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Effects of Wind Shear and Aerosol Conditions on the Organization of Precipitating Marine Stratocumulus Clouds
Here this study examines how wind shear affects precipitating marine stratocumulus clouds under different cloud droplet number concentrations (N d ). We performed a series of large eddy simulations (LES) of nocturnal marine stratocumulus clouds using Cloud Model 1 (CM1). The simulations show that N d is the dominant factor for cloud cellular organization in this cloud regime rather than wind shear. Low N d characterizes the open cellular structure with a high in-cloud liquid water path (LWP). When wind shear is increased, the cloud fraction tends to decrease along with LWP, suggesting the cloud top region is significantly influenced by the entrainment and mixing of dry air from the free troposphere. We also examine cold pools in open and closed cellular clouds. Open-cell clouds produce larger and deeper cold pools compared to closed-cell clouds. Interestingly, cold pools can exist without surface precipitation and are produced by evaporation of light precipitation (drizzle) below the cloud base with weak downdrafts. The evaporation of raindrops and drizzle play an important role in initiating new convection, particularly where colliding outflows occur downstream of the cloud. This secondary convection contributes to the development and maintenance of the cloud cellular organization and formation.
Simulating Mixed‐Phase Open Cellular Clouds Observed During COMBLE: Evaluation of Parameterized Turbulence Closure
Marine cold-air outbreaks, or CAOs, are airmass transformations whereby relatively cold boundary layer (BL) air is transported over relatively warm water. To more deeply understand BL and mixed-phase cloud properties during CAO conditions, the Cold-Air Outbreaks in the Marine Boundary Layer Experiment (COMBLE) took place from late 2019 into early 2020. During COMBLE, the U.S. Department of Energy's first Atmospheric Radiation Measurement Mobile Facility (AMF1) was deployed to Andenes, Norway, far downstream (~1,000 km) from the Arctic pack ice. This study examines the two most intense CAOs sampled at the AMF1 site. The observed BL structures are open cellular with high (~3–5 km) and cold (–30 to –50 °C) cloud tops, and they often have pockets of high liquid water paths (LWPs; up to ~1,000 g m –2 ) associated with strong updrafts and enhanced turbulence. We use a high-resolution mesoscale model to explore how well four turbulence closure methods represent open cellular clouds. After applying a radar simulator to model outputs for direct evaluation, cloud top properties agree well with AMF1 observations (within ~10%), but radar reflectivity and LWP agreement is more variable. Results suggest that the turbulent Prandtl number may play an important role for the simulated BL and cloud properties. All simulations produce enhanced precipitation rates that are well-correlated with a cloud transition. Finally, the eddy-diffusivity/mass-flux approach produces the deepest cloud layer and therefore the largest and most coherent cellular structures. Furthermore, we recommend the use of a non-local turbulence closure approach to better capture turbulent processes in intense CAOs.
Mapping 3D grain and precipitate structure during in situ mechanical testing of open-cell metal foam using micro-computed tomography and high-energy X-ray diffraction microscopy
Open-cell metal foams are ultra-low-density cellular metals with complex hierarchical structures that span bulk, cell, ligament, and sub-ligament scales and give rise to desirable properties such as high strength-to-weight ratio and excellent energy absorption. Although literature suggests that intrinsic material structures at sub-ligament length scales (e.g., grains and precipitates) play an important role in mechanical behavior of open-cell metal foams, there are very few experimental measurements of such structures in three dimensions and for meaningful volumes of foam. This study seeks to map and track the three-dimensional (3D) grain and precipitate structures of an intact volume of open-cell aluminum foam by advancing microstructural characterization techniques that leverage X-ray micro-computed tomography (μCT) and far-field high-energy X-ray diffraction microscopy (FF-HEDM). A 6%-relative-density aluminum foam sample was mechanically tested in compression while μCT and FF-HEDM measurements were collected at interrupted loading states at beamline 1-ID of the Advanced Photon Source. Further, a new scanning strategy and reconstruction algorithm were established to enable characterization of a foam volume with diameter approximately four times wider than the nominal width of the X-ray beam. The result is a set of maps that detail both the 3D grain and precipitate structures throughout the foam volume at successive strain steps. A novel grain tracking procedure was developed to track individual grains within the foam volume by accounting for the large rigid-body motions that individual ligaments can undergo during mechanical loading. The ability to track grains and precipitate structures in three dimensions throughout large bulk deformation of ultra-low-density polycrystalline materials enables new possibilities for validating numerical models and investigating local failure mechanisms. Furthermore, the methods and procedures developed in this study could be applied to other ultra-low-density structures, such as additively manufactured lattices.
