Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2.

The coronavirus disease 2019 (COVID-19) pandemic continues worldwide with many variants arising, some of which are variants of concern (VOCs). A recent VOC, omicron (B.1.1.529), which obtains a large number of mutations in the receptor-binding domain (RBD) of the spike protein, has risen to intense scientific and public attention. Here, we studied the binding properties between the human receptor ACE2 (hACE2) and the VOC RBDs and resolved the crystal and cryoelectron microscopy structures of the omicron RBD-hACE2 complex as well as the crystal structure of the delta RBD-hACE2 complex. We found that, unlike alpha, beta, and gamma, omicron RBD binds to hACE2 at a similar affinity to that of the prototype RBD, which might be due to compensation of multiple mutations for both immune escape and transmissibility. The complex structures of omicron RBD-hACE2 and delta RBD-hACE2 reveal the structural basis of how RBD-specific mutations bind to hACE2.

Antigenic cartography using sera from sequence-confirmed SARS-CoV-2 variants of concern infections reveals antigenic divergence of Omicron.

Large-scale vaccination campaigns have prevented countless hospitalizations and deaths due to COVID-19. However, the emergence of SARS-CoV-2 variants that escape from immunity challenges the effectiveness of current vaccines. Given this continuing evolution, an important question is when and how to update SARS-CoV-2 vaccines to antigenically match circulating variants, similarly to seasonal influenza viruses where antigenic drift necessitates periodic vaccine updates. Here, we studied SARS-CoV-2 antigenic drift by assessing neutralizing activity against variants of concern (VOCs) in a set of sera from patients infected with viral sequence-confirmed VOCs. Infections with D614G or Alpha strains induced the broadest immunity, whereas individuals infected with other VOCs had more strain-specific responses. Omicron BA.1 and BA.2 were substantially resistant to neutralization by sera elicited by all other variants. Antigenic cartography revealed that Omicron BA.1 and BA.2 were antigenically most distinct from D614G, associated with immune escape, and possibly will require vaccine updates to ensure vaccine effectiveness.

Synchronizing Efficient Purification of VOCs in Durable Solar Water Evaporation over a Highly Stable Cu/W18O49@Graphene Material.

Solar-driven clean water production is challenged by VOCs (volatile organic compounds), which pose health risks in distilled water. Herein, we developed a Cu/W18O49@Graphene photothermal-photocatalytic material addressing VOCs contamination. Plasmonic coupling between Cu and W18O49 enhances light absorption, and 1-2 layers of graphene encapsulation protects oxygen vacancies within W18O49 while facilitating hot electron extraction, effectively mitigating their ultrafast relaxation. Density functional theory calculations revealed enhanced VOCs adsorption on graphene. These synergies address oxygen vacancy decay in W18O49 and provide more active sites for gas-liquid-solid triphase photocatalytic reactions. Integrated with a three-dimensional floating evaporator substrate, the optimized Cu/W18O49@Graphene material achieved an effective water evaporation rate of 1.41 kg m-2 h-1 (efficiency of 88.6%), exceptional stability (>120 h), and remarkable 99% phenol removal under 1 sun irradiation (1 kW m-2). This work provides a promising solution to mitigate VOCs contamination in solar-driven water evaporation.

Yolk-Shell Hierarchical Pore Au@MOF Nanostructures: Efficient Gas Capture and Enrichment for Advanced Breath Analysis.

Surface-enhanced Raman scattering (SERS) offers a promising, cost-effective alternative for the rapid, sensitive, and quantitative analysis of potential biomarkers in exhaled gases, which is crucial for early disease diagnosis. However, a major challenge in SERS is the effective detection of gaseous analytes, primarily due to difficulties in enriching and capturing them within the substrate's "hotspot" regions. This study introduces an advanced gas sensor combining mesoporous gold (MesoAu) and metal-organic frameworks (MOFs), exhibiting high sensitivity and rapid detection capabilities. The MesoAu provides abundant active sites and interconnected mesopores, facilitating the diffusion of analytes for detection. A ZIF-8 shell enveloping MesoAu further enriches target molecules, significantly enhancing sensitivity. A proof-of-concept experiment demonstrated a detection limit of 0.32 ppb for gaseous benzaldehyde, indicating promising prospects for the rapid diagnosis of early stage lung cancer. This research also pioneers a novel approach for constructing hierarchical plasmonic nanostructures with immense potential in gas sensing.

