Vertical sleeve gastrectomy confers metabolic improvements by reducing intestinal bile acids and lipid absorption in mice

Vertical sleeve gastrectomy (VSG) is one of the most effective and durable therapies for morbid obesity and its related complications. Although bile acids (BAs) have been implicated as downstream mediators of VSG, the specific mechanisms through which BA changes contribute to the metabolic effects of VSG remain poorly understood. Here, we confirm that high fat diet-fed global farnesoid X receptor (Fxr) knockout mice are resistant to the beneficial metabolic effects of VSG. However, the beneficial effects of VSG were retained in high fat diet-fed intestine- or liver-specific Fxr knockouts, and VSG did not result in Fxr activation in the liver or intestine of control mice. Instead, VSG decreased expression of positive hepatic Fxr target genes, including the bile salt export pump (Bsep) that delivers BAs to the biliary pathway. This reduced small intestine BA levels in mice, leading to lower intestinal fat absorption. These findings were verified in sterol 27-hydroxylase (Cyp27a1) knockout mice, which exhibited low intestinal BAs and fat absorption and did not show metabolic improvements following VSG. In addition, restoring small intestinal BA levels by dietary supplementation with taurocholic acid (TCA) partially blocked the beneficial effects of VSG. Altogether, these findings suggest that reductions in intestinal BAs and lipid absorption contribute to the metabolic benefits of VSG.

To date, bariatric surgery remains the most effective and long-lasting treatment for morbid obesity and its related complications, including type 2 diabetes (T2D) and fatty liver diseases (1, 2). The Roux-en-Y gastric bypass (RYGB) and vertical sleeve gastrectomy (VSG) surgical procedures represent two of the most commonly performed variations of bariatric surgery (3, 4). Because VSG results in fewer complications and a lower incidence of dumping syndrome, it thus has surpassed RYGB to become the most commonly performed bariatric procedure in the United States (4–6). Nevertheless, the precise relationship between the metabolic benefits of VSG and its underlying molecular mechanisms remains unclear.Several molecular mechanisms associated with the metabolic benefits of bariatric surgery have been reported (7). While a number of studies have focused on the role of glucagon-like peptide 1 (GLP-1), whose circulating levels increase 5- to 10-fold after VSG (8, 9), glucagon-like peptide 1 receptor (GLP-1r) in β-cells appears dispensable for mediating improvements in glucose tolerance after surgery (10). Additional mechanisms underlying the benefits of VSG have been described and involve improved insulin secretion, substantial changes to islet gene expression (11), and alterations in the composition and concentration of bile acid (BA) digestive surfactants (12). For example, patients who receive bariatric surgery not only exhibit compositional changes to their pool of BAs but also experience an increase in their circulating concentrations (9, 13–15). In diet-induced obese rodent models, VSG recapitulates several of the observations perceived postsurgically in human patients, including significant changes in BA dynamics (16, 17). More interestingly, several studies have shown that the benefits of VSG may require two BA receptors: farnesoid X receptor (Fxr) and G protein-coupled BA receptor (also known as Tgr5) (18, 19). Although these observations underscore the potential importance of BA circulation and signaling in the metabolic benefits of bariatric surgery, the fundamental mechanisms through which BA changes confer such benefits remain unknown. Here, we analyze and compare the effects of VSG in different mouse lines (Fxr whole-body knockout [Fxr^−/−], liver-specific knockout [Fxr^ΔL], intestine-specific knockout [Fxr^ΔIN], and Cyp27a1 knockout [Cyp27a1^−/−]) and demonstrate that reduced intestinal BAs and lipid absorption may underlie the metabolic benefits of VSG.     

Superelastic oxide micropillars enabled by surface tension–modulated 90° domain switching with excellent fatigue resistance

Superelastic materials capable of recovering large nonlinear strains are ideal for a variety of applications in morphing structures, reconfigurable systems, and robots. However, making oxide materials superelastic has been a long-standing challenge due to their intrinsic brittleness. Here, we fabricate ferroelectric BaTiO₃ (BTO) micropillars that not only are superelastic but also possess excellent fatigue resistance, lasting over 1 million cycles without accumulating residual strains or noticeable variation in stress–strain curves. Phase field simulations reveal that the large recoverable strains of BTO micropillars arise from surface tension–modulated 90° domain switching and thus are size dependent, while the small energy barrier and ultralow energy dissipation are responsible for their unprecedented cyclic stability among superelastic materials. This work demonstrates a general strategy to realize superelastic and fatigue-resistant domain switching in ferroelectric oxides for many potential applications.

Superelastic materials are capable of recovering large amount of nonlinear “plastic” strains, way beyond their linear elastic regimes (1–4). They are ideal for a variety of applications from morphing structures, reconfigurable systems, to robots (5–8). The effects have traditionally been associated with macroscopically compliant/ductile rubbers (2) or microscopically phase-transforming shape memory alloys (SMAs) (7–11). The only macroscopically brittle oxide recently discovered to be superelastic is ZrO₂-based micropillars or particles (12–20), which is realized via austenite-martensite phase transformation similar to SMAs. Although ultimate strengths approaching the theoretical limit have been demonstrated in nanoscale samples (21, 22), long fatigue life is elusive, which is arguably more important for most applications. As a matter of fact, poor fatigue life has been a long-standing challenge for oxide ceramics in general (23, 24). Even for ductile SMAs that enjoy excellent fatigue life, irrecoverable residual strains gradually accumulate over cycling, leading to substantial variations in stress–strain curves at different cycles (9, 10, 25). We overcome these difficulties by reporting superelastic barium titanate (BaTiO₃ [BTO]) micropillars enabled by surface tension–modulated 90° domain switching, which exhibit excellent fatigue resistance, while bulk BTO crystals or ceramics are rather brittle. The demonstration of over one million cycles of loading and unloading without accumulating residual strains or noticeable variation in stress–strain curves is unprecedented among superelastic materials.BTO is a ferroelectric oxide exhibiting modest piezoelectric strains around 0.1 to 0.2% (26) and fracture toughness of ∼1 MPa ⋅ m^1/2, and thus it is quite brittle (27). Considerable research efforts have been devoted to enhancing its electric field–induced strain via 90° ferroelectric domain switching (28–30). However, the process is often irreversible, and external mechanisms such as restoring force (28, 29) and internal mechanisms such as defect pinning (30) have to be invoked to make the electrostrain recoverable. Nevertheless, it hints at the possibility of BTO being made superelastic by taking advantage of the stress-induced 90° domain switching (6). Earlier works suggest that surface tension induces an in-plane compressive stress that favors the axial polarization in one-dimensional ferroelectrics at small size (31, 32), which may provide the necessary restoring mechanism for the stress-switched domains. Thus, if a compressive axial force is applied, reversible domain switching may occur during unloading, leading to superelasticity. To verify this hypothesis, we fabricated single-crystalline BTO micropillars from [001]-oriented bulk crystals (SI Appendix, Fig. S1A) via focused ion beam (FIB), as detailed in Materials and Methods and SI Appendix, Fig. S1B. The diameters (Φ) of the micropillars range from 0.5 μm to 5 μm, with their height to diameter ratio fixed at 3. No visible defects can be seen from the scanning electron microscopy (SEM) images of these micropillars shown in Fig. 1 A–D, and their surfaces appear to be quite smooth, suggesting that no apparent damages are induced by FIB.Open in a separate windowFig. 1.Superelastic BTO micropillars below a critical size. (A–D) SEM images of the micropillars with Φ = 5, 3, 2, and 0.5 μm. (E–G) The first and second cycles of stress–strain curves for BTO micropillars with Φ = 5, 2, and 0.5 μm. (H) S_r/S_max and ΔW/W_max during the first cycle for BTO micropillars of different diameters. Here, S_r and S_max denote the residual strain and the maximum strain (SI Appendix, Fig. S6A), while ΔW and W_max are energy dissipated and stored in the first cycle, respectively (SI Appendix, Fig. S6F).     

Optical vector field rotation and switching with near-unity transmission by fully developed chiral photonic crystals

State-of-the-art nanostructured chiral photonic crystals (CPCs), metamaterials, and metasurfaces have shown giant optical rotatory power but are generally passive and beset with large optical losses and with inadequate performance due to limited size/interaction length and narrow operation bandwidth. In this work, we demonstrate by detailed theoretical modeling and experiments that a fully developed CPC, one for which the number of unit cells N is high enough that it acquires the full potentials of an ideal (N → ∞) crystal, will overcome the aforementioned limitations, leading to a new generation of versatile high-performance polarization manipulation optics. Such high-N CPCs are realized by field-assisted self-assembly of cholesteric liquid crystals to unprecedented thicknesses not possible with any other means. Characterization studies show that high-N CPCs exhibit broad transmission maxima accompanied by giant rotatory power, thereby enabling large (>π) polarization rotation with near-unity transmission over a large operation bandwidth. Polarization rotation is demonstrated to be independent of input polarization orientation and applies equally well on continuous-wave or ultrafast (picosecond to femtosecond) pulsed lasers of simple or complex (radial, azimuthal) vector fields. Liquid crystal–based CPCs also allow very wide tuning of the operation spectral range and dynamic polarization switching and control possibilities by virtue of several stimuli-induced index or birefringence changing mechanisms.