Open cells exhibit weaker entrainment of free-tropospheric biomass burning aerosol into the south-east Atlantic boundary layer
This work presents synergistic satellite, airborne and surface-based observations of a pocket of open cells (POC) in the remote south-east Atlantic. The observations were obtained over and upwind of Ascension Island during the CLouds and Aerosol Radiative Impacts and Forcing (CLARIFY) and the Layered Smoke Interacting with Clouds (LASIC) field experiments. A novel aspect of this case study is that an extensive free-tropospheric biomass burning aerosol plume that had been transported from the African continent was observed to be in contact with the boundary layer inversion over the POC and the surrounding closed cellular cloud regime. The in situ measurements show marked contrasts in the boundary layer thermodynamic structure, cloud properties, precipitation and aerosol conditions between the open cells and surrounding overcast cloud field. The data demonstrate that the overlying biomass burning aerosol was mixing down into the boundary layer in the stratocumulus cloud downwind of the POC, with elevated carbon monoxide, black carbon mass loadings and accumulation-mode aerosol concentrations measured beneath the trade-wind inversion. The stratocumulus cloud in this region was moderately polluted and exhibited very little precipitation falling below cloud base. A rapid transition to actively precipitating cumulus clouds and detrained stratiform remnants in the form of thin quiescent veil clouds was observed across the boundary into and deep within the POC. The subcloud layer in the POC was much cleaner than that in the stratocumulus region. The clouds in the POC formed within an ultra-clean layer (accumulation-mode aerosol concentrations of approximately a few cm -3 ) in the upper region of the boundary layer, which was likely to have been formed via efficient collision–coalescence and sedimentation processes. Enhanced Aitken-mode aerosol concentrations were also observed intermittently in this ultra-clean layer, suggesting that new particle formation was taking place. Across the boundary layer inversion and immediately above the ultra-clean layer, accumulation-mode aerosol concentrations were ~1000 cm -3 . Importantly, the air mass in the POC showed no evidence of elevated carbon monoxide over and above typical background conditions at this location and time of year. As carbon monoxide is a good tracer for biomass burning aerosol that is not readily removed by cloud processing and precipitation, it demonstrates that the open cellular convection in the POC is not able to entrain large quantities of the free-tropospheric aerosol that was sitting directly on top of the boundary layer inversion. This suggests that the structure of the mesoscale cellular convection may play an important role in regulating the transport of aerosol from the free troposphere down into the marine boundary layer. We then develop a climatology of open cellular cloud conditions in the south-east Atlantic from 19 years of September Moderate Resolution Imaging Spectroradiometer (MODIS) Terra imagery. This shows that the maxima in open cell frequency (> 0.25) occurs far offshore and in a region where subsiding biomass burning aerosol plumes may often come into contact with the underlying boundary layer cloud. If the results from the observational case study applied more broadly, then the apparent low susceptibility of open cells to free-tropospheric intrusions of additional cloud condensation nuclei could have some important consequences for aerosol–cloud interactions in the region.