A Noncoding A-to-U Kozak Site Change Related to the High Transmissibility of Alpha, Delta, and Omicron VOCs.

Three prevalent SARS-CoV-2 variants of concern (VOCs) emerged and caused epidemic waves. It is essential to uncover advantageous mutations that cause the high transmissibility of VOCs. However, viral mutations are tightly linked, so traditional population genetic methods, including machine learning-based methods, cannot reliably detect mutations conferring a fitness advantage. In this study, we developed an approach based on the sequential occurrence order of mutations and the accelerated furcation rate in the pandemic-scale phylogenomic tree. We analyzed 3,777,753 high-quality SARS-CoV-2 genomic sequences and the epidemiology metadata using the Coronavirus GenBrowser. We found that two noncoding mutations at the same position (g.a28271-/u) may be crucial to the high transmissibility of Alpha, Delta, and Omicron VOCs although the noncoding mutations alone cannot increase viral transmissibility. Both mutations cause an A-to-U change at the core position -3 of the Kozak sequence of the N gene and significantly reduce the protein expression ratio of ORF9b to N. Using a convergent evolutionary analysis, we found that g.a28271-/u, S:p.P681H/R, and N:p.R203K/M occur independently on three VOC lineages, suggesting that coordinated changes of S, N, and ORF9b proteins are crucial to high viral transmissibility. Our results provide new insights into high viral transmissibility co-modulated by advantageous noncoding and nonsynonymous changes.

Enhanced Sensitivity in Photovoltaic 2D MoS2/Te Heterojunction VOC Sensors.

Volatile organic compound (VOC) sensors have a broad range of applications including healthcare monitoring, product quality control, and air quality management. However, many such applications are demanding, requiring sensors with high sensitivity and selectivity. 2D materials are extensively used in many VOC sensing devices due to their large surface-to-volume ratio and fascinating electronic properties. These properties, along with their exceptional flexibility, low power consumption, room-temperature operation, chemical functionalization potential, and defect engineering capabilities, make 2D materials ideal for high-performance VOC sensing. Here, a 2D MoS2/Te heterojunction is reported that significantly improves the VOC detection compared to MoS2 and Te sensors on their own. Density functional theory (DFT) analysis shows that the MoS2/Te heterojunction significantly enhances the adsorption energy and therefore sensing sensitivity of the sensor. The sensor response, which denotes the percentage change in the sensor's conductance upon VOC exposure, is further enhanced under photo-illumination and zero-bias conditions to values up to ≈7000% when exposed to butanone. The MoS2/Te heterojunction is therefore a promising device architecture for portable and wearable sensing applications.

The heat is on: reduced detection of floral scents after heatwaves in bumblebees.

Global climate change disrupts key ecological processes and biotic interactions. The recent increase in heatwave frequency and severity prompts the evaluation of physiological processes that ensure the maintenance of vital ecosystem services such as pollination. We used experimental heatwaves to determine how high temperatures affect the bumblebees' ability to detect floral scents. Heatwaves induced strong reductions in antennal responses to floral scents in both tested bumblebee species (Bombus terrestris and Bombus pascuorum). These reductions were generally stronger in workers than in males. Bumblebees showed no consistent pattern of recovery 24 h after heat events. Our results suggest that the projected increased frequency and severity of heatwaves may jeopardize bumblebee-mediated pollination services by disrupting the chemical communication between plants and pollinators. The reduced chemosensitivity can decrease the bumblebees' abilities to locate food sources and lead to declines in colonies and populations.

Recent developments and applications of selected ion flow tube mass spectrometry (SIFT-MS).