Optical vector field (more commonly called polarization) rotators and switches are essential components of all modern optical and photonic systems for communications, ellipsometry, metrology, biological/chemical detection, and quantum processing/computing (1–10). There are, however, some inherent limitations. Wave plates made with birefringent crystals, for example, require strict alignment of the optic axis with respect to the polarization orientation of incident light and generally do not work with laser vector beams of complex polarization fields; Faraday rotators that do not have this requirement are generally too cumbersome and bulky due to their weak optical rotatory powers. One promising approach to circumvent these limitations is to employ chiral optical materials such as chiral photonic crystals and metasurfaces. Nevertheless, structural chirality, such as chiral metamaterials, metasurfaces, and photonic crystals that are capable of very large optical rotatory power (up to ∼100,000°/mm), are inevitably accompanied by large absorption losses (11–15). In metamaterials/surfaces, the intrinsic noncircular absorption and nanofabrication difficulty also add to the limitation of their practical scalability in the interaction length, resulting in small (<π) net polarization rotation angle, very small aperture, and narrow operating spectral bandwidth (11–13). Similar issues confront most chiral photonic crystals (CPCs) due to the limitations of molecular self-assembly or nanofabrication/processing technique and high transmission loss associated with operation near the Bragg reflection band (14, 15).Here, we show by theory and experimental corroborations that a fully developed liquid crystal–based CPC, one for which the number of unit cells N approaches that (N → ∞) of an ideal crystal, can circumvent all the aforementioned limitations and possess several advantageous characteristics impossible with conventional low-N thin counterparts. Such high-period–number chiral photonic crystals (HN-CPCs) are achieved by fabricating cholesteric liquid crystals (CLCs) to thicknesses several hundred times that of conventional ones using a refined field-assisted self-assembly (FASA) technique (16, 17; see SI Appendix, Note 1, for more details). Optical properties of CLCs as CPCs arise from complex “collective” responses from many unit cells. While thicker crystals obviously give rise to larger effects, the resulting properties as the crystal thickness or period number N evolves from low values to a very high value do not lend themselves to such simple linear extrapolation; as a function of N, pleasant surprises and new insights and possibilities abound. Our studies show that for N > 500, these CLCs exhibit simultaneously broad transmission maxima and large polarization rotation power in the off-Bragg-resonance spectral regime. Polarization rotation is independent of input polarization orientation and acts equally well on simple or complex vector fields (18–22) of continuous-wave (CW) or ultrafast pulsed laser beams. Liquid crystal–based CPCs also allow dynamic polarization switching and control by virtue of field–induced index/birefringence changing mechanisms at modest or ultrafast (picosecond to femtosecond) speeds (23–34).     

Crystal structure of a far-red–sensing cyanobacteriochrome reveals an atypical bilin conformation and spectral tuning mechanism

Cyanobacteriochromes (CBCRs) are small, linear tetrapyrrole (bilin)-binding photoreceptors in the phytochrome superfamily that regulate diverse light-mediated adaptive processes in cyanobacteria. More spectrally diverse than canonical red/far-red–sensing phytochromes, CBCRs were thought to be restricted to sensing visible and near UV light until recently when several subfamilies with far-red–sensing representatives (frCBCRs) were discovered. Two of these frCBCRs subfamilies have been shown to incorporate bilin precursors with larger pi-conjugated chromophores, while the third frCBCR subfamily uses the same phycocyanobilin precursor found in the bulk of the known CBCRs. To elucidate the molecular basis of far-red light perception by this third frCBCR subfamily, we determined the crystal structure of the far-red–absorbing dark state of one such frCBCR Anacy_2551g3 from Anabaena cylindrica PCC 7122 which exhibits a reversible far-red/orange photocycle. Determined by room temperature serial crystallography and cryocrystallography, the refined 2.7-Å structure reveals an unusual all-Z,syn configuration of the phycocyanobilin (PCB) chromophore that is considerably less extended than those of previously characterized red-light sensors in the phytochrome superfamily. Based on structural and spectroscopic comparisons with other bilin-binding proteins together with site-directed mutagenesis data, our studies reveal protein–chromophore interactions that are critical for the atypical bathochromic shift. Based on these analyses, we propose that far-red absorption in Anacy_2551g3 is the result of the additive effect of two distinct red-shift mechanisms involving cationic bilin lactim tautomers stabilized by a constrained all-Z,syn conformation and specific interactions with a highly conserved anionic residue.

Cyanobacteria have developed elaborate, spectrally tuned photoreceptors and light-harvesting systems for adaptation and survival in a wide range of ecological niches (1–5). Many photoreceptor systems are modular components of much larger signaling proteins that integrate different sensor and effector modules into a single protein molecule to interface with diverse signal transduction pathways. Photoreceptors in the phytochrome superfamily utilize a specific lineage of GAF (cGMP phosphodiesterase, adenylyl cyclase and FhlA) domain that binds a thioether-linked linear tetrapyrrole (bilin) chromophore for light perception (6–11). Bilin-based photoreceptors play critical roles in plant development as well as in regulating cyanobacterial phototaxis, development, and light harvesting (2, 3, 12–17). Protein structural changes following the primary photochemical event then alter the downstream enzymatic activities and/or protein–protein interactions via an interdomain allosteric mechanism (18).Phytochromes possess a tripartite photosensory region consisting of three N-terminal domains (PAS, GAF, and PHY), known as the photosensory core module, in which the PAS and GAF domains are tethered via a “figure-eight knot” (14, 19, 20). In prototypical phytochromes, the bilin chromophore embedded in the GAF domain adopts a protonated 5-Z,syn, 10-Z,syn, 15-Z,anti configuration in the dark-adapted state. Light absorption triggers photoisomerization of the 15,16 double bond to generate a 15E,anti photoproduct, which typically absorbs far-red light (9, 14, 21). A long extension from the adjacent PHY domain is responsible for stabilizing the far-red–absorbing Pfr state (14, 20). In cyanobacteria, the phytochrome superfamily has diversified to yield a large family of more streamlined sensors, designated cyanobacteriochromes (CBCRs) (2, 4, 22–26). Unlike canonical phytochromes, CBCR photosensory modules consist of one or more GAF domains that are sufficient for covalent attachment of bilin and photoconversion. These small CBCR domains have also been used as light-sensing modules in a variety of synthetic biology applications (27–32). In contrast to canonical red/far-red phytochromes, CBCRs are able to sense light from near UV to far-red, utilizing a common phycocyanobilin (PCB) chromophore precursor (22–24, 26).The remarkable spectral diversity of CBCRs (SI Appendix, Fig. S1A) arises from extensive molecular evolution of the GAF domain scaffold. Many CBCRs leverage two thioether linkages to sense blue, violet, or near-UV light (8, 22, 23, 25, 33–35). Such “two-Cys” CBCRs possess an additional thioether linkage to the C10 methine bridge of the bilin that splits the chromophore in half, significantly shortening the conjugated π-system. Rupture of this covalent bond can occur upon 15Z/15E photoisomerization, which restores bilin conjugation across C10 to generate a photostate absorbing at wavelengths from teal to red (8, 33, 36, 37). Dual cysteine CBCRs have evolved multiple times, yielding a wide range of photocycles with (ultra)violet, blue, teal, green, orange, and red states (22).Red/green CBCRs such as AnPixJg2 and NpR6012g4 have red-absorbing dark states similar to phytochromes that photoconvert to green-absorbing lit states. In this CBCR subfamily, the molecular mechanism responsible for photoproduct tuning relies on trapping the 15E bilin in a twisted geometry that results in blue-shifted absorption (10, 11). In contrast, green/red CBCRs exhibit a reversed photocycle: the green-absorbing 15Z dark state photoconverts to yield a red-absorbing 15E photoproduct. This subfamily uses a protochromic mechanism first reported for the light-regulated histidine kinase RcaE (SI Appendix, Fig. S1B) in which photoconversion triggers a proton transfer to an uncharged chromophore inducing a spectral red shift (2, 38).Until recently, the light-sensing range of CBCRs appeared limited to the visible spectrum, thereby implicating phytochromes to be exclusively responsible for far-red sensing in cyanobacteria. Indeed, far-red–dependent remodeling of the photosynthetic apparatus in multiple cyanobacterial species is mediated by the red/far-red phytochrome RfpA (3, 39). The discovery of two lineages of CBCRs with far-red-absorbing dark states (frCBCRs) was thus surprising (40). Upon far-red light absorption, these frCBCRs convert to either an orange- or red-absorbing photoproduct state. These frCBCRs evolved from green/red CBCRs as part of a greater green/red (GGR) lineage and independent from evolution of other frCBCRs within the XRG (extended red/green) lineage (35, 40, 41). Owing to their small size and spectral overlap with the therapeutic window of optimum tissue penetrance (700 to 800 nm) (42–46), frCBCRs represent tantalizing scaffolds for development of FR-responsive optogenetic reagents for biomedical research and imaging applications (45, 47–50).To understand the molecular basis of far-red spectral tuning of the frCBCR family that evolved within GGR lineage, we determined the crystal structures of the FR-absorbing dark state of the representative FR/O CBCR Anacy_2551g3 from Anabaena cylindrica PCC 7122 at both ambient and cryogenic temperatures. These structures revealed an all-Z,syn configuration of its PCB chromophore that differs from those found in all known CBCRs and phytochromes. Based upon these crystallographic results, spectra of site-directed mutants of Anacy_2551g3 and related frCBCRs in the GGR lineage, and comparisons with other bilin-binding proteins, we identify key protein–chromophore interactions that support two tuning mechanisms simultaneously at work for far-red light detection in this family of frCBCRs.     

