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115 records · Page 7

Site specific N- and O-glycosylation mapping of the spike proteins of SARS-CoV-2 variants of concern

Abstract The glycosylation on the spike (S) protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, modulates the viral infection by altering conformational dynamics, receptor interaction and host immune responses. Several variants of concern (VOCs) of SARS-CoV-2 have evolved during the pandemic, and crucial mutations on the S protein of the virus have led to increased transmissibility and immune escape. In this study, we compare the site-specific glycosylation and overall glycomic profiles of the wild type Wuhan-Hu-1 strain (WT) S protein and five VOCs of SARS-CoV-2: Alpha, Beta, Gamma, Delta and Omicron. Interestingly, both N- and O-glycosylation sites on the S protein are highly conserved among the spike mutant variants, particularly at the sites on the receptor-binding domain (RBD). The conservation of glycosylation sites is noteworthy, as over 2 million SARS-CoV-2 S protein sequences have been reported with various amino acid mutations. Our detailed profiling of the glycosylation at each of the individual sites of the S protein across the variants revealed intriguing possible association of glycosylation pattern on the variants and their previously reported infectivity. While the sites are conserved, we observed changes in the N- and O-glycosylation profile across the variants. The newly emerged variants, which showed higher resistance to neutralizing antibodies and vaccines, displayed a decrease in the overall abundance of complex-type glycans with both fucosylation and sialylation and an increase in the oligomannose-type glycans across the sites. Among the variants, the glycosylation sites with significant changes in glycan profile were observed at both the N -terminal domain and RBD of S protein, with Omicron showing the highest deviation. The increase in oligomannose-type happens sequentially from Alpha through Delta. Interestingly, Omicron does not contain more oligomannose-type glycans compared to Delta but does contain more compared to the WT and other VOCs. O-glycosylation at the RBD showed lower occupancy in the VOCs in comparison to the WT. Our study on the sites and pattern of glycosylation on the SARS-CoV-2 S proteins across the VOCs may help to understand how the virus evolved to trick the host immune system. Our study also highlights how the SARS-CoV-2 virus has conserved both N - and O - glycosylation sites on the S protein of the most successful variants even after undergoing extensive mutations, suggesting a correlation between infectivity/ transmissibility and glycosylation.

60 APPLIED LIFE SCIENCES↗

Cleavage at the nsp5–nsp6 site of SARS-CoV-2 main protease intermediate precursor is faster from a monomer than a dimer form

Our previous studies of severe acute respiratory syndrome coronavirus 2 main protease (MPro) precursor monomer indicate that the initial N-terminal nonstructural protein (nsp)4/nsp5 cleavage occurs intramolecularly, with a small fraction of the active site loop equilibrium being in the active state. To understand the influence of dimer formation of MPro upon N-terminal cleavage on the subsequent C-terminal nsp5/nsp6 intermolecular cleavage kinetics, the stepwise processing of a monomeric, inactive precursor containing the native terminal cleavage sites of MPro (MBP- (−6) MPro C145A(+3) -GB1-6H, 86.2 kDa) by mature WT MPro (MPro WT ) was investigated. Differential scanning fluorimetry and analytical ultracentrifugation measurements of various MPro constructs suggest that the C145A mutation decreases the dimer dissociation constant (K dimer ) by ∼26-fold, relative to WT C145 and H41A. The monomeric precursor’s nsp4–nsp5 site appears to saturate MProWT’s active sites and cleave faster, followed by a slower first-order cleavage at the C-terminal site. No detectable product resulting from the C-terminal cleavage is observed until most of the N-terminal cleavage is complete. The initial intermediate product (termed MPro C145A-IP ) is a homodimer with an estimated K dimer of <0.05 μM. In contrast, the first-order kinetics observed for the cleavage of the monomeric form of the intermediate product is at least 300 times faster than that of the dimer form. Room-temperature X-ray structure of the MPro C145A-IP –ensitrelvir complex is like that of the MPro WT –ensitrelvir complex and reveals a dynamic C-terminal region including MPro residues 302 to 306. These results are interpreted from the point of view of a mechanism in which nsp5–nsp6 cleavage may occur from a monomeric intermediate, and dimer formation restricts this cleavage.

60 APPLIED LIFE SCIENCES↗

Assessing and Promoting Functional Resilience in Flight Crews During Exploration Missions