Selected ion flow tube mass spectrometry (SIFT-MS) is now recognized as the most versatile analytical technique for the identification and quantification of trace gases down to the parts-per-trillion by volume, pptv, range. This statement is supported by the wide reach of its applications, from real-time analysis, obviating sample collection of very humid exhaled breath, to its adoption in industrial scenarios for air quality monitoring. This review touches on the recent extensions to the underpinning ion chemistry kinetics library and the alternative challenge of using nitrogen carrier gas instead of helium. The addition of reagent anions in the Voice200 series of SIFT-MS instruments has enhanced the analytical capability, thus allowing analyses of volatile trace compounds in humid air that cannot be analyzed using reagent cations alone, as clarified by outlining the anion chemistry involved. Case studies are reviewed of breath analysis and bacterial culture volatile organic compound (VOC), emissions, environmental applications such as air, water, and soil analysis, workplace safety such as transport container fumigants, airborne contamination in semiconductor fabrication, food flavor and spoilage, drugs contamination and VOC emissions from packaging to demonstrate the stated qualities and uniqueness of the new generation SIFT-MS instrumentation. Finally, some advancements that can be made to improve the analytical capability and reach of SIFT-MS are mentioned.

Green leaf volatiles co-opt proteins involved in molecular pattern signalling in plant cells.

The green leaf volatiles (GLVs) Z-3-hexen-1-ol (Z3-HOL) and Z-3-hexenyl acetate (Z3-HAC) are airborne infochemicals released from damaged plant tissues that induce defenses and developmental responses in receiver plants, but little is known about their mechanism of action. We found that Z3-HOL and Z3-HAC induce similar but distinctive physiological and signaling responses in tomato seedlings and cell cultures. In seedlings, Z3-HAC showed a stronger root growth inhibition effect than Z3-HOL. In cell cultures, the two GLVs induced distinct changes in MAP kinase (MAPK) activity and proton fluxes as well as rapid and massive changes in the phosphorylation status of proteins within 5 min. Many of these phosphoproteins are involved in reprogramming the proteome from cellular homoeostasis to stress and include pattern recognition receptors, a receptor-like cytoplasmic kinase, MAPK cascade components, calcium signaling proteins and transcriptional regulators. These are well-known components of damage-associated molecular pattern (DAMP) signaling pathways. These rapid changes in the phosphoproteome may underly the activation of defense and developmental responses to GLVs. Our data provide further evidence that GLVs function like DAMPs and indicate that GLVs coopt DAMP signaling pathways.

Diverse pro-inflammatory ability of mutated spike protein derived from variant strains of SARS-CoV-2.

The severity of COVID-19 has been reported to differ among SARS-CoV-2 mutant variants. The overactivation of macrophages is involved in severe COVID-19, yet the effects of SARS-CoV-2 mutations on macrophages remain poorly understood. To clarify the effects, we examined whether mutations of spike proteins (S-proteins) affect macrophage activation. CD14+ monocyte-derived macrophages were stimulated with the recombinant S-protein of the wild-type, Delta, and Omicron strains or live viral particles of individual strains. Regarding IL-6 and TNF-α, Delta or Omicron S-protein had stronger or weaker pro­inflammatory ability, respectively, than the wild-type. Similar trends were observed between S-proteins and viral particles. S-protein mutations could be related to the diversity in macrophage activation and severity rates in COVID-19 caused by various SARS-CoV-2 strains.

High-quality identification of volatile organic compounds (VOCs) originating from breath.