African burned area and fire carbon emissions are strongly impacted by small fires undetected by coarse resolution satellite data

Fires are a major contributor to atmospheric budgets of greenhouse gases and aerosols, affect soils and vegetation properties, and are a key driver of land use change. Since the 1990s, global burned area (BA) estimates based on satellite observations have provided critical insights into patterns and trends of fire occurrence. However, these global BA products are based on coarse spatial-resolution sensors, which are unsuitable for detecting small fires that burn only a fraction of a satellite pixel. We estimated the relevance of those small fires by comparing a BA product generated from Sentinel-2 MSI (Multispectral Instrument) images (20-m spatial resolution) with a widely used global BA product based on Moderate Resolution Imaging Spectroradiometer (MODIS) images (500 m) focusing on sub-Saharan Africa. For the year 2016, we detected 80% more BA with Sentinel-2 images than with the MODIS product. This difference was predominately related to small fires: we observed that 2.02 Mkm² (out of a total of 4.89 Mkm²) was burned by fires smaller than 100 ha, whereas the MODIS product only detected 0.13 million km² BA in that fire-size class. This increase in BA subsequently resulted in increased estimates of fire emissions; we computed 31 to 101% more fire carbon emissions than current estimates based on MODIS products. We conclude that small fires are a critical driver of BA in sub-Saharan Africa and that including those small fires in emission estimates raises the contribution of biomass burning to global burdens of (greenhouse) gases and aerosols.

Fire plays an important role in the Earth system, impacting climate and air quality and affecting vegetation, soils, and human assets (1–3). Global annual BA is currently estimated to be between 4.2 and 4.7 million km² (4–6). Fires burn naturally in many ecosystems, but currently, the majority of fires have an anthropogenic origin and are often used as a land management tool [e.g., in the deforestation process (4, 5)]. Fires impact climate by releasing greenhouse gases and aerosols and by modifying surface albedo (6–8).Satellite sensors are the preferred way to estimate BA, as they provide frequent and comprehensive observations of surface reflectance and thermal properties (9). However, most existing products are based on coarse spatial-resolution images (≥500 m), which provide a global view of fire occurrence almost daily but may have important omission and commission errors, particularly where fires are small in size (10). In fact, several regional assessments of those global BA products have identified substantial omission errors when compared to fire perimeters (11–15). Omission of small fires may be the cause of observing higher omission than commission errors in existing validation efforts of global BA products (15–17).A first approach to estimate the contribution of these small fires was proposed by Randerson et al. (18) based on a statistical method overlaying BA and active fire detections. They estimated that small fires led to an additional 24 to 54% BA compared to previous estimates. Thanks to recent developments in satellite instruments and computing power, we can now map BA with substantially higher spatial resolution (≤30 m) and for large geographic regions (19–21), reducing the dependency on statistical methods and active fire detections.Our main goal was to compare a new BA dataset generated from medium-resolution images and its resulting fire carbon emissions with existing information based on global BA datasets derived from coarse-resolution data. We focused our analysis on Africa, as it accounts for about 70% of global BA (22) and about half of global fire carbon emissions (23). The medium-resolution BA product was developed from Sentinel-2 MultiSpectral Instrument (MSI) data under the Fire Disturbance project of the European Space Agency’s Climate Change Initiative (CCI) program. The product, named FireCCISFD11, covers the whole of sub-Saharan Africa at 20-m resolution for the year 2016 (21) (see Materials and Methods). We have compared this product with three global BA datasets derived from MODIS data: MCD64A1C6 (22), the Global Fire Emission Database version 4s (GFED4s) (23), and the Global Fire Atlas (GFA) (24). MCD64A1C6 is the most recent version of a widely used BA product for global analysis of biomass burning impacts (9, 25). GFED4s is based on an older version of the MCD64A1 dataset (C5.1) but includes BA estimates from small fires based on a statistical approach. This product is only available at 0.25° spatial resolution (23). The GFA was derived from the MCD64A1C6 product. It generates burned patches from detected burned pixels using contextual analysis (24). Our comparative analysis between FireCCISFD11 and global products included total BA (with MCD64A1 and GFED4s), fire size distribution (with MCD64A1 and GFA), BA stratified by land cover (MCD64A1), and fire emissions (derived from MCD64A1 and GFED4s).     

Transfer-printed,tandem microscale light-emitting diodes for full-color displays

Inorganic semiconductor-based microscale light-emitting diodes (micro-LEDs) have been widely considered the key solution to next-generation, ubiquitous lighting and display systems, with their efficiency, brightness, contrast, stability, and dynamic response superior to liquid crystal or organic-based counterparts. However, the reduction of micro-LED sizes leads to the deteriorated device performance and increased difficulties in manufacturing. Here, we report a tandem device scheme based on stacked red, green, and blue (RGB) micro-LEDs, for the realization of full-color lighting and displays. Thin-film micro-LEDs (size ∼100 μm, thickness ∼5 μm) based on III–V compound semiconductors are vertically assembled via epitaxial liftoff and transfer printing. A thin-film dielectric-based optical filter serves as a wavelength-selective interface for performance enhancement. Furthermore, we prototype arrays of tandem RGB micro-LEDs and demonstrate display capabilities. These materials and device strategies provide a viable path to advanced lighting and display systems.

Microscale light-emitting diodes (micro-LEDs) based on inorganic semiconductors have been widely regarded as one of the most promising solutions to the next generation of emissive display technologies for versatile applications, from televisions, smartphones and wearable watches, to advanced virtual, augmented, and mixed realities (1–4). Constructed from single-crystalline–compound semiconductors like gallium arsenide (GaAs), gallium phosphide (GaP), and gallium nitride (GaN), these micro-LEDs present significant benefits over conventional liquid crystal displays (LCDs) (5), organic LEDs (OLEDs) (6–9), and more recent quantum dot (10, 11) and perovskite-based LEDs (12), in terms of their efficiencies, brightness, contrast, dynamic response, and long-time stability. High-resolution displays rely on arrays of polychromatic (red, green, and blue [RGB]) emissive elements with dimensions of less than 100 μm or even 10 μm, which are massively and heterogeneously assembled onto silicon, glass, or plastic substrates (13–17). This scaling down of device sizes enhances the display resolution and reduces the raw material cost; however, it is also accompanied by significant challenges. First, reducing LED size causes dramatic efficiency decreases for all types of LEDs (18–21), particularly GaAs- or GaP-based red LEDs that are more susceptible to sidewall defects (SI Appendix, Fig. S1). Second, device shrinkage also results in deteriorated uniformity, which influences the reliability and performance of display systems. Third, fabricating and transferring smaller devices demand higher accuracies for alignment and positioning (22), imposing greatly increased manufacturing expenses (SI Appendix, Fig. S2).Alternatively, device arrays with a single-pixel, spectrally tunable LED (23) or vertically stacked tandem LEDs (24) relieve the above constraints associated with conventional laterally arranged RGB micro-LEDs. However, color-tunable LEDs based on voltage-dependent spectral change can neither achieve full-range tunability nor obtain independent color/intensity controllability (25, 26). On the other hand, the current state-of-the-art wafer-bonding–based assembly methods only realize double-layer stacking with the capability of dual-color tuning (green/blue or red/blue) (22, 27, 28). Although there are some reports on full-color stacked inorganic and organic RGB LEDs (24, 29–31), these demonstrations are only limited to a few of chip-scale, large or thick LEDs for lighting purposes.In this paper, we report a tandem thin-film RGB micro-LED architecture with full-range color tunability to overcome the limitations of previously explored technologies. Based on the epitaxial liftoff and transfer printing method, arrays of thin-film, high-performance, inorganic RGB micro-LEDs made of different III–V compounds are assembled in a vertical stack. Embedded into the stacked structure, a thin-film dielectric filter serves as a wavelength selective interlayer to improve the LED light output. Independently addressable active arrays show full-color electroluminescent patterns, demonstrating the display capability of the tandem micro-LEDs.     

Heading perception depends on time-varying evolution of optic flow

There is considerable support for the hypothesis that perception of heading in the presence of rotation is mediated by instantaneous optic flow. This hypothesis, however, has never been tested. We introduce a method, termed “nonvarying phase motion,” for generating a stimulus that conveys a single instantaneous optic flow field, even though the stimulus is presented for an extended period of time. In this experiment, observers viewed stimulus videos and performed a forced-choice heading discrimination task. For nonvarying phase motion, observers made large errors in heading judgments. This suggests that instantaneous optic flow is insufficient for heading perception in the presence of rotation. These errors were mostly eliminated when the velocity of phase motion was varied over time to convey the evolving sequence of optic flow fields corresponding to a particular heading. This demonstrates that heading perception in the presence of rotation relies on the time-varying evolution of optic flow. We hypothesize that the visual system accurately computes heading, despite rotation, based on optic acceleration, the temporal derivative of optic flow.

