Preparing Better Samples for Cryo-Electron Microscopy: Biochemical Challenges Do Not End with Isolation and Purification.

The preparation of extremely thin samples, which are required for high-resolution electron microscopy, poses extreme risk of damaging biological macromolecules due to interactions with the air-water interface. Although the rapid increase in the number of published structures initially gave little indication that this was a problem, the search for methods that substantially mitigate this hazard is now intensifying. The two main approaches under investigation are (a) immobilizing particles onto structure-friendly support films and (b) reducing the length of time during which such interactions may occur. While there is little possibility of outrunning diffusion to the interface, intentional passivation of the interface may slow the process of adsorption and denaturation. In addition, growing attention is being given to gaining more effective control of the thickness of the sample prior to vitrification.

Capturing carbon dioxide from air with charged-sorbents.

Emissions reduction and greenhouse gas removal from the atmosphere are both necessary to achieve net-zero emissions and limit climate change1. There is thus a need for improved sorbents for the capture of carbon dioxide from the atmosphere, a process known as direct air capture. In particular, low-cost materials that can be regenerated at low temperatures would overcome the limitations of current technologies. In this work, we introduce a new class of designer sorbent materials known as 'charged-sorbents'. These materials are prepared through a battery-like charging process that accumulates ions in the pores of low-cost activated carbons, with the inserted ions then serving as sites for carbon dioxide adsorption. We use our charging process to accumulate reactive hydroxide ions in the pores of a carbon electrode, and find that the resulting sorbent material can rapidly capture carbon dioxide from ambient air by means of (bi)carbonate formation. Unlike traditional bulk carbonates, charged-sorbent regeneration can be achieved at low temperatures (90-100 °C) and the sorbent's conductive nature permits direct Joule heating regeneration2,3 using renewable electricity. Given their highly tailorable pore environments and low cost, we anticipate that charged-sorbents will find numerous potential applications in chemical separations, catalysis and beyond.

Precipitation regime changes in High Mountain Asia driven by cleaner air.

High Mountain Asia (HMA) has experienced a spatial imbalance in water resources in recent decades, partly because of a dipolar pattern of precipitation changes known as South Drying-North Wetting1. These changes can be influenced by both human activities and internal climate variability2,3. Although climate projections indicate a future widespread wetting trend over HMA1,4, the timing and mechanism of the transition from a dipolar to a monopolar pattern remain unknown. Here we demonstrate that the observed dipolar precipitation change in HMA during summer is primarily driven by westerly- and monsoon-associated precipitation patterns. The weakening of the Asian westerly jet, caused by the uneven emission of anthropogenic aerosols, favoured a dipolar precipitation trend from 1951 to 2020. Moreover, the phase transition of the Interdecadal Pacific Oscillation induces an out-of-phase precipitation change between the core region of the South Asian monsoon and southeastern HMA. Under medium- or high-emission scenarios, corresponding to a global warming of 0.6-1.1 °C compared with the present, the dipolar pattern is projected to shift to a monopolar wetting trend in the 2040s. This shift in precipitation patterns is mainly attributed to the intensified jet stream resulting from reduced emissions of anthropogenic aerosols. These findings underscore the importance of considering the impact of aerosol emission reduction in future social planning by policymakers.

Molecular basis of methyl-salicylate-mediated plant airborne defence.

Aphids transmit viruses and are destructive crop pests1. Plants that have been attacked by aphids release volatile compounds to elicit airborne defence (AD) in neighbouring plants2-5. However, the mechanism underlying AD is unclear. Here we reveal that methyl-salicylate (MeSA), salicylic acid-binding protein-2 (SABP2), the transcription factor NAC2 and salicylic acid-carboxylmethyltransferase-1 (SAMT1) form a signalling circuit to mediate AD against aphids and viruses. Airborne MeSA is perceived and converted into salicylic acid by SABP2 in neighbouring plants. Salicylic acid then causes a signal transduction cascade to activate the NAC2-SAMT1 module for MeSA biosynthesis to induce plant anti-aphid immunity and reduce virus transmission. To counteract this, some aphid-transmitted viruses encode helicase-containing proteins to suppress AD by interacting with NAC2 to subcellularly relocalize and destabilize NAC2. As a consequence, plants become less repellent to aphids, and more suitable for aphid survival, infestation and viral transmission. Our findings uncover the mechanistic basis of AD and an aphid-virus co-evolutionary mutualism, demonstrating AD as a potential bioinspired strategy to control aphids and viruses.

Giant lungfish genome elucidates the conquest of land by vertebrates.

Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, 'conquered' the land and ultimately gave rise to all land vertebrates, including humans1-3. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14× larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods4,5, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution.

Uncovering global-scale risks from commercial chemicals in air.

Commercial chemicals are used extensively across urban centres worldwide1, posing a potential exposure risk to 4.2 billion people2. Harmful chemicals are often assessed on the basis of their environmental persistence, accumulation in biological organisms and toxic properties, under international and national initiatives such as the Stockholm Convention3. However, existing regulatory frameworks rely largely upon knowledge of the properties of the parent chemicals, with minimal consideration given to the products of their transformation in the atmosphere. This is mainly due to a dearth of experimental data, as identifying transformation products in complex mixtures of airborne chemicals is an immense analytical challenge4. Here we develop a new framework-combining laboratory and field experiments, advanced techniques for screening suspect chemicals, and in silico modelling-to assess the risks of airborne chemicals, while accounting for atmospheric chemical reactions. By applying this framework to organophosphate flame retardants, as representative chemicals of emerging concern5, we find that their transformation products are globally distributed across 18 megacities, representing a previously unrecognized exposure risk for the world's urban populations. More importantly, individual transformation products can be more toxic and up to an order-of-magnitude more persistent than the parent chemicals, such that the overall risks associated with the mixture of transformation products are also higher than those of the parent flame retardants. Together our results highlight the need to consider atmospheric transformations when assessing the risks of commercial chemicals.

Prey can detect predators via electroreception in air.

Predators and prey benefit from detecting sensory cues of each other's presence. As they move through their environment, terrestrial animals accumulate electrostatic charge. Because electric charges exert forces at a distance, a prey animal could conceivably sense electrical forces to detect an approaching predator. Here, we report such a case of a terrestrial animal detecting its predators by electroreception. We show that predatory wasps are charged, thus emit electric fields, and that caterpillars respond to such fields with defensive behaviors. Furthermore, the mechanosensory setae of caterpillars are deflected by these electrostatic forces and are tuned to the wingbeat frequency of their insect predators. This ability unveils a dimension of the sensory interactions between prey and predators and is likely widespread among terrestrial animals.

Defining Physiological Normoxia for Improved Translation of Cell Physiology to Animal Models and Humans.

The extensive oxygen gradient between the air we breathe (Po2 ~21 kPa) and its ultimate distribution within mitochondria (as low as ~0.5-1 kPa) is testament to the efforts expended in limiting its inherent toxicity. It has long been recognized that cell culture undertaken under room air conditions falls short of replicating this protection in vitro. Despite this, difficulty in accurately determining the appropriate O2 levels in which to culture cells, coupled with a lack of the technology to replicate and maintain a physiological O2 environment in vitro, has hindered addressing this issue thus far. In this review, we aim to address the current understanding of tissue Po2 distribution in vivo and summarize the attempts made to replicate these conditions in vitro. The state-of-the-art techniques employed to accurately determine O2 levels, as well as the issues associated with reproducing physiological O2 levels in vitro, are also critically reviewed. We aim to provide the framework for researchers to undertake cell culture under O2 levels relevant to specific tissues and organs. We envisage that this review will facilitate a paradigm shift, enabling translation of findings under physiological conditions in vitro to disease pathology and the design of novel therapeutics.

Correcting datasets leads to more homogeneous early-twentieth-century sea surface warming.

Existing estimates of sea surface temperatures (SSTs) indicate that, during the early twentieth century, the North Atlantic and northeast Pacific oceans warmed by twice the global average, whereas the northwest Pacific Ocean cooled by an amount equal to the global average1-4. Such a heterogeneous pattern suggests first-order contributions from regional variations in forcing or in ocean-atmosphere heat fluxes5,6. These older SST estimates are, however, derived from measurements of water temperatures in ship-board buckets, and must be corrected for substantial biases7-9. Here we show that correcting for offsets among groups of bucket measurements leads to SST variations that correlate better with nearby land temperatures and are more homogeneous in their pattern of warming. Offsets are identified by systematically comparing nearby SST observations among different groups10. Correcting for offsets in German measurements decreases warming rates in the North Atlantic, whereas correcting for Japanese measurement offsets leads to increased and more uniform warming in the North Pacific. Japanese measurement offsets in the 1930s primarily result from records having been truncated to whole degrees Celsius when the records were digitized in the 1960s. These findings underscore the fact that historical SST records reflect both physical and social dimensions in data collection, and suggest that further opportunities exist for improving the accuracy of historical SST records9,11.

Quantitative detection of hydrogen peroxide in rain, air, exhaled breath, and biological fluids by NMR spectroscopy.