INTRODUCTION: Volatile organic compounds (VOCs) can arise from underlying metabolism and are detectable in exhaled breath, therefore offer a promising route to non-invasive diagnostics. Robust, precise, and repeatable breath measurement platforms able to identify VOCs in breath distinguishable from background contaminants are needed for the confident discovery of breath-based biomarkers. OBJECTIVES: To build a reliable breath collection and analysis method that can produce a comprehensive list of known VOCs in the breath of a heterogeneous human population. METHODS: The analysis cohort consisted of 90 pairs of breath and background samples collected from a heterogenous population. Owlstone Medical's Breath Biopsy® OMNI® platform, consisting of sample collection, TD-GC-MS analysis and feature extraction was utilized. VOCs were determined to be "on-breath" if they met at least one of three pre-defined metrics compared to paired background samples. On-breath VOCs were identified via comparison against purified chemical standards, using retention indexing and high-resolution accurate mass spectral matching. RESULTS: 1471 VOCs were present in > 80% of samples (breath and background), and 585 were on-breath by at least one metric. Of these, 148 have been identified covering a broad range of chemical classes. CONCLUSIONS: A robust breath collection and relative-quantitative analysis method has been developed, producing a list of 148 on-breath VOCs, identified using purified chemical standards in a heterogenous population. Providing confirmed VOC identities that are genuinely breath-borne will facilitate future biomarker discovery and subsequent biomarker validation in clinical studies. Additionally, this list of VOCs can be used to facilitate cross-study data comparisons for improved standardization.

Bispidine Based Hg(II) 1D Coordination Polymers of Helical Topology: Stability, Selective Adsorption and 1D to 2D Dimensionality Change Via SC-to-SC Transformation.

Bispidine based Hg(II) coordination polymers of helical topology CP-MeOH and CP-EtOH are almost isostructural (they mainly differ for the solvent included in their lattice and by a small % in unit cell parameters) but they differ for everything else: i) their intrinsic stability, ii) their ability to adsorb solvents upon prior evacuation, iii) their accessible structural transformations. In particular, one of the two starting materials, once evacuated, is capable to adsorb methanol from atmospheres containing binary and ternary mixtures of volatile organic compounds (MeOH, CHCl3 and EtOH) under ambient conditions (25 °C, 1 atm) and with a marked selectivity. The other one is not, but undergoes a 1D to 2D dimensionality change which can be monitored in situ by SC-XRD through a SC-to-SC process.

Identification of volatile biomarkers for lung cancer from different histological sources: A comprehensive study.

The identification of noninvasive volatile biomarkers for lung cancer is a significant clinical challenge. Through in vitro studies, the recognition of altered metabolism in cell volatile organic compound (VOC) emitting profile, along with the occurrence of oncogenesis, provides insight into the biochemical pathways involved in the production and metabolism of lung cancer volatile biomarkers. In this research, for the first time, a comprehensive comparative analysis of the volatile metabolites in NSCLS cells (A549), SCLC cells (H446), lung normal cells (BEAS-2B), as well as metabolites in both the oxidative stress (OS) group and control group. Specifically, the combination of eleven VOCs, including n-dodecane, acetaldehyde, isopropylbenzene, p-ethyltoluene and cis-1,3-dichloropropene, exhibited potential as volatile biomarkers for lung cancer originating from two different histological sources. Furthermore, the screening process in A549 cell lines resulted in the identification of three exclusive biomarkers, isopropylbenzene, formaldehyde and bromoform. Similarly, the exclusive biomarkers 1,2,4-trimethylbenzene, p-ethyltoluene, and cis-1,3-dichloropropene were present in the H446 cell line. Additionally, significant changes in trans-2-pentene, acetaldehyde, 1,2,4-trimethylbenzene, and bromoform were observed, indicating a strong association with OS. These findings highlight the potential of volatile biomarkers profiling as a means of noninvasive identification for lung cancer diagnosis.

Male dingo urinary scents code for age class and wild dingoes respond to this information.

Chemical information in canid urine has been implicated in territoriality and influences the spacing of individuals. We identified the key volatile organic compound (VOC) components in dingo (Canis lupus dingo) urine and investigated the potential role of scents in territorial spacing. VOC analysis, using headspace gas chromatography-mass spectrometry (GC-MS), demonstrated that the information in fresh urine from adult male dingoes was sufficient to allow statistical classification into age categories. Discriminant function analyses demonstrated that the relative amounts or combinations of key VOCs from pre-prime (3-4 years), prime (5-9 years), and post-prime (≥10 years) males varied between these age categories, and that scents exposed to the environment for 4 (but not 33) days could still be classified to age categories. Further, a field experiment showed that dingoes spent less time in the vicinity of prime male dingo scents than other scents. Collectively, these results indicate that age-related scent differences may be discriminable by dingoes. Previous authors have suggested the potential to use scent as a management tool for wild canids by creating an artificial territorial boundary/barrier. Our results suggest that identifying the specific signals in prime-age male scents could facilitate the development of scent-based tools for non-lethal management.