James Gibson first remarked that the instantaneous motion of points on the retina (Fig. 1A) can be formally described as a two-dimensional (2D) field of velocity vectors called the “optic flow field” (or “optic flow”) (1). Such optic flow, caused by an observer’s movement relative to the environment, conveys information about self-motion and the structure of the visual scene (1–15). When an observer translates in a given direction along a straight path, the optic flow field radiates from a point in the image with zero velocity, or singularity, called the focus of expansion (Fig. 1B). It is well known that under such conditions, one can accurately estimate one’s “heading” (i.e., instantaneous direction of translation in retinocentric coordinates) by simply locating the focus of expansion (SI Appendix). However, if there is angular rotation in addition to translation (by moving along a curved path or by a head or eye movement), the singularity in the optic flow field will be displaced such that it no longer corresponds to the true heading (Fig. 1 C and D). In this case, if one estimates heading by locating the singularity, the estimate will be biased away from the true heading. This is known as the rotation problem (14).Open in a separate windowFig. 1.Projective geometry, the rotation problem, time-varying optic flow, and the optic acceleration hypothesis. (A) Viewer-centered coordinate frame and perspective projection. Because of motion between the viewpoint and the scene, a 3D surface point traverses a path in 3D space. Under perspective projection, the 3D path of this point projects onto a 2D path in the image plane (retina), the temporal derivative of which is called image velocity. The 2D velocities associated with all visible points define a dense 2D vector field called the optic flow field. (B–D) Illustration of the rotation problem. (B) Optic flow for pure translation (1.5-m/s translation speed, 0° heading, i.e., heading in the direction of gaze). Optic flow singularity (red circle) corresponds to heading (purple circle). (C) Pure rotation, for illustrative purposes only and not corresponding to any experimental condition (2°/s rightward rotation). (D) Translation + rotation (1.5 m/s translation speed, 0° heading, 2°/s rightward rotation). Optic flow singularity (red circle) is displaced away from heading (purple circle). (E) Three frames from a video depicting movement along a circular path with the line-of-sight initially perpendicular to a single fronto-parallel plane composed of black dots. (F) Time-varying evolution of optic flow. The first optic flow field reflects image motion between the first and second frames of the video. The second optic flow field reflects image motion between the second and third frames of the video. For this special case (circular path), the optic flow field evolves (and the optic flow singularity drifts) only due to the changing depth of the environment relative to the viewpoint. (G) Illustration of the optic acceleration hypothesis. Optic acceleration is the derivative of optic flow over time (here, approximated as the difference between the second and first optic flow fields). The singularity of the optic acceleration field corresponds to the heading direction. Acceleration vectors autoscaled for visibility.Computer vision researchers and vision scientists have developed a variety of algorithms that accurately and precisely extract observer translation and rotation from optic flow, thereby solving the rotation problem. Nearly all of these rely on instantaneous optic flow (i.e., a single optic flow field) (4, 9, 16–25) with few exceptions (26–29). However, it is unknown whether these algorithms are commensurate with the neural computations underlying heading perception.The consensus of opinion in the experimental literature is that human observers can estimate heading (30, 31) from instantaneous optic flow, in the absence of additional information (5, 10, 15, 32–34). Even so, there are reports of systematic biases in heading perception (11); the visual consequences of rotation (eye, head, and body) can bias heading judgments (10, 15, 35–37), with the amount of bias typically proportional to the magnitude of rotation. Other visual factors, such as stereo cues (38, 39), depth structure (8, 10, 40–43), and field of view (FOV) (33, 42–44) can modulate the strength of these biases. Errors in heading judgments have been reported to be greater when eye (35–37, 45, 46) or head movements (37) are simulated versus when they are real, which has been taken to mean that observers require extraretinal information, although there is also evidence to the contrary (10, 15, 33, 40, 41, 44, 47–50). Regardless, to date no one has tested whether heading perception (even with these biases) is based on instantaneous optic flow or on the information available in how the optic flow field evolves over time. Some have suggested that heading estimates rely on information accumulated over time (32, 44, 51), but no one has investigated the role of time-varying optic flow without confounding it with stimulus duration (i.e., the duration of evidence accumulation).In this study, we employed an application of an image processing technique that ensured that only a single optic flow field was available to observers, even though the stimulus was presented for an extended period of time. We called this condition “nonvarying phase motion” or “nonvarying”: The phases of two component gratings comprising each stationary stimulus patch shifted over time at a constant rate, causing a percept of motion in the absence of veridical movement (52). Phase motion also eliminated other cues that may otherwise have been used for heading judgments, including image point trajectories (15, 32) and their spatial compositions (i.e., looming) (53, 54). For nonvarying phase motion, observers exhibited large biases in heading judgments in the presence of rotation. A second condition, “time-varying phase motion,” or “time-varying,” included acceleration by varying the velocity of phase motion over time to match the evolution of a sequence of optic flow fields. Doing so allowed observers to compensate for the confounding effect of rotation on optic flow, making heading perception nearly veridical. This demonstrates that heading perception in the presence of rotation relies on the time-varying evolution of optic flow.     

From the Cover: Evidence from South Africa for a protracted end-Permian extinction on land

Earth’s largest biotic crisis occurred during the Permo–Triassic Transition (PTT). On land, this event witnessed a turnover from synapsid- to archosauromorph-dominated assemblages and a restructuring of terrestrial ecosystems. However, understanding extinction patterns has been limited by a lack of high-precision fossil occurrence data to resolve events on submillion-year timescales. We analyzed a unique database of 588 fossil tetrapod specimens from South Africa’s Karoo Basin, spanning ∼4 My, and 13 stratigraphic bin intervals averaging 300,000 y each. Using sample-standardized methods, we characterized faunal assemblage dynamics during the PTT. High regional extinction rates occurred through a protracted interval of ∼1 Ma, initially co-occurring with low origination rates. This resulted in declining diversity up to the acme of extinction near the Daptocephalus–Lystrosaurus declivis Assemblage Zone boundary. Regional origination rates increased abruptly above this boundary, co-occurring with high extinction rates to drive rapid turnover and an assemblage of short-lived species symptomatic of ecosystem instability. The “disaster taxon” Lystrosaurus shows a long-term trend of increasing abundance initiated in the latest Permian. Lystrosaurus comprised 54% of all specimens by the onset of mass extinction and 70% in the extinction aftermath. This early Lystrosaurus abundance suggests its expansion was facilitated by environmental changes rather than by ecological opportunity following the extinctions of other species as commonly assumed for disaster taxa. Our findings conservatively place the Karoo extinction interval closer in time, but not coeval with, the more rapid marine event and reveal key differences between the PTT extinctions on land and in the oceans.

Mass extinctions are major perturbations of the biosphere resulting from a wide range of different causes including glaciations and sea level fall (1), large igneous provinces (2), and bolide impacts (3, 4). These events caused permanent changes to Earth’s ecosystems, altering the evolutionary trajectory of life (5). However, links between the broad causal factors of mass extinctions and the biological and ecological disturbances that lead to species extinctions have been difficult to characterize. This is because ecological disturbances unfold on timescales much shorter than the typical resolution of paleontological studies (6), particularly in the terrestrial record (6–8). Coarse-resolution studies have demonstrated key mass extinction phenomena including high extinction rates and lineage turnover (7, 9), changes in species richness (10), ecosystem instability (11), and the occurrence of disaster taxa (12). However, finer time resolutions are central to determining the association and relative timings of these effects, their potential causal factors, and their interrelationships. Achieving these goals represents a key advance in understanding the ecological mechanisms of mass extinctions.The end-Permian mass extinction (ca. 251.9 Ma) was Earth’s largest biotic crisis as measured by taxon last occurrences (13–15). Large outpourings from Siberian Trap volcanism (2) are the likely trigger of calamitous climatic changes, including a runaway greenhouse effect and ocean acidification, which had profound consequences for life on land and in the oceans (16–18). An estimated 81% of marine species (19) and 89% of tetrapod genera became extinct as established Permian ecosystems gave way to those of the Triassic. In the ocean, this included the complete extinction of reef-forming tabulate and rugose corals (20, 21) and significant losses in previously diverse ammonoid, brachiopod, and crinoid families (22). On land, many nonmammalian synapsids became extinct (16), and the glossopterid-dominated floras of Gondwana also disappeared (23). Stratigraphic sequences document a global “coral gap” and “coal gap” (24, 25), suggesting reef and forest ecosystems were rare or absent for up to 5 My after the event (26). Continuous fossil-bearing deposits documenting patterns of turnover across the Permian–Triassic transition (PTT) on land (27) and in the oceans (28) are geographically widespread (29, 30), including marine and continental successions that are known from China (31, 32) and India (33). Continental successions are known from Russia (34), Australia (35), Antarctica (36), and South Africa’s Karoo Basin (Fig. 1 and 37–40), the latter providing arguably the most densely sampled and taxonomically scrutinized (41–43) continental record of the PTT. The main extinction has been proposed to occur at the boundary between two biostratigraphic zones with distinctive faunal assemblages, the Daptocephalus and Lystrosaurus declivis assemblage zones (Fig. 1), which marks the traditional placement of the Permian–Triassic geologic boundary [(37) but see ref. 44]. Considerable research has attempted to understand the anatomy of the PTT in South Africa (38, 39, 45–52) and to place it in the context of biodiversity changes across southern Gondwana (53, 54) and globally (29, 31, 32, 44, 47, 55).Open in a separate windowFig. 1.Map of South Africa depicting the distribution of the four tetrapod fossil assemblage zones (Cistecephalus, Daptocephalus, Lystrosaurus declivis, Cynognathus) and our two study sites where fossils were collected in this study (sites A and B). Regional lithostratigraphy and biostratigraphy within the study interval are shown alongside isotope dilution–thermal ionization mass spectrometry dates retrieved by Rubidge et al., Botha et al., and Gastaldo et al. (37, 44, 80). The traditional (dashed red line) and associated PTB hypotheses for the Karoo Basin (37, 44) are also shown. Although traditionally associated with the PTB, the Daptocephalus–Lystrosaurus declivis Assemblage Zone boundary is defined by first appearances of co-occurring tetrapod assemblages, so its position relative to the three PTB hypotheses is unchanged. The Ripplemead member (*) has yet to be formalized by the South African Committee for Stratigraphy.Decades of research have demonstrated the richness of South Africa’s Karoo Basin fossil record, resulting in hundreds of stratigraphically well-documented tetrapod fossils across the PTT (37, 39, 56). This wealth of data has been used qualitatively to identify three extinction phases and an apparent early postextinction recovery phase (39, 45, 51). Furthermore, studies of Karoo community structure and function have elucidated the potential role of the extinction and subsequent recovery in breaking the incumbency of previously dominant clades, including synapsids (11, 57). Nevertheless, understanding patterns of faunal turnover and recovery during the PTT has been limited by the scarcity of quantitative investigations. Previous quantitative studies used coarsely sampled data (i.e., assemblage zone scale, 2 to 3 Ma time intervals) to identify low species richness immediately after the main extinction, potentially associated with multiple “boom and bust” cycles of primary productivity based on δ¹³C variation during the first 5 My of the Triassic (41, 58). However, many details of faunal dynamics in this interval remain unknown. Here, we investigate the dynamics of this major tetrapod extinction at an unprecedented time resolution (on the order of hundreds of thousands of years), using sample-standardized methods to quantify multiple aspects of regional change across the Cistecephalus, Daptocephalus, and Lystrosaurus declivis assemblage zones.     