Hydrogen peroxide (H2O2) plays a key role in environmental chemistry, biology, and medicine. H2O2 concentrations typically are 6 to 10 orders of magnitude lower than that of water, making its quantitative detection challenging. We demonstrate that optimized NMR spectroscopy allows direct, interference-free, quantitative measurements of H2O2 down to submicromolar levels in a wide range of fluids, ranging from exhaled breath and air condensate to rain, blood, urine, and saliva. NMR measurements confirm the previously reported spontaneous generation of H2O2 in microdroplets that form when condensing water vapor on a hydrophobic surface, which can interfere with atmospheric H2O2 measurements. Its antimicrobial activity and strong seasonal variation speculatively could be linked to the seasonality of respiratory viral diseases.

Integrated mRNA and miRNA analysis reveals the regulatory network of oxidative stress and inflammation in Coilia nasus brains during air exposure and salinity mitigation.

BACKGROUND: Air exposure is an inevitable source of stress that leads to significant mortality in Coilia nasus. Our previous research demonstrated that adding 10‰ NaCl to aquatic water could enhance survival rates, albeit the molecular mechanisms involved in air exposure and salinity mitigation remained unclear. Conversely, salinity mitigation resulted in decreased plasma glucose levels and improved antioxidative activity. To shed light on this phenomenon, we characterized the transcriptomic changes in the C. nasus brain upon air exposure and salinity mitigation by integrated miRNA-mRNA analysis. RESULTS: The plasma glucose level was elevated during air exposure, whereas it decreased during salinity mitigation. Antioxidant activity was suppressed during air exposure, but was enhanced during salinity mitigation. A total of 629 differentially expressed miRNAs (DEMs) and 791 differentially expressed genes (DEGs) were detected during air exposure, while 429 DEMs and 1016 DEGs were identified during salinity mitigation. GO analysis revealed that the target genes of DEMs and DEGs were enriched in biological process and cellular component during air exposure and salinity mitigation. KEGG analysis revealed that the target genes of DEMs and DEGs were enriched in metabolism. Integrated analysis showed that 24 and 36 predicted miRNA-mRNA regulatory pairs participating in regulating glucose metabolism, Ca2+ transport, inflammation, and oxidative stress. Interestingly, most of these miRNAs were novel miRNAs. CONCLUSION: In this study, substantial miRNA-mRNA regulation pairs were predicted via integrated analysis of small RNA sequencing and RNA-Seq. Based on predicted miRNA-mRNA regulation and potential function of DEGs, miRNA-mRNA regulatory network involved in glucose metabolism and Ca2+ transport, inflammation, and oxidative stress in C. nasus brain during air exposure and salinity mitigation. They regulated the increased/decreased plasma glucose and inhibited/promoted antioxidant activity during air exposure and salinity mitigation. Our findings would propose novel insights to the mechanisms underlying fish responses to air exposure and salinity mitigation.

Revealing the pathogenesis of gastric intestinal metaplasia based on the mucosoid air-liquid interface.

BACKGROUND: Gastric intestinal metaplasia (GIM) is an essential precancerous lesion. Although the reversal of GIM is challenging, it potentially brings a state-to-art strategy for gastric cancer therapeutics (GC). The lack of the appropriate in vitro model limits studies of GIM pathogenesis, which is the issue this work aims to address for further studies. METHOD: The air-liquid interface (ALI) model was adopted for the long-term culture of GIM cells in the present work. This study conducted Immunofluorescence (IF), quantitative real-time polymerase chain reaction (qRT-PCR), transcriptomic sequencing, and mucoproteomic sequencing (MS) techniques to identify the pathways for differential expressed genes (DEGs) enrichment among different groups, furthermore, to verify novel biomarkers of GIM cells. RESULT: Our study suggests that GIM-ALI model is analog to the innate GIM cells, which thus can be used for mucus collection and drug screening. We found genes MUC17, CDA, TRIM15, TBX3, FLVCR2, ONECUT2, ACY3, NMUR2, and MAL2 were highly expressed in GIM cells, while GLDN, SLC5A5, MAL, and MALAT1 showed down-regulated, which can be used as potential biomarkers for GIM cells. In parallel, these genes that highly expressed in GIM samples were mainly involved in cancer-related pathways, such as the MAPK signal pathway and oxidative phosphorylation signal pathway. CONCLUSION: The ALI model is validated for the first time for the in vitro study of GIM. GIM-ALI model is a novel in vitro model that can mimic the tissue micro-environment in GIM patients and further provide an avenue for studying the characteristics of GIM mucus. Our study identified new markers of GIM as well as pathways associated with GIM, which provides outstanding insight for exploring GIM pathogenesis and potentially other related conditions.

