not those of rhinovirus 14, contain hydrophobic pockets, which are filled by molecules called pocket factors (17, 21, 23, 24). It has been speculated that pocket factors are fatty acids or lipids (25). The pockets are positioned immediately below the canyons. The exposure of rhinoviruses to acidic pH induces expulsion of the pocket factors, which leads to the formation of activated particles and genome release (17, 26–32). The activated particles are characterized by capsid expansion, a reduction in interpentamer contacts, the release of VP4 subunits, externalization of N termini of VP1 subunits, and changes in the distribution of RNA genomes (17, 26–29, 33, 34). Artificial hydrophobic compounds that bind to VP1 pockets with high affinity inhibit infection by rhinoviruses (35, 36).ICAM-1 is an endothelial- and leukocyte-associated protein that stabilizes cell–cell interactions and facilitates the movement of leukocytes through endothelia (37). ICAM-1 can be divided into an extracellular amino-terminal part composed of five immunoglobulin domains, a single transmembrane helix, and a 29-residue–long carboxyl-terminal cytoplasmic domain. The immunoglobulin domains are characterized by a specific fold that consists of seven to eight β-strands, which form two antiparallel β-sheets in a sandwich arrangement (38–40). The immunoglobulin domains of ICAM-1 are stabilized by disulfide bonds and glycosylation (38–41). The connections between the immunoglobulin domains are formed by flexible linkers that enable bending of the extracellular part of ICAM-1. For example, the angle between domains 1 and 2 differs by 8° between molecules in distinct crystal forms (38, 42). As a virus receptor, ICAM-1 enables the virus particles to sequester at the cell surface and mediates their endocytosis (5). The structures of complexes of rhinoviruses 3, 14, and 16, and CVA21 with ICAM-1 have been determined to resolutions of 9 to 28 Å (42–46). It was shown that ICAM-1 molecules bind into the canyons at the rhinovirus surface, approximately between fivefold and twofold symmetry axes (42–46). ICAM-1 interacts with residues from all three major capsid proteins. It has been speculated that the binding of ICAM-1 triggers the transition of virions of rhinovirus 14 to activated particles and initiates genome release (45, 47). However, the limited resolution of the previous studies prevented characterization of the corresponding molecular mechanism.Here, we present the cryo-electron microscopy (cryo-EM) reconstruction of the rhinovirus 14 virion, which contains resolved density of octanucleotide segments of the RNA genome that interact with VP2 subunits. Furthermore, we show that the binding of ICAM-1 to rhinovirus 14 induces changes in its capsid and genome, which are required for subsequent virus activation and genome release at acidic pH.     

Photosynthesis tunes quantum-mechanical mixing of electronic and vibrational states to steer exciton energy transfer

Photosynthetic species evolved to protect their light-harvesting apparatus from photoxidative damage driven by intracellular redox conditions or environmental conditions. The Fenna–Matthews–Olson (FMO) pigment–protein complex from green sulfur bacteria exhibits redox-dependent quenching behavior partially due to two internal cysteine residues. Here, we show evidence that a photosynthetic complex exploits the quantum mechanics of vibronic mixing to activate an oxidative photoprotective mechanism. We use two-dimensional electronic spectroscopy (2DES) to capture energy transfer dynamics in wild-type and cysteine-deficient FMO mutant proteins under both reducing and oxidizing conditions. Under reducing conditions, we find equal energy transfer through the exciton 4–1 and 4–2-1 pathways because the exciton 4–1 energy gap is vibronically coupled with a bacteriochlorophyll-a vibrational mode. Under oxidizing conditions, however, the resonance of the exciton 4–1 energy gap is detuned from the vibrational mode, causing excitons to preferentially steer through the indirect 4–2-1 pathway to increase the likelihood of exciton quenching. We use a Redfield model to show that the complex achieves this effect by tuning the site III energy via the redox state of its internal cysteine residues. This result shows how pigment–protein complexes exploit the quantum mechanics of vibronic coupling to steer energy transfer.