Integrative analysis reveals unique structural and functional features of the Smc5/6 complex

Structural maintenance of chromosomes (SMC) complexes are critical chromatin modulators. In eukaryotes, the cohesin and condensin SMC complexes organize chromatin, while the Smc5/6 complex directly regulates DNA replication and repair. The molecular basis for the distinct functions of Smc5/6 is poorly understood. Here, we report an integrative structural study of the budding yeast Smc5/6 holo-complex using electron microscopy, cross-linking mass spectrometry, and computational modeling. We show that the Smc5/6 complex possesses several unique features, while sharing some architectural characteristics with other SMC complexes. In contrast to arm-folded structures of cohesin and condensin, Smc5 and Smc6 arm regions do not fold back on themselves. Instead, these long filamentous regions interact with subunits uniquely acquired by the Smc5/6 complex, namely the Nse2 SUMO ligase and the Nse5/Nse6 subcomplex, with the latter also serving as a linchpin connecting distal parts of the complex. Our 3.0-Å resolution cryoelectron microscopy structure of the Nse5/Nse6 core further reveals a clasped-hand topology and a dimeric interface important for cell growth. Finally, we provide evidence that Nse5/Nse6 uses its SUMO-binding motifs to contribute to Nse2-mediated sumoylation. Collectively, our integrative study identifies distinct structural features of the Smc5/6 complex and functional cooperation among its coevolved unique subunits.

Structural maintenance of chromosomes (SMC) complexes regulate genome organization and maintenance in both prokaryotic and eukaryotic cells. Each complex contains a pair of SMC subunits and a set of non-SMC subunits (1). Studies of several SMC proteins reveal that they form tripartite filamentous structures. An SMC subunit folds back on itself at its middle “hinge” region, enabling its N- and C-terminal ATPase domains to associate forming a “head” region, and its two long coiled-coil regions located in between the hinge and the head to pair in an antiparallel manner, forming an “arm” region (SI Appendix, Fig. S1A) (1). The two SMC subunits of each complex form its backbone and can associate with each other at hinge, head, and arm regions (1).Much of the molecular understanding of SMC complexes has come from studies of those acting as DNA organization and separation factors, such as prokaryotic Smc-ScpAB and MukBEF complexes and eukaryotic cohesin and condensin. These complexes can entrap and loop DNA, resulting in DNA tethering and folding (2–4). One emerging feature of these complexes is that their long arm regions bend sharply at so-called “elbow” sites (SI Appendix, Fig. S1A). Elbow bending causes the hinge to contact the head-proximal coiled-coil or head-bound non-SMC proteins, a conformation thought to facilitate DNA loop extrusion (5–8). In these SMCs, the head and hinge regions that associate with other proteins and DNA are conserved, while the arm regions are not and act mainly as connecting elements (9).Differing from cohesin (containing Smc1/3) and condensin (containing Smc2/4), the third eukaryotic SMC complex, containing Smc5 and Smc6, does not appear to affect chromatid intertwining or mitotic chromosome structures (10–12). Rather, the Smc5/6 complex directly regulates DNA replication and recombinational repair (13–15). These unique functions correlate with the acquisition of a special set of six subunits, namely non-SMC elements (Nse)1 to 6. Three Nse subunits, Nse2, Nse5, and Nse6, are not found in any other SMC complexes in either prokaryotes or eukaryotes. Nse2 (also known as Mms21) is a SUMO ligase that promotes the sumoylation of more than a dozen genome maintenance factors (16–19). Nse5 and Nse6 are thought to act distinctly from Nse2 by forming a subcomplex that recruits the Smc5/6 complex to DNA damage sites (13–15, 20–22). The acquisition of the Nse2, Nse5, and Nse6 subunits is one of the most unique features that sets the Smc5/6 complex apart from other SMC complexes.Our understanding of how the Smc5/6 complex gained unique functions among the SMC family of complexes is hindered by the limited structural information of its holo-complex. Studies of subunits and their fragments or subcomplexes have provided insights into potential intersubunit interactions (23–25). However, these data may not reflect structures and interactions within the entire complex. Thus, it is imperative to determine, in the context of the holo-complex, whether Smc5 and Smc6 adopt distinct conformations relative to other SMCs, how they associate with Nse subunits, and what the functional relationships are among the complex-specific Nse2, -5, and -6 subunits. Here, we provide an integrative structural analysis of the Smc5/6 holo-complex isolated from budding yeast that addresses these challenges. We use negative-staining electron microscopy (EM), cross-linking mass spectrometry (CL-MS), single-particle cryo-EM, structural modeling, and functional analyses to identify several unique features of the Smc5/6 complex that distinguish it from the other SMC complexes. We also provide evidence that the coevolved Nse2, -5, and -6 subunits are connected at both structural and functional levels.     

“You” speaks to me: Effects of generic-you in creating resonance between people and ideas

Creating resonance between people and ideas is a central goal of communication. Historically, attempts to understand the factors that promote resonance have focused on altering the content of a message. Here we identify an additional route to evoking resonance that is embedded in the structure of language: the generic use of the word “you” (e.g., “You can’t understand someone until you’ve walked a mile in their shoes”). Using crowd-sourced data from the Amazon Kindle application, we demonstrate that passages that people highlighted—collectively, over a quarter of a million times—were substantially more likely to contain generic-you compared to yoked passages that they did not highlight. We also demonstrate in four experiments (n = 1,900) that ideas expressed with generic-you increased resonance. These findings illustrate how a subtle shift in language establishes a powerful sense of connection between people and ideas.

Consider the feeling evoked by watching a gripping scene in a film, hearing a moving song, or coming across a quotation that seems to be written just for you. Experiencing resonance, a sense of connection, is a pervasive human experience. Prior research examining the processes that promote this experience suggests that altering a message to evoke emotion (1–7), highlighting its applicability to a person’s life (2, 6, 8–10), or appealing to a person’s beliefs (4, 8, 11) can all contribute to an idea’s resonance. Here we examine an additional route to cultivating this experience, which is grounded in a message’s form rather than its content: the use of a linguistic device that frames an idea as applying broadly.The ability to frame an idea as general rather than specific is a universal feature of language (12–15). One frequently used device is the generic usage of the pronoun “you” (15–17). Although “you” is often used to refer to a specific person or persons (e.g., “How did you get to work today?”), in many languages, it can also be used to refer to people in general (e.g., “You avoid rush hour if you can.”). This general use of “you” is comparable to the more formal “one,” but is used much more frequently (18).Research indicates that people often use “you” in this way to generalize from their own experiences. For example, a person reflecting on getting fired from their job might say, “It makes you feel betrayed” (18). Here, we propose that using “you” to refer to people in general has additional social implications, affecting whether an idea evokes resonance.Two features of the general usage of “you” (hereafter, “generic-you”) motivate this hypothesis. First, generic-you conveys that ideas are generalizable. Rather than expressing information that applies to a particular situation (e.g., “Leo broke your heart”), generic-you expresses information that is timeless and applies across contexts (e.g., “Eventually, you recover from heartbreak”; 18–23). Second, generic-you is expressed with the same word ("you") that is used in nongeneric contexts to refer to the addressee. Thus, even when “you” is used generically, the association to its specific meaning may further pull in the addressee, heightening resonance. Together, these features suggest that generic-you should promote the resonance of an idea. We tested this hypothesis across five preregistered studies (24–28), using a combination of crowd-sourced data and online experimental paradigms. Data, code, and materials are publicly available via the Open Science Framework (https://osf.io/6J2ZC/) (29). Study 1 used publicly available data from the Amazon Kindle application. Studies 2–5 were approved by the University of Michigan Health Sciences and Behavioral Sciences institutional review board (IRB) under HUM00172473 and deemed exempt from ongoing IRB review. All participants who participated in studies 2–5 provided informed consent via a checkbox presented through the online survey platform, Qualtrics.     

Distinct architecture and composition of mouse axonemal radial spoke head revealed by cryo-EM

The radial spoke (RS) heads of motile cilia and flagella contact projections of the central pair (CP) apparatus to coordinate motility, but the morphology is distinct for protozoa and metazoa. Here we show the murine RS head is compositionally distinct from that of Chlamydomonas. Our reconstituted murine RS head core complex consists of Rsph1, Rsph3b, Rsph4a, and Rsph9, lacking Rsph6a and Rsph10b, whose orthologs exist in the protozoan RS head. We resolve its cryo-electron microscopy (cryo-EM) structure at 3.2-Å resolution. Our atomic model further reveals a twofold symmetric brake pad-shaped structure, in which Rsph4a and Rsph9 form a compact body extended laterally with two long arms of twisted Rsph1 β-sheets and potentially connected dorsally via Rsph3b to the RS stalk. Furthermore, our modeling suggests that the core complex contacts the periodic CP projections either rigidly through its tooth-shaped Rsph4a regions or elastically through both arms for optimized RS–CP interactions and mechanosignal transduction.