Computational analysis of affinity dynamics between the variants of SARS-CoV-2 spike protein (RBD) and human ACE-2 receptor.

The novel coronavirus SARS-CoV-2 resulted in a significant worldwide health emergency known as the COVID-19 pandemic. This crisis has been marked by the widespread of various variants, with certain ones causing notable apprehension. In this study, we harnessed computational techniques to scrutinize these Variants of Concern (VOCs), including various Omicron subvariants. Our approach involved the use of protein structure prediction algorithms and molecular docking techniques, we have investigated the effects of mutations within the Receptor Binding Domain (RBD) of SARS-CoV-2 and how these mutations influence its interactions with the human angiotensin-converting enzyme 2 (hACE-2) receptor. Further we have predicted the structural alterations in the RBD of naturally occurring SARS-CoV-2 variants using the tr-Rosetta algorithm. Subsequent docking and binding analysis employing HADDOCK and PRODIGY illuminated crucial interactions occurring at the Receptor-Binding Motif (RBM). Our findings revealed a hierarchy of increased binding affinity between the human ACE2 receptor and the various RBDs, in the order of wild type (Wuhan-strain) < Beta < Alpha < Gamma < Omicron-B.1.1.529 < Delta < Omicron-BA.2.12.1 < Omicron-BA.5.2.1 < Omicron-BA.1.1. Notably, Omicron-BA.1.1 demonstrated the highest binding affinity of -17.4 kcal mol-1 to the hACE2 receptor when compared to all the mutant complexes. Additionally, our examination indicated that mutations occurring in active residues of the Receptor Binding Domain (RBD) consistently improved the binding affinity and intermolecular interactions in all mutant complexes. Analysis of the differences among variants has laid a foundation for the structure-based drug design targeting the RBD region of SARS-CoV-2.

Anisotropic sensing based on single ReS2flake for VOCs discrimination.

Selective and sensitive detection of volatile organic compounds (VOCs) holds paramount importance in real-world applications. This study proposes an innovative approach utilizing a single ReS2field-effect transistor (FET) characterized by distinct in-plane anisotropy, specifically tailored for VOC recognition. The unique responses of ReS2, endowed with robust in-plane anisotropic properties, demonstrate significant difference along thea-axis andb-axis directions when exposed to four kinds of VOCs: acetone, methanol, ethanol, and IPA. Remarkably, the responses of ReS2were significantly magnified under ultraviolet (UV) illumination, particularly in the case of acetone, where the response amplified by 10-15 times and the detection limit decreasing from 70 to 4 ppm compared to the dark conditions. Exploiting the discernible variances in responses along thea-axis andb-axis under both UV and dark conditions, the data points of acetone, ethanol, methanol and IPA gases were clearly separated in the principal component space without any overlap through principal component analysis, indicating that the single ReS2FET has a high ability to distinguish various gas species. The exploration of anisotropic sensing materials and light excitation strategies can be applied to a broad range of sensing platforms based on two-dimensional materials for practical applications.

How Does Personal Hygiene Influence Indoor Air Quality?

Humans are known to be a continuous and potent indoor source of volatile organic compounds (VOCs). However, little is known about how personal hygiene, in terms of showering frequency, can influence these emissions and their impact on indoor air chemistry involving ozone. In this study, we characterized the VOC composition of the air in a controlled climate chamber (22.5 m3 with an air change rate at 3.2 h-1) occupied by four male volunteers on successive days under ozone-free (∼0 ppb) and ozone-present (37-40 ppb) conditions. The volunteers either showered the evening prior to the experiments or skipped showering for 24 and 48 h. Reduced shower frequency increased human emissions of gas-phase carboxylic acids, possibly originating from skin bacteria. With ozone present, increasing the number of no-shower days enhanced ozone-skin surface reactions, yielding higher levels of oxidation products. Wearing the same clothing over several days reduced the level of compounds generated from clothing-ozone reactions. When skin lotion was applied, the yield of the skin ozonolysis products decreased, while other compounds increased due to ozone reactions with lotion ingredients. These findings help determine the degree to which personal hygiene choices affect the indoor air composition and indoor air exposures.