Photosynthetic organisms convert solar photons into chemical energy by taking advantage of the quantum mechanical nature of their molecular systems and the chemistry of their environment (1–4). Antenna complexes, composed of one or more pigment–protein complexes, facilitate the first steps in the photosynthesis process: They absorb photons and determine which proportion of excitations to move to reaction centers, where charge separation occurs (4). In oxic environments, excitations can generate highly reactive singlet oxygen species. These pigment–protein complexes can quench excess excitations in these environments with molecular moieties such as quinones and cysteine residues (1, 5–7).The Fenna–Matthews–Olson (FMO) complex, a trimer of pigment–protein complexes found in the green sulfur bacterium Chlorobaculum tepidum (8), has emerged as a model system to study the photophysical properties of photosynthetic antenna complexes (9–19). Each subunit in the FMO complex contains eight bacteriochlorophyll-a site molecules (Protein Data Bank, ID code: 3ENI) that are coupled to form a basis of eight partially delocalized excited states called excitons (Fig. 1) (20–23). Previous experiments on FMO have observed the presence of long-lived coherences in nonlinear spectroscopic signals at both cryogenic and physiological temperatures (11, 13). The coherent signals are thought to arise from some combination of electronic (24–26), vibrational (16–18), and vibronic (27) coherences in the system (28–30). One previous study reported that the coherent signals in FMO remain unchanged upon mutagenesis of the protein, suggesting that the signals are ground state vibrational coherences (17). Others discuss the role of vibronic coupling, where electronic and nuclear degrees of freedom become coupled (29). Other dimeric model systems have demonstrated the regimes in which these vibronically coupled states produce coherent or incoherent transport and vibronic coherences (31–33). Recent spectroscopic data has suggested that vibronic coupling plays a role in driving efficient energy transfer through photosynthetic complexes (27, 31, 33, 34), but to date there is no direct experimental evidence suggesting that biological systems use vibronic coupling as part of their biological function.Open in a separate windowFig. 1.(Left) Numbered sites and sidechains of cysteines C353 and C49 in the FMO pigment–protein complex (PDB ID code: 3ENI) (20). (Right) Site densities for excitons 4, 2, and 1 in reducing conditions with the energy transfer branching ratios for the WT oxidized and reduced protein. The saturation of pigments in each exciton denotes the relative contribution number to the exciton. The C353 residue is located near excitons 4 and 2, which have most electron density along one side of the complex, and other redox-active residues such as the Trp/Tyr chain. C353 and C49 surround site III, which contains the majority of exciton 1 density. Excitons 2 and 4 are generally delocalized over sites IV, V, and VII.It has been shown that redox conditions affect excited state properties in pigment-protein complexes, yet little is known about the underlying microscopic mechanisms for these effects (1, 9). Many commonly studied light-harvesting complexes—including the FMO complex (20), light-harvesting complex 2 (LH2) (35), the PC645 phycobiliprotein (36), and the cyanobacterial antenna complex isiA (37)—contain redox-active cysteine residues in close proximity to their chromophores. As the natural low light environment of C. tepidum does not necessitate photoprotective responses to light quantity and quality, its primary photoprotective mechanism concerns its response to oxidative stress. C. tepidum is an obligate anaerobe, but the presence of many active anoxygenic genes such as sodB for superoxide dismutase and roo for rubredoxin oxygen oxidoreductase (38) suggests that it is frequently exposed to molecular oxygen (7, 39). Using time-resolved fluorescence measurements, Orf et al. demonstrated that two cysteine residues in the FMO complex, C49 and C353, quench excitons under oxidizing conditions (1), which could protect the excitation from generating reactive oxygen species (7, 40–42). In two-dimensional electronic spectroscopy (2DES) experiments, Allodi et al. showed that redox conditions in both the wild-type and C49A/C353A double-mutant proteins affect the ultrafast dynamics through the FMO complex (9, 43). The recent discovery that many proteins across the evolutionary landscape possess chains of tryptophan and tyrosine residues provides evidence that these redox-active residues may link the internal protein behavior with the chemistry of the surrounding environment (41, 43).In this paper, we present data showing that pigment–protein complexes tune the vibronic coupling of their chromophores and that the absence of this vibronic coupling activates an oxidative photoprotective mechanism. We use 2DES to show that a pair of cysteine residues in FMO, C49 and C353, can steer excitations toward quenching sites in oxic environments. The measured reaction rate constants demonstrate unusual nonmonotonic behavior. We then use a Redfield model to determine how the exciton energy transfer (EET) time constants arise from changing chlorophyll site energies and their system-bath couplings (44, 45). The analysis reveals that the cysteine residues tune the resonance between exciton 4–1 energy gap and an intramolecular chlorophyll vibration in reducing conditions to induce vibronic coupling and detune the resonance in oxidizing conditions. This redox-dependent modulation of the vibronic coupling steers excitations through different pathways in the complex to change the likelihood that they interact with exciton quenchers.     