The majority of motile cilia and flagella are composed of nine dynein arm-containing peripheral doublet microtubules (DMTs) surrounding a central pair (CP) of MTs (the “9+2” axoneme). The radial spoke (RS) is a T-shaped protein complex with an orthogonal head pointing toward the CP and a stalk anchored on each A-tubule of the DMTs (1–5). It acts as the mechanochemical transducer between the CP and axonemal dynein arms to regulate flagellar/ciliary motility (6–11). The flagella of Chlamydomonas reinhardtii, a widely used model organism, contain two full-size RSs (RS1 and RS2) in each 96-nm repeat unit of the axoneme. In contrast, motile cilia/flagella of Tetrahymena thermophila and metazoa possess triplet RSs (RS1 to RS3) (2–4, 11). The Chlamydomonas RS is composed of at least 23 subunit proteins (RSP1 to RSP23) (2, 12, 13). Seventeen of them have mammalian homologs (14). Mutations leading to the loss of the entire RS or RS head result in immotile flagella in Chlamydomonas (6–8) but in rotatory ciliary beat in mammals, causing primary ciliary dyskinesia (PCD), a genetic syndrome characterized by recurrent respiratory infections, situs inversus, infertility, and hydrocephalus (4, 15–21).The most striking morphological differences in the RS lie in the RS head, the key structural domain that mediates the mechanosignaling by directly contacting projections of the CP (9–11). The heads of RS1 and RS2 consist of two structurally identical, rotationally symmetric halves that differ largely from that of RS3 (3, 4). Furthermore, their morphologies differ dramatically between protozoa and metazoa. In Chlamydomonas and Tetrahymena, for instance, the heads of RS1 and RS2 are rich in lateral branches that also form a connection between the two heads (2, 4). In contrast, in sea urchin (Strongylocentrotus purpuratus) and human, the heads of RS1 and RS2 resemble a pair of ice skate blades with many fewer interfaces toward the CP (3, 4). Despite the importance of the RS and RS head in cilia/flagella motility, the structural details of the RS and the RS–CP interactions remain poorly understood, especially in mammals.The RS heads have probably been remodeled to comply with both structural and functional alterations of the axoneme during evolution. How the morphological changes occurred, however, remains unclear. The Chlamydomonas RS head is composed of RSP1, -4, -6, -9, and -10 and part (the C terminus) of the stalk component, RSP3. Each of the symmetrical halves of the head contains one copy of these components (2, 10, 22). All the head components have mammalian orthologs (Rsph1, -4a, -6a, -9, -10b, and -3b) (11, 14). In sharp contrast to the markedly reduced surface area of metazoan RS heads, the peptides of human RSPH4A, -6A, and -10B are longer than their Chlamydomonas orthologs by 1.5-, 1.3-, and 4-fold, respectively (11). Only RSPH1 (309 amino acids [aa]) is shorter than RSP1 (814 aa) (11). The lengths of mouse RS head proteins are also similarly changed as their human counterparts (SI Appendix, Fig. S1A). Furthermore, while murine Rsph4a is essential for the head formation of RS1 to RS3 in motile multicilia of the trachea, ependyma, and oviduct (15), Rsph6a is specifically expressed in sperm for their normal flagellar formation (23). RSP4/Rsph4a and RSP6/Rsph6a are paralogs: RSP4 and RSP6 share 48% sequence identity (24), whereas murine Rsph4a is 63% identical to Rsph6a (SI Appendix, Fig. S1B). Sea urchin and Ciona, however, have only one ortholog (11, 25). These results suggest that, unlike the protozoan RS heads, the metazoan ones may not simultaneously contain Rsph4a and Rsph6a. The general shapes of the RS structure in axonemes have been determined by conventional electron microscopy (EM) (26–28) and cryo-electron tomography (cryo-ET) (2–5). Recently, a 15-Å-resolution RS structure of Chlamydomonas was resolved by cryo-EM single-particle analysis (29). The resolutions, however, do not suffice for the delineation of the locations of individual RS subunits.In the present study, by biochemical and structural analyses, we show the murine RS head is both compositionally and morphologically distinct from that of Chlamydomonas. Our study suggests that the RS head has experienced profound remodeling to probably comply with both structural and functional alterations of the axoneme during evolution for coordinated ciliary or flagellar motility.     

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.     

Stage-specific overcompensation,the hydra effect,and the failure to eradicate an invasive predator

As biological invasions continue to increase globally, eradication programs have been undertaken at significant cost, often without consideration of relevant ecological theory. Theoretical fisheries models have shown that harvest can actually increase the equilibrium size of a population, and uncontrolled studies and anecdotal reports have documented population increases in response to invasive species removal (akin to fisheries harvest). Both findings may be driven by high levels of juvenile survival associated with low adult abundance, often referred to as overcompensation. Here we show that in a coastal marine ecosystem, an eradication program resulted in stage-specific overcompensation and a 30-fold, single-year increase in the population of an introduced predator. Data collected concurrently from four adjacent regional bays without eradication efforts showed no similar population increase, indicating a local and not a regional increase. Specifically, the eradication program had inadvertently reduced the control of recruitment by adults via cannibalism, thereby facilitating the population explosion. Mesocosm experiments confirmed that adult cannibalism of recruits was size-dependent and could control recruitment. Genomic data show substantial isolation of this population and implicate internal population dynamics for the increase, rather than recruitment from other locations. More broadly, this controlled experimental demonstration of stage-specific overcompensation in an aquatic system provides an important cautionary message for eradication efforts of species with limited connectivity and similar life histories.

Theoretical population models can produce counterintuitive predictions regarding the consequences of harvest or removal of predatory species. These models show that for simple predator-prey systems, there can be positive population responses to predator mortality resulting from harvest for fisheries or population management, which can create an increased equilibrium level of that predator species (1–5). Among these mortality processes is the “hydra effect,” named after the mythical multi-headed serpent that grew two new heads for each one that was removed (6, 7). This counterintuitive outcome can be driven by a density-dependent process known as overcompensation. The hydra effect typically refers to higher equilibrium or time-averaged densities in response to increased mortality, typically involving consumer populations undergoing population cycles. Population increases in response to mortality can be the result of stage-specific overcompensation, which involves an increase in a specific life history stage or a size class following increased mortality. The first analysis of overcompensatory responses to mortality did not depend on stage specificity and was applied initially to fisheries harvests (1). Subsequent models have included stage specificity and have been applied to a broad range of systems in which species have been harvested for consumption or removed for population control of non-native species (4, 5, 8–15).Theory suggests that overcompensation in response to harvest or removal can occur for a variety of reasons, including 1) reduced competition for resources and increased adult reproduction rates, 2) faster rates of juvenile maturation or greater success in reaching the adult stage, and 3) increased juvenile or adult survival rates (1–7). An increase in reproductive output in response to reduced adult density can be the result of a reduction in resource competition (SI Appendix, Fig. S1).While there is substantial evidence that conditions that could produce density-dependent overcompensation occur frequently, evidence for overcompensation in natural populations is rare. For only a few populations do we have the long-term demographic data collected over a sufficiently long duration and for population densities over a wide enough range to detect this effect. Unfortunately, recent reviews of population increases in response to increased mortality do not include field studies with explicit controls for removals (13–17).There are examples of density-dependent overcompensation from field populations (4, 13–15), as well as a larger number of studies from the laboratory and greenhouse typically involving plant and insect populations (18–22). Among the field examples is a population control program for smallmouth bass in a lake in upstate New York, which paradoxically resulted in greater bass abundance, primarily of juveniles, after 7 y of removal efforts (23, 24). Another field study in the United Kingdom showed that perch populations responded similarly when an unidentified pathogen decimated adults (25). Other programs that attempted to remove invasive fishes, including pikeperch in England (26), brook trout in Idaho (27), and Tilapia in Australia (28), showed similar results. However, although many of these examples involved well-executed studies with substantial field data, none had explicit controls for removal, such as comparable populations without harvest (or disease). Thus, despite the support of current theory in these studies, the contribution of external factors to observed population responses to harvest remains uncertain. To date, we are unaware of any experimental studies with comparable controls in a field population that demonstrates overcompensation in a single species (13–15).     

The feeding system of Tiktaalik roseae: an intermediate between suction feeding and biting

Changes to feeding structures are a fundamental component of the vertebrate transition from water to land. Classically, this event has been characterized as a shift from an aquatic, suction-based mode of prey capture involving cranial kinesis to a biting-based feeding system utilizing a rigid skull capable of capturing prey on land. Here we show that a key intermediate, Tiktaalik roseae, was capable of cranial kinesis despite significant restructuring of the skull to facilitate biting and snapping. Lateral sliding joints between the cheek and dermal skull roof, as well as independent mobility between the hyomandibula and palatoquadrate, enable the suspensorium of T. roseae to expand laterally in a manner similar to modern alligator gars and polypterids. This movement can expand the spiracular and opercular cavities during feeding and respiration, which would direct fluid through the feeding apparatus. Detailed analysis of the sutural morphology of T. roseae suggests that the ability to laterally expand the cheek and palate was maintained during the fish-to-tetrapod transition, implying that limited cranial kinesis was plesiomorphic to the earliest limbed vertebrates. Furthermore, recent kinematic studies of feeding in gars demonstrate that prey capture with lateral snapping can synergistically combine both biting and suction, rather than trading off one for the other. A “gar-like” stage in early tetrapod evolution might have been an important intermediate step in the evolution of terrestrial feeding systems by maintaining suction-generation capabilities while simultaneously elaborating a mechanism for biting-based prey capture.