Molecular determinants of pH sensing in the proton-activated chloride channel
In response to acidic pH, the widely expressed proton-activated chloride (PAC) channel opens and conducts anions across cellular membranes. By doing so, PAC plays an important role in both cellular physiology (endosome acidification) and diseases associated with tissue acidosis (acid-induced cell death). Despite the available structural information, how proton binding in the extracellular domain (ECD) leads to PAC channel opening remains largely unknown. Here, through comprehensive mutagenesis and electrophysiological studies, we identified several critical titratable residues, including two histidine residues (H130 and H131) and an aspartic acid residue (D269) at the distal end of the ECD, together with the previously characterized H98 at the transmembrane domain–ECD interface, as potential pH sensors for human PAC. Mutations of these residues resulted in significant changes in pH sensitivity. Some combined mutants also exhibited large basal PAC channel activities at neutral pH. By combining molecular dynamics simulations with structural and functional analysis, we further found that the β12 strand at the intersubunit interface and the associated “joint region” connecting the upper and lower ECDs allosterically regulate the proton-dependent PAC activation. Our studies suggest a distinct pH-sensing and gating mechanism of this new family of ion channels sensitive to acidic environment.
Contrasting characteristics of open- and closed-cellular stratocumulus cloud in the eastern North Atlantic
Abstract. Extensive regions of marine boundary layer cloud impact the radiative balance through their significant shortwave albedo while having little impact on outgoing longwave radiation. Despite this importance, these cloud systems remain poorly represented in large-scale models due to difficulty in representing the processes that drive their life cycle and coverage. In particular, the mesoscale organization and cellular structure of marine boundary clouds have important implications for the subsequent cloud feedbacks. In this study, we use long-term (2013–2018) observations from the Atmospheric Radiation Measurement (ARM) Facility's Eastern North Atlantic (ENA) site on Graciosa Island, Azores, Portugal, to identify cloud cases with open- or closed-cellular organization. More than 500 h of each organization type are identified. The ARM observations are combined with reanalysis and satellite products to quantify the cloud, precipitation, aerosol, thermodynamic, and large-scale synoptic characteristics associated with these cloud types. Our analysis shows that both cloud organization populations occur during similar sea surface temperature conditions, but the open-cell cases are distinguished by stronger cold-air advection and large-scale subsidence compared to the closed-cell cases, consistent with their formation during cold-air outbreaks. We also find that the open-cell cases were associated with deeper boundary layers, stronger low-level winds, and higher rain rates compared to their closed-cell counterparts. Finally, raindrops with diameters larger than 1 mm were routinely recorded at the surface during both populations, with a higher number of large drops during the open-cellular cases. The similarities and differences noted herein provide important insights into the environmental and cloud characteristics during varying marine boundary layer cloud mesoscale organization and will be useful for the evaluation of model simulations for ENA marine clouds.
Prediction of α $IIb$ $β$ 3 integrin structures along its minimum free energy activation pathway
The adhesion protein integrin is a transmembrane heterodimer that plays a pivotal role in cellular processes such as cell signaling and cell migration. To execute its function, integrin undergoes extensive conformational changes from a bent-closed to an extended-open state. Resolving the structures across these changes remains a challenge with both experimental and computational methods, but it is crucial for understanding the activation mechanism of integrin. We address this challenge for the platelet integrin α IIb β 3 by employing finite temperature string method with structures of the images along the initial guess path generated by a multiscale data-driven framework. The full-length all-atom structures along the resulting minimum free energy path between the inactive bent-closed and active extended-open states of α IIb β 3 integrin are consistent with a variety of experimentally resolved structures. Changes in these predicted structures along the path show that the extension and separation of the α and β subunits from the bent-closed to the extended-open state require correlated movements between the subdomain pairs in α IIb β 3 . Furthermore, these results provide new insights into integrin activation mechanism, and the predicted structures have potential applications in guiding the design of integrin-targeting therapeutics.
The remarkable inefficiency of stratocumulus
Marine stratocumulus clouds play a central role in Earth's climate system by reflecting incoming solar radiation and exerting a strong cooling effect. Their organization into open and closed mesoscale cellular morphologies can be thought of as an example of bistable dynamics driven by aerosol–cloud interactions and mesoscale processes. From the perspective of non-equilibrium thermodynamics, these structures are an example of a far-from-equilibrium open system that continuously produces and exports entropy. While entropy production has been studied in idealized deep convective systems, it has not yet been quantified for shallow clouds. Here, we compute and decompose the internal entropy production of open- and closed-cell stratocumulus using an ensemble of large-eddy simulations. We show that the overall entropy production of stratocumulus is low, reflecting the limited vertical extent and corresponding reduced ability to utilize the energy fluxes at the system's boundaries. Moist processes dominate the overall irreversibility, which, combined with their low entropy production, leads to a mechanical efficiency about an order of magnitude smaller than in deep convective systems. Although the dominant irreversible processes differ between open- and closed-cell regimes, the distributions of total entropy production largely overlap across the ensemble, limiting the ability to distinguish the dynamics of individual cases based solely on total entropy production.