Rules of contact inhibition of locomotion for cells on suspended nanofibers

Contact inhibition of locomotion (CIL), in which cells repolarize and move away from contact, is now established as a fundamental driving force in development, repair, and disease biology. Much of what we know of CIL stems from studies on two-dimensional (2D) substrates that do not provide an essential biophysical cue—the curvature of extracellular matrix fibers. We discover rules controlling outcomes of cell–cell collisions on suspended nanofibers and show them to be profoundly different from the stereotyped CIL behavior on 2D substrates. Two approaching cells attached to a single fiber do not repolarize upon contact but rather usually migrate past one another. Fiber geometry modulates this behavior; when cells attach to two fibers, reducing their freedom to reorient, only one cell repolarizes on contact, leading to the cell pair migrating as a single unit. CIL outcomes also change when one cell has recently divided and moves with high speed—cells more frequently walk past each other. Our computational model of CIL in fiber geometries reproduces the core qualitative results of the experiments robustly to model parameters. Our model shows that the increased speed of postdivision cells may be sufficient to explain their increased walk-past rate. We also identify cell–cell adhesion as a key mediator of collision outcomes. Our results suggest that characterizing cell–cell interactions on flat substrates, channels, or micropatterns is not sufficient to predict interactions in a matrix—the geometry of the fiber can generate entirely new behaviors.

Cell migration is an essential component of various physiological processes such as morphogenesis, wound healing, and metastasis (1). Cell–cell interactions in which cell–cell contact reorients cell polarity are necessary for the correct function of many developmental events (2). One of the earliest such interactions known was termed “contact inhibition of locomotion” (CIL) by Abercombie and Heaysman over five decades ago in chick fibroblasts cultured on flat two-dimensional (2D) substrates (2–4). In CIL, two approaching cells isolated from the rest of the cell population first make contact, followed by protrusion inhibition at the site of contact, which leads to cell repolarization through formation of new protrusions away from the site of contact. Subsequently, cells migrate away from each other in the direction of newly formed protrusions (1). This sequence can, however, be altered in specific conditions such as metastasis in which a loss of CIL allows malignant cells to invade fibroblast cultures—this is a loss of CIL between different cell types (heterotypic CIL) (4, 5). Recent work has also begun to identify the molecular players that initiate and regulate CIL, including Rac activity, microtubules, Eph/Ephrin binding, and E- and N-cadherin expression (6–10).CIL is most commonly studied and analyzed on flat 2D substrates using several invasion and collision assays (2, 3, 11). By contrast, cells traveling in matrix in vivo are constrained to move along narrow fibers. A common shortcoming in featureless 2D assays is thus the inability to study CIL under natural constraints (11–13). Recently, micropatterned substrates have been used to understand restricted motility, developing one-dimensional (1D) collision assays where cell migration is constrained to straight lines, allowing for a greater occurrence of cell–cell collisions to quantify rates and outcomes of different types of cell–cell interactions (11, 13–15). These interactions do not necessarily resemble the stereotyped CIL behavior. Broadly, experiments and simulations (16–18) have observed the following: 1) the classical stereotype of CIL with two cells contacting head-on, with both cells repolarizing (referred to as “reversal” or “mutual CIL”); 2) after a head-on collision, only one cell reverses (“training” or “nonmutual CIL”); and 3) cells manage to crawl past or over one another, exchanging positions (“walk past” or “sliding”). Within the well-studied neural-crest cell explants, walk past is extremely rare (11), but it can occur in epithelial cells, especially in those that have been metastatically transformed or that have decreased E-cadherin expression (15).Both 2D substrates and micropatterned stripes provide controllable and reproducible environments but neither fully models the details of in vivo native cellular environments, which consist of extracellular matrices (ECM) of fibrous proteins, with these fibers having different radii. Our earlier in vitro recapitulation of the effects of fiber curvature showed that both protrusive and migratory behavior is sensitive to fiber diameter (19–21). Furthermore, we have shown that suspended, flat 2D ribbons do not capture the protrusive behavior observed on suspended round fibers (19); thus, we wanted to inquire if the CIL rules developed on 1D collision and 2D assays extend to contextually relevant fibrous environments. To understand CIL in fibrous environments that mimic native ECM, we use suspended and aligned nanofiber networks to study CIL behavior in NIH/3T3 fibroblast cell–cell pairs exhibiting two distinct elongated morphologies: spindle, attached to a single fiber and parallel cuboidal, attached to two fibers (22). We further investigate the effect of cell division on CIL by studying the encounters of cells that have recently divided (daughter cells) with other cells; these recently divided cells are much faster, consistent with earlier work (23). Our work allows us to determine the types and rates of cell–cell contact outcomes—the “rules of CIL”—in a biologically relevant system with a controlled geometry. These rules are radically different from the known stereotypical behavior in 2D assays, but the essential features of these rules emerge robustly from a minimal computational model of CIL in confined geometries.     