Although suction feeding is a primary mode of prey capture among aquatic vertebrates (1), it is physically impractical on land due to the lower viscosity of air as compared to water (2–4). Terrestrial-feeding vertebrates must resort to other means, such as biting or tongue capture, to procure food (2). Naturally, researchers seeking to understand shifts in feeding strategies in tetrapodomorph vertebrates during the water-to-land transition have focused primarily on whether feeding systems in fossil forms showed adaptations for either suction or biting (2, 5). Generally, plesiomorphic “fish-like” morphology is interpreted as a means to create suction during the feeding cycle, and derived “tetrapod-like” morphology is interpreted as suggestive of biting (5–8). Suction feeding in fish is typically associated with jointed, kinetic skulls that allow for large volumetric expansion to draw in food (1, 9). In contrast, many lineages of modern tetrapods have consolidated skulls, such as mammals, crocodilians, and amphibians, thought to strengthen the skull for biting (9–12). While there is evidence for kinetic joints in the palate and skull roof of multiple early stem tetrapods (6, 13–16), it is uncertain if they represent plesiomorphic holdovers of limited fish-like cranial kinesis (13, 17, 18) or were independently derived mechanisms to improve biting capabilities on land (17, 19).A central challenge of paleontology has been to understand how, and when, transitions in the feeding system of early terrestrial vertebrates occurred. Late Devonian finned tetrapodomorphs, typified by Eusthenopteron foordi, have expansive, kinetic skulls with open sutures, robust gill covers, large hyomandibulae, tall palatal elements, and a jointed neurocranium all thought to be features that play a role in suction feeding (5, 9, 20). In contrast, the Late Devonian limbed tetrapodomorph Acanthostega gunnari has a flat skull, interdigitating sutures between the bones of the skull roof, absent gill covers, reduced hyomandibulae, horizontal palatal elements, and a consolidated neurocranium that are hypothesized to be derived adaptations for biting (5, 6, 21, 22). Analyses of tetrapodomorph lower jaws have produced equivocal results, noting few differences between presumed aquatic and terrestrial forms (7, 8). These results suggest that either a fish-like suction-based feeding mechanism was maintained well into the Carboniferous (7, 8, 23) or that a biting-based feeding mechanism had evolved in water prior to the origin of terrestrial tetrapods (24).To understand how feeding modes shifted among tetrapodomorphs and assess the origin of novel feeding mechanisms in the tetrapod lineage, we use high-resolution microcomputed tomography (µCT) to analyze multiple specimens of a well-preserved elpistostegalian-grade tetrapodomorph, Tiktaalik roseae, and compare the anatomy resolved from those µCT scans to features of other extinct tetrapodomorphs and extant fishes with analogous features. T. roseae is a tetrapodomorph from the Upper Devonian (Frasnian, ∼375 Mya) of Arctic Canada (Ellesmere Island, Nunavut Territory) (25, 26) that, according to most-recent phylogenies (27, 28), is representative of the outgroup of limbed vertebrates (tetrapods). Although plesiomorphic in lower jaw morphology (7, 8, 29), elpistostegalian-grade tetrapodomorphs (a group also including Panderichthys rhombolepis and Elpistostege watsoni) represent a period of rapid cranial evolution that could nevertheless suggest shifts in feeding strategies (5, 26, 30, 31). µCT was performed on four specimens of T. roseae from the Nunavut Fossil Vertebrate Collection (NUFV) consisting of three-dimensionally (3D) preserved palatal material in articulation with the cranium, as well as individual bones from multiple disarticulated specimens (SI Appendix, Table S1). Sutural cross-sections were compared with homologous sutures reported for E. foordi (5, 20) and A. gunnari (5, 21). Cranial joints were compared with possible modern analogs, alligator gar (Atractosteus spatula) (32–34) and ornate bichir (Polypterus ornatipinnis) (5, 32, 35), which were selected on the basis of convergent feeding morphologies with T. roseae. Finally, joints between the palate, hyomandibula, and braincase were modeled with the same kinematic range of motion as reported in A. spatula for comparison purposes (34).     

Early Holocene greening of the Sahara requires Mediterranean winter rainfall

The greening of the Sahara, associated with the African Humid Period (AHP) between ca. 14,500 and 5,000 y ago, is arguably the largest climate-induced environmental change in the Holocene; it is usually explained by the strengthening and northward expansion of the African monsoon in response to orbital forcing. However, the strengthened monsoon in Early to Middle Holocene climate model simulations cannot sustain vegetation in the Sahara or account for the increased humidity in the Mediterranean region. Here, we present an 18,500-y pollen and leaf-wax δD record from Lake Tislit (32° N) in Morocco, which provides quantitative reconstruction of winter and summer precipitation in northern Africa. The record from Lake Tislit shows that the northern Sahara and the Mediterranean region were wetter in the AHP because of increased winter precipitation and were not influenced by the monsoon. The increased seasonal contrast of insolation led to an intensification and southward shift of the Mediterranean winter precipitation system in addition to the intensified summer monsoon. Therefore, a winter rainfall zone must have met and possibly overlapped the monsoonal zone in the Sahara. Using a mechanistic vegetation model in Early Holocene conditions, we show that this seasonal distribution of rainfall is more efficient than the increased monsoon alone in generating a green Sahara vegetation cover, in agreement with observed vegetation. This conceptual framework should be taken into consideration in Earth system paleoclimate simulations used to explore the mechanisms of African climatic and environmental sensitivity.

Moisture availability in northern Africa, from the Sahel to the Mediterranean coast, is a critical issue for both ecosystems and human societies yet represents one of the largest uncertainties in future climate simulations (1, 2). The humid time span in the African Sahel and Sahara, known as the African humid period (AHP) (3–13), occurred in northern Africa after the last glacial period (4, 10, 11, 14–16) and lasted from ca. 14.5 to 5 ky ago (ka), with an optimum between 11 and 6 ka (11, 16). This prominent climatic event allowed semiarid, subtropical, and tropical plant species to spread outside their modern ranges (14) into the Sahara and human populations to inhabit what is known as the green Sahara (5, 17).The green Sahara is an example of extreme environmental change, which highlights the region’s extraordinary sensitivity and the need to better understand its hydroclimatic variability. Current explanations for the greening of the Sahara point to the Earth’s orbital changes during the Early Holocene, leading to increased boreal summer (JJA) insolation, which drove the intensification and northward expansion of the JJA monsoon over northern Africa (15, 18), aided by strong positive feedbacks from the land surface (19–22). Reproducing the green Sahara has posed a lasting challenge for climate modelers. The influence of the African monsoon extends only to ∼24° N (with or without interactive vegetation) in most Middle Holocene simulations, which is insufficient to sustain a vegetated Sahara. Models that integrate vegetation, dust, and soil feedbacks push the monsoon influence further north but still have discrepancies with proxy data (18, 23, 24).When all surface feedbacks are prescribed, simulated precipitation in the northern Sahara is still too low compared to paleoclimatic evidence for substantially increased moisture at 31° N (11, 13) or too high in the 15 to 20° N range (20), creating incompatibility with prescribed vegetation (22). Additional sources of moisture (25, 26) may have contributed to an AHP that extended toward the Mediterranean borderlands through different mechanisms. However, identifying the moisture sources over North Africa during the AHP requires paleoclimate records of both winter (DJF) and JJA precipitation.In the High Atlas Mountains, we collected an 8.5-m sediment core from Lake Tislit (ca. 32° N). The lake traps pollen grains from the surrounding landscape and, as a closed lake, is highly sensitive to hydroclimate fluctuations. It is ideally located for capturing the climatic variability of the Mediterranean and northwestern Sahara (Fig. 1). The Tislit sequence yielded unique hydrological data from leaf-wax stable isotopes and ostracod stable oxygen isotopes (δ¹⁸O), as well as a quantified time series of seasonal rainfall from the fossil pollen assemblages. Based on the findings from the Tislit record, we propose a precipitation regime for the AHP, including both Mediterranean DJF precipitation and monsoon JJA precipitation increases. Using a dynamic vegetation model for a conceptual experiment with 9 ka boundary conditions, we evaluate how a change in the seasonal distribution of precipitation over the Sahara can affect its revegetation.Open in a separate windowFig. 1.Maps showing the location of Lake Tislit, core GC27 (11), and Lake Yoa (6), along with the schematic position of the Inter Tropical Convergence Zone, with modern mean JJA (A) and DJF (B) rainfall (56). Map C shows the correlation coefficients (r) between Tislit and northern Morocco for DJF precipitation variability over the 1901 to 2010 time period (using the 20th century reanalysis of National Oceanic and Atmospheric Administration; https://psl.noaa.gov/data/20thC_Rean/). The limit of statistical significance (0.05 level) is shown by the dashed black line. Gray contours indicate annual precipitation isohyets (millimeter/year).     

Capillary equilibrium of bubbles in porous media

In geologic, biologic, and engineering porous media, bubbles (or droplets, ganglia) emerge in the aftermath of flow, phase change, or chemical reactions, where capillary equilibrium of bubbles significantly impacts the hydraulic, transport, and reactive processes. There has previously been great progress in general understanding of capillarity in porous media, but specific investigation into bubbles is lacking. Here, we propose a conceptual model of a bubble’s capillary equilibrium associated with free energy inside a porous medium. We quantify the multistability and hysteretic behaviors of a bubble induced by multiple state variables and study the impacts of pore geometry and wettability. Surprisingly, our model provides a compact explanation of counterintuitive observations that bubble populations within porous media can be thermodynamically stable despite their large specific area by analyzing the relationship between free energy and bubble volume. This work provides a perspective for understanding dispersed fluids in porous media that is relevant to CO₂ sequestration, petroleum recovery, and fuel cells, among other applications.