Emerging use of air eDNA and its application to forensic investigations - A review.

Biological material is routinely collected at crime scenes and from exhibits and is a key type of evidence during criminal investigations. Improvements in DNA technologies allow collection and profiling of trace samples, comprised of few cells, significantly expanding the types of exhibits targeted for DNA analysis to include touched surfaces. However, success rates from trace and touch DNA samples tend to be poorer compared to other biological materials such as blood. Simultaneously, there have been recent advances in the utility of environmental DNA collection (eDNA) in identification and tracking of different biological organisms and species from bacteria to naked mole rats in different environments, including, soil, ice, snow, air and aquatic. This paper examines the emerging methods and research into eDNA collection, with a special emphasis on the potential forensic applications of human DNA collection from air including challenges and further studies required to progress implementation.

Up in the air: Presence and collection of DNA from air and air conditioner units.

Biological material is routinely collected at crime scenes and from exhibits and is a key type of evidence during criminal investigations. Touch or trace DNA samples from surfaces and objects deemed to have been contacted are frequently collected. However, a person of interest may not leave any traces on contacted surfaces, for example, if wearing gloves. A novel means of sampling human DNA from air offers additional avenues for DNA collection. In the present study, we report on the results of a pilot study into the prevalence and persistence of human DNA in the air. The first aspect of the pilot study investigates air conditioner units that circulate air around a room, by sampling units located in four offices and four houses at different time frames post-cleaning. The second aspect investigates the ability to collect human DNA from the air in rooms, with and without people, for different periods of time and with different types of collection filters. Results of this pilot study show that human DNA can be collected on air conditioner unit surfaces and from the air, with air samples representing the more recent occupation while air conditioner units showing historic use of the room.

An experimental and modeling approach to describe the deactivation of cellulases at the air-liquid interface.

Understanding the reaction mechanisms involved in the enzymatic hydrolysis of cellulose is important because it is kinetically the most limiting step of the bioethanol production process. The present work focuses on the enzymatic deactivation at the air-liquid interface, which is one of the aspects contributing to this global deactivation. This phenomenon has already been experimentally proven, but this is the first time that a model has been proposed to describe it. Experiments were performed by incubating Celluclast cocktail solutions on an orbital stirring system at different enzyme concentrations and different surface-to-volume ratios. A 5-day follow-up was carried out by measuring the global FPase activity of cellulases for each condition tested. The activity loss was proven to depend on both the air-liquid surface area and the enzyme concentration. Both observations suggest that the loss of activity takes place at the air-liquid surface, the total amount of enzymes varying with volume or enzyme concentration. Furthermore, tests performed using five individual enzymes purified from a Trichoderma reesei cocktail showed that the only cellulase that is deactivated at the air-liquid interface is cellobiohydrolase II. From the experimental data collected by varying the initial enzyme concentration and the ratio surface to volume, it was possible to develop, for the first time, a model that describes the loss of activity at the air-liquid interface for this configuration.

Riddled with holes: Understanding air space formation in plant leaves.

Plants use energy from sunlight to transform carbon dioxide from the air into complex organic molecules, ultimately producing much of the food we eat. To make this complex chemistry more efficient, plant leaves are intricately constructed in 3 dimensions: They are flat to maximise light capture and contain extensive internal air spaces to increase gas exchange for photosynthesis. Many years of work has built up an understanding of how leaves form flat blades, but the molecular mechanisms that control air space formation are poorly understood. Here, I review our current understanding of air space formation and outline how recent advances can be harnessed to answer key questions and take the field forward. Increasing our understanding of plant air spaces will not only allow us to understand a fundamental aspect of plant development, but also unlock the potential to engineer the internal structure of crops to make them more efficient at photosynthesis with lower water requirements and more resilient in the face of a changing environment.

Mechanisms of Air Entraining of Proteins in Cementitious Materials.