A general model of hippocampal and dorsal striatal learning and decision making

Humans and other animals use multiple strategies for making decisions. Reinforcement-learning theory distinguishes between stimulus–response (model-free; MF) learning and deliberative (model-based; MB) planning. The spatial-navigation literature presents a parallel dichotomy between navigation strategies. In “response learning,” associated with the dorsolateral striatum (DLS), decisions are anchored to an egocentric reference frame. In “place learning,” associated with the hippocampus, decisions are anchored to an allocentric reference frame. Emerging evidence suggests that the contribution of hippocampus to place learning may also underlie its contribution to MB learning by representing relational structure in a cognitive map. Here, we introduce a computational model in which hippocampus subserves place and MB learning by learning a “successor representation” of relational structure between states; DLS implements model-free response learning by learning associations between actions and egocentric representations of landmarks; and action values from either system are weighted by the reliability of its predictions. We show that this model reproduces a range of seemingly disparate behavioral findings in spatial and nonspatial decision tasks and explains the effects of lesions to DLS and hippocampus on these tasks. Furthermore, modeling place cells as driven by boundaries explains the observation that, unlike navigation guided by landmarks, navigation guided by boundaries is robust to “blocking” by prior state–reward associations due to learned associations between place cells. Our model, originally shaped by detailed constraints in the spatial literature, successfully characterizes the hippocampal–striatal system as a general system for decision making via adaptive combination of stimulus–response learning and the use of a cognitive map.