SHP2 genetic variants in NSML-associated RASopathies disrupt the PZR–IRX transcription factor signaling axis
Noonan syndrome with multiple lentigines (NSML) is a rare autosomal dominant disorder caused by mutations inPTPN11(protein tyrosine phosphatase nonreceptor type 11) which encodes for the protein tyrosine phosphatase, SHP2. Approximately 85% of NSML patients develop hypertrophic cardiomyopathy (HCM). Here, we show that SHP2 is recruited to tyrosyl phosphorylated protein-zero related (PZR) in NSML mice. This recruitment is required for the Iroquois homeobox (IRX) transcription factors 3 and 5 to suppress BMP10 which negatively regulates postnatal cardiac growth. The protein expression of IRX3 and IRX5 was elevated in hypertrophied NSML hearts. IRX3 and IRX5 upregulation was rescued in NSML mice harboring a knock-in mutation of PZR that fails to become tyrosyl phosphorylated and recruit SHP2. NSML mice treated with low-dose dasatinib also exhibited normalized IRX3 and IRX5 expression levels. Consistent with this, BMP10 expression levels were reduced in NSML mice and rescued in PZR tyrosyl phosphorylation-deficient and low-dose dasatinib-treated NSML mice. A crystal structure of the tandem SH2 domains of SHP2 bound to tyrosyl phosphorylated PZR reveals that recruitment constrains the open SHP2 conformation to facilitate cellular-Src (c-Src) binding. Disruption of c-Src binding to SHP2 abolished IRX activation and failure to suppress BMP10. Hence, NSML-associated SHP2 genetic variants disrupt IRX transcription factor signaling to BMP10, implicating this axis as a target for RASopathy-associated HCM.
Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion
Bacterial biofilms are complex cell communities within a self-produced extracellular matrix, crucial in various fields but challenging to analyze in 3D. We developed a "biofilm-in-capillary" growth method compatible with full-rotation soft X-ray tomography, enabling high-resolution 3D imaging of bacterial cells and their matrix during biofilm formation. This approach offers 50 nm isotropic spatial resolution, rapid imaging, and quantitative native analysis of biofilm structure. Using Bacillus subtilis biofilms, we detected coherent alignment and chaining of wild-type cells towards the oxygen-rich capillary tip. In contrast, the ΔtasA genetic knock-out showed a loss of cellular orientation and changes in the extracellular matrix. Adding TasA protein to the ΔtasA strain restored matrix density and led to cell assembly compaction, but without the chaining observed in wild-type biofilms. This scalable and transferable approach opens new avenues for examining biofilm structure and function across various species, including mixed biofilms, and response to genetic and environmental factors.
Vertical Structure of Clouds and Precipitation During Arctic Cold–Air Outbreaks and Warm–Air Intrusions: Observations From COMBLE
The Arctic is marked by deep intrusions of warm, moist air, alternating with outbreaks of cold air down to lower latitudes. The typical vertical structure of clouds and precipitation during these two synoptic weather extremes is examined at a coastal site at 69°N in Norway. The Norwegian Sea is a corridor for warm-air intrusions (WAIs) and frequently witnesses cold-air outbreaks (CAOs). This study uses data from profiling radar, lidar, and microwave radiometer, radiosondes and other probes that were collected during the CAOs in the Marine Boundary Layer Experiment (COMBLE) between 1 December 2019 and 31 May 2020. Marine CAOs are defined in terms of thermal instability relative to the sea surface temperature, and WAIs in terms of equivalent potential temperature stratification between the surface and 850 hPa. Cloud structures in CAOs are convective, driven by strong surface heat fluxes over a long fetch of open water, with cloud tops rarely exceeding 6 km above sea level. The mostly open-cellular convection produces intermittent moderately-heavy precipitation at the observational site, notwithstanding the low precipitable water vapor (PWV). In contrast, WAIs are marked by high values of PWV and integrated vapor transport. Here, WAI clouds are synoptically driven, stratiform, with cloud tops often exceeding 5 km, sometimes layered, and generally producing persistent precipitation that can be heavier than in CAOs.