While few prior studies examined the air-entraining properties of proteins in cementitious materials, the underlying mechanisms of proteins' air entraining and the interactions between proteins and cement have not been studied in the past. The significance of this article is to address this knowledge gap by investigating the effect of proteins on relevant factors that affect air entraining in cement paste and establishing an understanding of the mechanism of air entrainment with proteins. These factors include the surface tension of pore solution, protein adsorption on cement particles, cement paste hydrophobization, and flow of fresh paste. Thirteen different proteins were used to investigate the effect of a wide range of protein characteristics on air entraining. Proteins decreased the pore solution surface tension to different degrees. At low concentrations, the adsorption of proteins on cement particles slightly affected the pore solution surface tension. Protein adsorption on cement particles showed a wide range of adsorption isotherms. Proteins generally increased the flow of paste due to electrostatic repulsion between cement particles because of the adsorption of negatively charged proteins on cement particles, as well as the ball-bearing effect of bubbles in fresh paste. The surface hydrophobicity was increased in pastes with proteins. A detailed microcomputed tomography (micro-CT) analysis showed very different air void microstructures in pastes with various proteins. While a relatively strong correlation was observed between air void porosity and surface hydrophobicity, the correlation between air void porosity and the surface tension of pore solution was weak. This indicates that the accumulation of hydrophobized cement particles on the air bubble in the fresh paste, refered to as the Pickering effect, is the main mechanism of air entraining of proteins in the paste. It was shown that a high air void porosity occurs in an intermediate range of flow.

Turkey vultures tune their airspeed to changing air density.

Animals must tune their physical performance to changing environmental conditions, and the breadth of environmental tolerance may contribute to delineating the geographic range of a species. A common environmental challenge that flying animals face is the reduction of air density at high elevation and the reduction in the effectiveness of lift production that accompanies it. As a species, turkey vultures (Cathartes aura) inhabit a >3000 m elevation range, and fly considerably higher, necessitating that they accommodate for a 27% change in air density (0.890 to 1.227 kg m-3) through behavior, physiology or biomechanics. We predicted that birds flying at high elevation would maintain aerodynamic lift performance behaviorally via higher flight speeds, rather than increases in power output or local phenotypic adaptation. We used three-dimensional videography to track turkey vultures flying at three elevations, and data supported the hypothesized negative relationship between median airspeed and air density. Additionally, neither the ratio of horizontal speed to sinking speed nor flapping behavior varied with air density.

Learning Electronic Polarizations in Aqueous Systems.

The polarization of periodically repeating systems is a discontinuous function of the atomic positions, a fact which seems at first to stymie attempts at their statistical learning. Two approaches to build models for bulk polarizations are compared: one in which a simple point charge model is used to preprocess the raw polarization to give a learning target that is a smooth function of atomic positions and the total polarization is learned as a sum of atom-centered dipoles and one in which instead the average position of Wannier centers around atoms is predicted. For a range of bulk aqueous systems, both of these methods perform perform comparatively well, with the former being slightly better but often requiring an extra effort to find a suitable point charge model. As a challenging test, we also analyze the performance of the models at the air-water interface. In this case, while the Wannier center approach delivers accurate predictions without further modifications, the preprocessing method requires augmentation with information from isolated water molecules to reach similar accuracy. Finally, we present a simple protocol to preprocess the polarizations in a data-driven way using a small number of derivatives calculated at a much lower level of theory, thus overcoming the need to find point charge models without appreciably increasing the computation cost. We believe that the training strategies presented here help the construction of accurate polarization models required for the study of the dielectric properties of realistic complex bulk systems and interfaces with ab initio accuracy.

Dense Monolayer Network Structures of Double Hydrophilic Hyperbranched Copolymers at the Air/Water Interface.

Influences of subphase pH and temperature on the interfacial aggregation behavior of two double hydrophilic hyperbranched copolymers of poly[oligo(ethylene glycol) methacrylate-co-(2-diisopropylamino)ethyl methacrylate] (P(OEGMA-co-DIPAEMA)) at the air/water interface are studied by the Langmuir film balance technique. Morphologies of their Langmuir-Blodgett (LB) films are characterized by atomic force microscopy (AFM). At the interface, P(OEGMA-co-DIPAEMA) copolymers tend to form a dense network structure of circular micelles composed of branching agent-connected carbon backbone cores and mixed shells of OEGMA and DIPAEMA segments (pendant groups). This network structure containing many honeycomb-like holes with diameters of 6-8 nm is identified for the first time and clearly observed in the enlarged AFM images of their LB films. Under acidic conditions, surface pressure versus molecular area isotherms of the two copolymers in the low-pressure region show larger mean molecular area than those under neutral and alkaline conditions due to the lack of impediment from DIPAEMA segments. Upon further compression, each isotherm exhibits a wide pseudo-plateau, which corresponds to OEGMA segments being pressed into the subphase. Furthermore, the isotherms under neutral and alkaline conditions exhibit the lower critical solution temperature behavior of OEGMA segments, and the critical temperature is lower when the hyperbranched copolymer contains higher OEGMA content.