Behavioral and neuroscientific studies suggest that animals can apply multiple strategies to the problem of maximizing future reward, referred to as the reinforcement-learning (RL) problem (1, 2). One strategy is to build a model of the environment that can be used to simulate the future to plan optimal actions (3) and the past for episodic memory (4–6). An alternative, model-free (MF) approach uses trial and error to estimate a direct mapping from the animal’s state to its expected future reward, which the agent caches and looks up at decision time (7, 8), potentially supporting procedural memory (9). This computation is thought to be carried out in the brain through prediction errors signaled by phasic dopamine responses (10). These strategies are associated with different tradeoffs (2). The model-based (MB) approach is powerful and flexible, but computationally expensive and, therefore, slow at decision time. MF methods, in contrast, enable rapid action selection, but these methods learn slowly and adapt poorly to changing environments. In addition to MF and MB methods, there are intermediate solutions that rely on learning useful representations that reduce burdens on the downstream RL process (11–13).In the spatial-memory literature, a distinction has been observed between “response learning” and “place learning” (14–16). When navigating to a previously visited location, response learning involves learning a sequence of actions, each of which depends on the preceding action or sensory cue (expressed in egocentric terms). For example, one might remember a sequence of left and right turns starting from a specific landmark. An alternative place-learning strategy involves learning a flexible internal representation of the spatial layout of the environment (expressed in allocentric terms). This “cognitive map” is thought to be supported by the hippocampal formation, where there are neurons tuned to place and heading direction (17–19). Spatial navigation using this map is flexible because it can be used with arbitrary starting locations and destinations, which need not be marked by immediate sensory cues.We posit that the distinction between place and response learning is analogous to that between MB and MF RL (20). Under this view, associative reinforcement is supported by the DLS (21, 22). Indeed, there is evidence from both rodents (23–25) and humans (26, 27) that spatial-response learning relies on the same basal ganglia structures that support MF RL. Evidence also suggests an analogy between MB reasoning and hippocampus (HPC)-based place learning (28, 29). However, this equivalence is not completely straightforward. For example, in rodents, multiple hippocampal lesion and inactivation studies failed to elicit an effect on action-outcome learning, a hallmark of MB planning (30–35). Nevertheless, there are indications that HPC might contribute to a different aspect of MB RL: namely, the representation of relational structure. Tasks that require memory of the relationships between stimuli do show dependence on HPC (36–42).Here, we formalize the perspective that hippocampal contributions to MB learning and place learning are the same, as are the dorsolateral striatal contributions to MF and response learning. In our model, HPC supports flexible behavior by representing the relational structure among different allocentric states, while dorsolateral striatum (DLS) supports associative reinforcement over egocentric sensory features. The model arbitrates between the use of these systems by weighting each system’s action values by the reliability of the system, as measured by a recent average of prediction errors, following Wan Lee et al. (43). We show that HPC and DLS maintain these roles across multiple task domains, including a range of spatial and nonspatial tasks. Our model can quantitatively explain a range of seemingly disparate findings, including the choice between place and response strategies in spatial navigation (23, 44) and choices on nonspatial multistep decision tasks (45, 46). Furthermore, it explains the puzzling finding that landmark-guided navigation is sensitive to the blocking effect, whereas boundary-guided navigation is not (27), and that these are supported by the DLS and HPC, respectively (26). Thus, different RL strategies that manage competing tradeoffs can explain a longstanding body of spatial navigation and decision-making literature under a unified model.     

The mitochondrial thioredoxin reductase system (TrxR2) in vascular endothelium controls peroxynitrite levels and tissue integrity

The mitochondrial thioredoxin/peroxiredoxin system encompasses NADPH, thioredoxin reductase 2 (TrxR2), thioredoxin 2, and peroxiredoxins 3 and 5 (Prx3 and Prx5) and is crucial to regulate cell redox homeostasis via the efficient catabolism of peroxides (TrxR2 and Trxrd2 refer to the mitochondrial thioredoxin reductase protein and gene, respectively). Here, we report that endothelial TrxR2 controls both the steady-state concentration of peroxynitrite, the product of the reaction of superoxide radical and nitric oxide, and the integrity of the vascular system. Mice with endothelial deletion of the Trxrd2 gene develop increased vascular stiffness and hypertrophy of the vascular wall. Furthermore, they suffer from renal abnormalities, including thickening of the Bowman’s capsule, glomerulosclerosis, and functional alterations. Mechanistically, we show that loss of Trxrd2 results in enhanced peroxynitrite steady-state levels in both vascular endothelial cells and vessels by using a highly sensitive redox probe, fluorescein-boronate. High steady-state peroxynitrite levels were further found to coincide with elevated protein tyrosine nitration in renal tissue and a substantial change of the redox state of Prx3 toward the oxidized protein, even though glutaredoxin 2 (Grx2) expression increased in parallel. Additional studies using a mitochondria-specific fluorescence probe (MitoPY1) in vessels revealed that enhanced peroxynitrite levels are indeed generated in mitochondria. Treatment with Mn(III)tetrakis(1-methyl-4-pyridyl)porphyrin [Mn(III)TMPyP], a peroxynitrite-decomposition catalyst, blunted intravascular formation of peroxynitrite. Our data provide compelling evidence for a yet-unrecognized role of TrxR2 in balancing the nitric oxide/peroxynitrite ratio in endothelial cells in vivo and thus establish a link between enhanced mitochondrial peroxynitrite and disruption of vascular integrity.