Characterizing Mesoscale Cellular Convection in Marine Cold Air Outbreaks With a Machine Learning Approach
Abstract During marine cold‐air outbreaks (MCAOs), when cold polar air moves over warmer ocean, a well‐recognized cloud pattern develops, with open or closed mesoscale cellular convection (MCC) at larger fetch over open water. The Cold‐Air Outbreaks in the Marine Boundary Layer Experiment provided a comprehensive set of ground‐based in situ and remote sensing observations of MCAOs at a coastal location in northern Norway. MCAO periods that unambiguously exhibit open or closed MCC are determined. Individual cells observed with a profiling Ka‐band radar are identified using a watershed segmentation method. Using self‐organizing maps (SOMs), these cells are then objectively classified based on the variability in their vertical structure. The SOM nodes contain some information about the location of the cell transect relative to the center of the MCC. This adds classification noise, requiring numerous cell transects to isolate cell dynamical information. The SOM‐based classification shows that comparatively intense convection occurs only in open MCC. This convection undergoes an apparent lifecycle. Developing cells are associated with stronger updrafts, large spectrum width, larger amounts of liquid water, lower surface precipitation rates, and lower cloud tops than mature and weakening cells. The weakening of these cells is associated with the development of precipitation‐induced cold pools. The SOM classification also reveals less intense convection, with a similar lifecycle. More stratiform vertical cloud structures with weak vertical motions are common during closed MCC periods and are separated into precipitating and non‐precipitating stratiform cores. Convection is observed only occasionally in the closed MCC environment.
Transforming our understanding of chloroplast-associated genes through comprehensive characterization of protein localizations and protein-protein interactions
Bioenergy crops are a renewable source of fuels and are a critical base for building a carbon-neutral economy. Rational engineering of bioenergy crops has the potential to enhance the yields. However, our ability to engineer plants is limited because the functions of most genes remain unknown. Systematic characterization of gene function in plants thus has the potential to greatly accelerate bioenergy research. Here, we focus on the chloroplast, an underexplored energy-producing organelle that is a hallmark of plants. The chloroplast is one of the promising targets of biofuel crop engineering efforts because of its central role in photosynthesis, metabolism, and intracellular signaling. However, the protein composition of the chloroplast and the functions of most of its proteins remain poorly characterized. At the core of this project, we sought to comprehensively determine the localization of chloroplast-associated proteins and generate a spatially defined protein-protein interaction network for chloroplast. For this purpose, we used the leading model alga Chlamydomonas reinhardtii, which greatly increased experimental speed and throughput. We illustrated the value of our findings to land plants by determining the localization of Arabidopsis thaliana land plant homologs of the Chlamydomonas proteins. Altogether, we were successful in determining the localization of 1,034 chloroplast-associated proteins in Chlamydomonas. The localizations provide numerous insights into the spatial organization of chloroplasts and how they function to support photosynthesis. The localization patterns of distinct proteins revealed new chloroplast structures and revealed new spatial organization inside the chloroplast. We also identified new components of known chloroplast structures, such as the chloroplast envelope, nucleoid, plastoglobuli, and pyrenoid. We identified these new components by investigating the interacting partners of known proteins. Many proteins localized in both the chloroplast and other cellular structures, thereby hinting at new functions and communication between cellular structures. We also applied machine learning on the atlas to generate predictions for the location of all of the proteins in Chlamydomonas. This enabled us to assign putative functions to many uncharacterized proteins based on their cellular location. Altogether, this research establishes a rich resource that opens new avenues of investigation and guides future work in deciphering and manipulating chloroplast function. Next, we developed an extensive protein-protein interaction network for the chloroplast by performing affinity purification-mass spectrometry on ~1,150 tagged chloroplast-associated proteins, the first such large-scale study in any photosynthetic organism. This dataset reveals 4,694 high-confidence protein-protein interactions, offering insights into the functions of thousands of conserved poorly-characterized chloroplast proteins. This systematic identification of protein-protein interactions in the chloroplast also provides multiple exciting new research directions and a detailed blueprint of the chloroplast's operation. This research lays the groundwork to decipher the inner workings of the chloroplast, the cell structure at the heart of photosynthesis. The spatial atlas and protein-protein interactions reveal chloroplast organizational features that would not have been accessible with traditional approaches. The localization mapping, insights into the function, and research materials generated further provide a rich resource for the research community to advance the understanding of how the chloroplast is organized to enable engineering of enhanced photosynthetic organisms.