Quantification of Byproduct Formation from Portable Air Cleaners Using a Proposed Standard Test Method.

In response to the COVID-19 pandemic, air cleaning technologies were promoted as useful tools for disinfecting public spaces and combating airborne pathogen transmission. However, no standard method exists to assess the potentially harmful byproduct formation from air cleaners. Through a consensus standard development process, a draft standard test method to assess portable air cleaner performance was developed, and a suite of air cleaners employing seven different technologies was tested. The test method quantifies not only the removal efficiency of a challenge chemical suite and ultrafine particulate matter but also byproduct formation. Clean air delivery rates (CADRs) are used to quantify the chemical and particle removal efficiencies, and an emission rate framework is used to quantify the formation of formaldehyde, ozone, and other volatile organic compounds. We find that the tested photocatalytic oxidation and germicidal ultraviolet light (GUV) technologies produced the highest levels of aldehyde byproducts having emission rates of 202 and 243 µg h-1, respectively. Additionally, GUV using two different wavelengths, 222 and 254 nm, both produced ultrafine particulate matter.

Surface Hydroxyl and Oxygen Vacancies Engineering in ZnSnAl LDH: Synergistic Promotion of Photocatalytic Oxidation of Aromatic VOCs.

Photocatalytic oxidation has gained great interest in environmental remediation, but it is still limited by its low efficiency and catalytic deactivation in the degradation of aromatic VOCs. In this study, we concurrently regulated the surface hydroxyl and oxygen vacancies by introducing Al into ZnSn layered double hydroxide (LDH). The presence of distorted Al species induced local charge redistribution, leading to the remarkable formation of oxygen vacancies. These oxygen vacancies subsequently increased the amount of surface hydroxyl and elongated its bond length. The synergistic effects of surface hydroxyl and oxygen vacancies greatly enhanced reactant adsorption-activation and facilitated charge transfer to generate •OH, •O2-, and 1O2, resulting in highly efficient oxidation and ring-opening of various aromatic VOCs. Compared with commercial TiO2, the optimized ZnSnAl-50 catalyst exhibited about 2-fold activity for the toluene and styrene degradation and 10-fold activity for the chlorobenzene degradation. Moreover, ZnSnAl-50 demonstrated exceptional stability in the photocatalytic oxidation of toluene under a wide humidity range of 0-75%. This work marvelously improves the photocatalytic efficiency, stability, and adaptability through a novel strategy of surface hydroxyl and oxygen vacancies engineering.

Influence of Ventilation on Formation and Growth of 1-20 nm Particles via Ozone-Human Chemistry.

Ozone reaction with human surfaces is an important source of ultrafine particles indoors. However, 1-20 nm particles generated from ozone-human chemistry, which mark the first step of particle formation and growth, remain understudied. Ventilation and indoor air movement could have important implications for these processes. Therefore, in a controlled-climate chamber, we measured ultrafine particles initiated from ozone-human chemistry and their dependence on the air change rate (ACR, 0.5, 1.5, and 3 h-1) and operation of mixing fans (on and off). Concurrently, we measured volatile organic compounds (VOCs) and explored the correlation between particles and gas-phase products. At 25-30 ppb ozone levels, humans generated 0.2-7.7 × 1012 of 1-3 nm, 0-7.2 × 1012 of 3-10 nm, and 0-1.3 × 1012 of 10-20 nm particles per person per hour depending on the ACR and mixing fan operation. Size-dependent particle growth and formation rates increased with higher ACR. The operation of mixing fans suppressed the particle formation and growth, owing to enhanced surface deposition of the newly formed particles and their precursors. Correlation analyses revealed complex interactions between the particles and VOCs initiated by ozone-human chemistry. The results imply that ventilation and indoor air movement may have a more significant influence on particle dynamics and fate relative to indoor chemistry.