Bubbles are generated, trapped, and mobilized within porous media as a consequence of incomplete fluid–fluid displacements (1, 2), phase changes (3, 4), chemical and biochemical reactions (5, 6), or injection of emulsified fluids and foams (7, 8). Compared to continuously connected phases, the behavior of dispersed bubbles, or ganglia, are far less understood. In particular, the thermodynamic stability of bubbles, despite their large specific surface area, remains a puzzle. The difficulty comes from the fact that each bubble can attain a volume (V), topology, and capillary pressure (P_c) that is distinct from other bubbles in the medium (9). The variability poses challenges to understanding the transport and trapping mechanisms of bubbles in geologic CO₂ sequestration (10, 11), hydrocarbon recovery (12, 13), fuel cell water management (14, 15), and vadose zone oxygen supply (16, 17).The dominant factor controlling a bubble’s behavior in a porous medium is capillarity, which is typically much larger than either viscous, gravitational, or inertial forces (18, 19). Capillary pressure, P_c, allows a closure relationship for two-phase Darcy Eqs. (20–22) and influences thermodynamic properties like phase partition (23). Capillary pressure is derived from the Young–Laplace equation P_c = γκ, where γ is the interfacial tension and κ is the surface curvature. In an open space without obstacles, a bubble spontaneously evolves into a sphere to minimize its total interfacial energy. Thus, P_c is a continuous and monotonically decreasing function of V (Fig. 1A). However, in a porous medium, bubble’s P_c–V relation is more complicated due to the geometric confinement imposed by the porous structure and topological evolution (24). A bubble can no longer remain spherical as it grows in size but must conform to the geometry of the pore(s) it occupies. Therefore, a bubble’s P_c is a function of not only its volume and interfacial tension but also its topology as dictated by the confining porous medium, as confirmed by recent laboratory experiments and numerical simulations (25–29). The mere presence of confinement therefore engenders a host of phenomena that would otherwise be absent, such as capillary trapping (30, 31), anticoarsening of bubble populations (32, 33), and complex ganglion dynamics (11, 18). Furthermore, theoretical studies in mathematical topology (28, 34, 35) prove that immiscible fluids can be fully characterized by d+1 Minkowski functionals, where d is the problem dimension. Such characterizations remove the path-dependent (or hysteretic) behavior common to these systems (34, 35).Open in a separate windowFig. 1.(A) Spherical bubbles inside a bulk fluid. (B) Micromodel observations show that bubbles are nonspherical in porous media and may occupy multiple pores. This image is from SI Appendix, Movie S1. (C) A 2D porous medium comprised of an ordered array of identical circular grains. A bubble occupying multiple pores including a zoom-in to a portion of it. (D) Illustration of the full state. (E) Illustration of the critical state. (F) Decomposition of a bubble into four distinct parts: minor arc menisci shown by dark blue cap-shaped regions, throats shown by light blue diamond-shaped regions, inner bulk bodies shown by red star-shaped regions, and major arc menisci shown by dark green cap-shaped regions.Recent developments in microfluidics and micro computed tomography imaging allow detailed pore-scale visualizations of fluids inside porous media, including the morphology of bubbles and ganglia (25, 36–39). Garing et al. (25) experimentally measured the equilibrium capillary pressure of trapped air bubbles inside sandstone and bead-pack samples. They found that, unlike bubbles within a bulk fluid, the P_c of trapped bubbles shows no clear dependence on V and seems to fall within a bounded interval, except for vanishingly small V. Xu et al. (40) proposed an empirical correlation for the P_c trapped bubbles based on microfluidic observations. In this correlation, as V increases, P_c decreases until a minimum is reached and then increases linearly. In the first stage, the bubble is unconfined, whereas in the second, it is reshaped by the surrounding solid walls. The proposed correlation, however, is only valid for bubbles in a single pore and not bubbles that span multiple pores. The latter seems to be rather common in nature as evidenced by recent direct observations (Fig. 1B) (2, 25).Here, we propose a simple conceptual model to describe the equilibrium states of a bubble with arbitrary size trapped inside a porous medium. The model accounts for the bubble’s morphology, the geometry of the solid matrix, and the wettability between the two. We derive all metastable configurations of the bubble analytically and highlight the thermodynamic states the bubble assumes when it is static, growing, or shrinking. We also show that the relationship between surface free energy (F) and volume (V) of large bubbles is approximately linear, which explains the previously counterintuitive observation that such bubbles are thermodynamically stable despite having large surface areas. Our work provides a step toward understanding the capillary state, stability, and evolution of dispersed immiscible fluids in porous media.     

High-resolution multicontrast tomography with an X-ray microarray anode–structured target source

Multicontrast X-ray imaging with high resolution and sensitivity using Talbot–Lau interferometry (TLI) offers unique imaging capabilities that are important to a wide range of applications, including the study of morphological features with different physical properties in biological specimens. The conventional X-ray TLI approach relies on an absorption grating to create an array of micrometer-sized X-ray sources, posing numerous limitations, including technical challenges associated with grating fabrication for high-energy operations. We overcome these limitations by developing a TLI system with a microarray anode–structured target (MAAST) source. The MAAST features an array of precisely controlled microstructured metal inserts embedded in a diamond substrate. Using this TLI system, tomography of a Drum fish tooth with high resolution and tri-contrast (absorption, phase, and scattering) reveals useful complementary structural information that is inaccessible otherwise. The results highlight the exceptional capability of high-resolution multicontrast X-ray tomography empowered by the MAAST-based TLI method in biomedical applications.

Adding phase and scattering/darkfield contrast to the conventional absorption contrast in X-ray microscopy is a rapidly expanding research field because it offers tremendous advantages in a wide range of applications. The different contrast mechanisms are highly complementary, as they feature different sample–beam interactions that fingerprint different material properties. For example, the real and imaginary parts of the refractive index exhibit very significant differences in their absolute values (SI Appendix, Fig. S1) and represent the phase shift and attenuation of the X-ray, respectively (1–7). This has major implications for biomedical imaging, e.g., mammography (6, 8, 9), lung pathology (10–13), and industrial applications such as the structural investigation of carbon-reinforced polymer composites (14, 15). With this motivation, a variety of X-ray phase-contrast imaging (XPCI) techniques have been developed (2, 5–7, 9, 16), and there is a strong emphasis on achieving the phase-contrast efficiently and quantitatively (17–20). Among all these methods, grating-based XPCI (GXPCI), especially the Talbot–Lau interferometry (TLI) (3), is a leading contender for bringing XPCI into widespread adoption. Its unique advantages include 1) the compatibility with conventional, low-brilliance laboratory X-ray sources (3), 2) high sensitivity at high X-ray energy (20), and 3) desirable spatial resolution down to the micrometer level (21). Furthermore, it simultaneously provides three different contrast mechanisms: attenuation, refraction (differential phase-shift), and scattering (dark-field) in a single GXPCI dataset. The multicontrast modalities of TLI can offer valuable and complementary information for better discrimination of different structural components with different physical properties (4, 19). The GXPCI-enabled scattering contrast corresponds to the ultra-small-angle scattering strength of a material and offers excellent sensitivity to the morphological features that are much finer than the nominal spatial resolution (22–24). The phase-contrast component, on the other hand, quantitatively reconstructs the spatial distribution of the electron density, which is a fundamental material property that has different implications in different applications (20, 25). For example, the electron density of a battery cathode material fingerprints its state of charge and evolves as the battery is charged and discharged (26). Therefore, the three-dimensional (3D) electron density map of a battery electrode can be used to quantify the reaction heterogeneity, which is critical to the battery performance. The extraordinary potential of TLI tomography is reflected by the broad interest in applying this method to biological and medical imaging (5, 6, 8, 9, 12, 13), nondestructive testing (14, 27), materials science (19), and security screening (28). There are, however, key limitations of this technique that have yet to be addressed.A main advantage of TLI is its compatibility with a high-power laboratory X-ray source, which could largely improve the throughput of the experiment (3). In a conventional TLI setup, an absorption source grating (G0) is utilized to formulate a structured illumination pattern (Fig. 1A). G0 is inserted near the exit window of the X-ray tube for improving the spatial coherence and for reinforcing a geometrical constraint that matches the configuration of the downstream optics (SI Appendix, Fig. S2). The drawback of using the source grating G0 is that more than half of the X-ray’s source flux is wasted, significantly jeopardizing the efficiency of the imaging system. To increase the imaging sensitivity, one needs to use G0 gratings with fine periods as small as a few micrometers (29). Meanwhile, to ensure a sufficient X-ray transmission contrast, the thickness of the G0 grating lines has to reach several tens of micrometers, manifesting a desire for a high aspect ratio (AR) that is technically very challenging (30). To overcome this issue, Thüring et al. tilted the gratings with respect to the beam to effectively increase the AR. This approach, however, significantly reduces the useful field of view (FOV), compromising the practicality of this technique (30). Additionally, a G0 with large AR collimates the X-ray beam, which is another reason for the diminished FOV (∝AR⁻¹) (SI Appendix, Fig. S3) (21). We acknowledge that curved and tiled gratings can potentially be fabricated to alleviate this issue; however, they are associated with great challenges in microfabrication, particularly when targeting high a AR and small radius (21, 31). Several approaches have been introduced to circumvent the use of G0 and its associated limitations. One demonstrated approach involves fabricating grooves on an anode target for structured illumination. However, this method has a rather limited FOV because the spatial coherence property changes as a function of the target position (32). Morimoto et al. developed a TLI with a transmission grating by using a structured X-ray source. They demonstrated two-dimensional imaging results with a rather low spatial resolution and at a low working energy (20 kV) (33, 34). Despite the tremendous research efforts devoted to this field, the aforementioned challenges have hindered the broad adoption of TLI as a standard tool for high-resolution structural investigations with high-energy X-rays.Open in a separate windowFig. 1.Schematic comparison of the conventional TLI setup and our approach with a MAAST source is shown in A. SEM images of the MAAST pattern with etched grooves (B) and with W-MMIs embedded in the polycrystalline diamond substrate (C).To tackle these challenges, we developed a TLI system with a microarray anode–structured target (MAAST) X-ray source. We overcome the limitations of the conventional configuration with an extended source and a G0 grating by designing and incorporating the illumination pattern into the MAAST source as a built-in feature. Our approach significantly improves the efficiency in the use of source X-rays for imaging at high resolution and with high sensitivity. We further present correlative tri-contrast tomography on a Drum fish tooth specimen and demonstrate a clear separation of biological features with different physical properties. Our results highlight the exceptional imaging capability empowered by the MAAST-based TLI method. Our approach also features a compact and robust setup that can potentially be made broadly available to academia research and industrial applications.