Selenocysteine-containing mitochondrial thioredoxin reductase (TrxR2) is the key regulator of the thioredoxin system and essential for mitochondrial redox homeostasis (1–3). This system constitutes a primary defense against peroxides produced in mitochondria, such as hydrogen peroxide and peroxynitrite (4). TrxR2 is necessary for maintaining thioredoxin 2 (Trx2) in its reduced state by using electrons from NADPH. In turn, Trx2 is a cofactor of mitochondrially localized peroxiredoxin 3 (Prx3) and peroxiredoxin 5 (Prx5) that reduce H₂O₂ and peroxynitrite^* generated by mitochondrial metabolism (1, 2, 4–7). The reaction rate constants of H₂O₂ and peroxynitrite with the fast reacting thiols of both Prx3 and Prx5 have been compiled recently (4). Notably, Prx3, the only peroxiredoxin which is exclusively localized in mitochondria (8, 9)^†, was reported to accept electrons also from glutaredoxin 2 (Grx2) (10). Among the biologically recognized functions, TrxR2 plays essential roles in hematopoiesis, heart development, and heart function (11, 12). In a previous study, we could show that loss of TrxR2 in endothelial cells (ECs) attenuated vascular remodeling processes following ischemic events and led to a prothrombotic and proinflammatory endothelium (13). While these studies pointed toward an important role of TrxR2 in the cardiovascular system, the underlying biochemical mechanisms, particularly in vivo, have remained largely unclear. Unlike many other cell types in the body, ECs are unique as they are constantly exposed to changing biochemical and mechanical stimuli. Furthermore, they do not just separate the circulating blood and the vascular smooth muscle cells but also have to fulfill a wide range of physiological tasks, including regulation of vascular tone, cellular adhesion, thromboresistance, smooth muscle cell proliferation, and inflammoresistance (14, 15). One of the most significant biomolecules that is involved in vascular endothelial function is the free radical nitric oxide (·NO) (16, 17). ·NO is not only an important vasodilator but also has antiinflammatory properties by inhibiting the synthesis and expression of cytokines and adhesion molecules that attract inflammatory cells and facilitate their entrance into the vessel wall (18, 19). Furthermore, ·NO suppresses platelet aggregation (20), vascular smooth muscle cell migration, and proliferation (21). Consequentially, a decreased synthesis of ·NO, as well as an enhanced inactivation, can result in endothelial dysfunction (22–24). Oxidative stress contributes to this phenomenon, starting with the diffusion-controlled reaction of ·NO with superoxide radical (O₂^·−), which shortens the biological half-life and compromises the signaling actions of ·NO (25–28). In addition, the oxidative inactivation of ·NO by O₂^·− yields a powerful oxidizing and nitrating species, peroxynitrite anion (28, 29). Moreover, peroxynitrite itself leads to uncoupling of endothelial nitric oxide synthase to become a dysfunctional O₂^·− and peroxynitrite-producing enzyme that additionally contributes to cellular oxidative stress (30, 31). A sustained overload of O₂^·− and, peroxynitrite combined with insufficient levels of ·NO may contribute to a switch of the endothelium from the quiescent stage toward an activated one, setting up a vicious cycle, causing endothelial dysfunction and inflammation. ECs are equipped with a number of antioxidant systems known to be potentially protective against vascular oxidative stress that, however, under persistent pathological stimuli, may become overwhelmed.In this context, it is increasingly recognized that mitochondrial-derived O₂^·− and the disruption of mitochondrial redox homeostasis contribute to alter the signaling actions of ·NO in vascular biology (32–34). Besides the mitochondrial thioredoxin system, a number of professional redox systems, including mitochondrial superoxide dismutase (MnSOD/SOD2), glutathione peroxidase, and glutathione reductase, are involved in maintaining mitochondrial redox homeostasis.However, the specific roles of these enzymes in the context of endothelial dysfunction are far from being understood. The fact that genetically modified mouse models revealed that many of the different antioxidant enzymes are indispensable for murine development (35–38) impedes further insights into their role for vascular homeostasis, and, to our knowledge, only a limited number of EC-specific transgenic mice have yet been described in this context (39–42). Interestingly, Trx2 transgenic mice that overexpress Trx2 specifically in the endothelium demonstrated an increased ·NO bioavailability and EC function, decreased oxidative stress, and reduced propensity to atheroma formation (3, 43).The aim of this study was to analyze the impact of endothelial TrxR2 on vascular homeostasis (in vitro, ex vivo, and in vivo), focusing on its role on mitochondrial peroxynitrite catabolism. The data support that enhanced mitochondrial steady-state levels of peroxynitrite in vascular ECs are connected with disruption of redox homeostasis and vascular structural and functional integrity.