Pharmacological inhibition of PRMT7 links arginine monomethylation to the cellular stress response
Protein arginine methyltransferases (PRMTs) regulate diverse biological processes and are increasingly being recognized for their potential as drug targets. Here we report the discovery of a potent, selective, and cell-active chemical probe for PRMT7. SGC3027 is a cell permeable prodrug, which in cells is converted to SGC8158, a potent, SAM-competitive PRMT7 inhibitor. Inhibition or knockout of cellular PRMT7 results in drastically reduced levels of arginine monomethylated HSP70 family stress-associated proteins. Structural and biochemical analyses reveal that PRMT7-driven in vitro methylation of HSP70 at R469 requires an ATP-bound, open conformation of HSP70. In cells, SGC3027 inhibits methylation of both constitutive and inducible forms of HSP70, and leads to decreased tolerance for perturbations of proteostasis including heat shock and proteasome inhibitors. These results demonstrate a role for PRMT7 and arginine methylation in stress response.
Structural and functional characterization of the dominant negative P-loop lysine mutation in the dy
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3D Temperature-Controlled Interchangeable Pattern for Size-Selective Nanoparticle Capture
Patterned surfaces with distinct regularity and structured arrangements have attracted great interest due to their extensive promising applications. Although colloidal patterning has conventionally been used to create such surfaces, herein, we introduce a novel 3D patterned poly(N-isopropylacrylamide) (PNIPAM) surface, synthesized by using a combination of colloidal templating and surface-initiated photoinduced electron transfer-reversible addition–fragmentation chain transfer (SI-PET-RAFT) polymerization. In order to investigate the temperature-driven 3D morphological variations at a lower critical solution temperature (LCST) of ~32 °C, multifaceted characterization techniques were employed. Atomic force microscopy confirmed the morphological transformations at 20 and 40 °C, while water contact angle measurements, upon heating, revealed distinct trends, offering insights into the correlation between surface wettability and topography adaptations. Moreover, quartz crystal microbalance with dissipation monitoring and electrochemical measurements were employed to detect the topographical adjustments of the unique hollow capsule structure within the LCST. Tests using different sizes of PSNPs shed light on the size-selective capture–release potential of the patterned PNIPAM, accentuating its biomimetic open–close behavior. Notably, our approach negates the necessity for expensive proteins, harnessing temperature adjustments to facilitate the noninvasive and efficient reversible capture and release of nanostructures. Finally, this advancement hopes to pave the way for future innovative cellular analysis platforms.
Systems and methods for periodic nodal surface based reactors, distributors, contactors and heat exchangers
The present disclosure relates to a transport mechanism apparatus for transporting at least one of a gas or a fluid. The transport mechanism may have an inlet, an outlet and an engineered cellular structure forming a periodic nodal surface, which may include a triply periodic minimal surface (TPMS) structure. The structure is formed in a layer-by-layer three dimensional (3D) printing operation to include cells propagating in three dimensions, where the cells include non-intersecting, continuously curving wall portions having openings, and where the opening in the cells form a plurality of flow paths throughout the transport mechanism from the inlet to the outlet, and where portions of the cells form the inlet and the outlet.