NASA plans to send humans to Mars in about 20 years. The NASA Human Research Program supports research to mitigate the major risks to human health and performance on extended missions. However, there will undoubtedly be unforeseen events on any mission of this nature - thus mitigation of known risks alone is not sufficient to ensure optimal crew health and performance. Research should be directed not only to mitigating known risks, but also to providing crews with the tools to assess and enhance resilience, as a group and individually. We can draw on ideas from complexity theory and network theory to assess crew and individual resilience. The entire crew or the individual crewmember can be viewed as a complex system that is composed of subsystems (individual crewmembers or physiological subsystems), and the interactions between subsystems are of crucial importance for overall health and performance. An understanding of the structure of the interactions can provide important information even in the absence of complete information on the component subsystems. This is critical in human spaceflight, since insufficient flight opportunities exist to elucidate the details of each subsystem. Enabled by recent advances in noninvasive measurement of physiological and behavioral parameters, subsystem monitoring can be implemented within a mission and also during preflight training to establish baseline values and ranges. Coupled with appropriate mathematical modeling, this can provide real-time assessment of health and function, and detect early indications of imminent breakdown. Since the interconnected web of physiological systems (and crewmembers) can be interpreted as a network in mathematical terms, we can draw on recent work that relates the structure of such networks to their resilience (ability to self-organize in the face of perturbation). There are many parameters and interactions to choose from. Normal variability is an established characteristic of a healthy physiological response. Healthy coupling has been investigated less extensively, but there are cases in which too tight or too loose coupling can be problematic. This might be in inter-individual behaviors, such as sleep cycles, coordination of work and meal times, and coupled motions during communication. Less apparent are couplings of physiological systems, nevertheless examples abound of coupled systems which might be monitored: cardio-respiratory rhythms; circadian rhythms, body temperature, and sleep; stress markers and cognition, sleep, and performance; profiles of biochemical markers related to immune function and nutritional status; sensorimotor aspects such as motion sickness, ataxia, reaction time, and manual control. Tools for resilience are then the means to measure and analyze these parameters, incorporate them into appropriate models of normal variability and interconnectedness, and recognize when parameters or their couplings are outside of normal limits. What to do when a problem is identified depends on its nature. Changes can be made to crew procedures, work pacing, interpersonal interactions, sleep cycles, meal timing and content, as guided by the model. Use and continued development of these methods could not only provide tools for resilience, but also meaningful autonomous work for the crew on an extended flight.

Shelhamer, Mark↗

Quantifying Impacts of Renewable Electricity Deployment on Air Quality and Human Health in Southeast Asia Based on Aims III Scenarios

Exposure to outdoor air pollution is the largest environmental risk factor for death and disease worldwide, associated with millions of cases of excess deaths (mortality) each year. Although there are many pollutants in the air that affect our health, the most important class of pollutants is fine particulate matter, PM 2.5 , which are airborne particles of diameter ≤2.5 micrometers (µm). These particles are small enough to deposit deep in the respiratory system where they can then enter the bloodstream, traveling and causing damage to other bodily systems. Exposure to outdoor (ambient) PM 2.5 has been found to be the most important environmental risk factor for mortality in Southeast Asia, associated with 130,000 - 320,000 excess deaths in Association of Southeast Asian Nations (ASEAN) member countries in 2019. Southeast Asia, especially its mega-cities, but also other areas, has some of the worst air quality in the world. Almost all human activity emits air pollutants. Fine particulate matter is both directly emitted and formed in the atmosphere through chemical reactions, the latter of which requires modeling to predict. Power generation is one of the major sources of air pollutants that lead to elevated concentrations of fine particulate matter, including in Southeast Asia. Fossil fuel combustion for power generation, especially coal but also diesel, is the main source of air pollutant emissions from power generation. While natural gas burns cleaner than coal or diesel, in the quantities combusted for power generation in Southeast Asia, it is also a significant emitter. This study augments the ASEAN Interconnection Masterplan Study III (AIMS III) by quantifying changes to air quality and human health that result from its renewable integration and transmission interconnection scenarios. Performing this analysis requires translation of the changes in projected generation from different power sector fuel sources in the AIMS III scenarios to changes in air pollutant emissions, developing what's known as an emissions inventory for each scenario and year evaluated. We then use for the first time a new global, reduced-complexity air quality model to transform the changes in emissions to changes in air pollutant concentration of the deadliest air pollutant for human health, fine particulate matter (or PM 2.5 ). The air quality model, Global InMAP, then utilizes the location of human population in ASEAN countries to calculate exposure to PM 2.5 concentration changes and translates that to estimates of excess mortality attributable to the AIMS III scenarios.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Harnessing Artificial Intelligence for Medical Diagnosis and Treatment During Space Exploration Missions

BACKGROUND The medical capabilities necessary for long-duration exploration missions (LDEMs) will differ tremendously from those currently available to crew medical officers (CMOs) on the International Space Station (ISS). Ground support will be more challenging due to distance-related communication delays and data transmission, and resource utilization must be optimized given limited ability for resupply. Clinical decision support systems (CDSSs) can help mitigate these limitations. The recent launch of generative artificial intelligence (AI) tools based upon large language models (LLM) support the creation of a smart assistant for onboard triage, diagnosis, and guided treatment of medical conditions during these missions. The Informing Mission Planning via Analysis of Complex Tradespaces (IMPACT) tool can help predict which clinical problems and outcomes are likely to occur for a design reference mission (DRM) and assist Medical Operations and systems engineering teams in creating a medical system that may optimally mitigate the predicted risks. The purpose of this study was to identify AI tools currently available or in development for the assistive diagnosis and care of medical conditions predicted for an extended duration Lunar mission. METHODS The 119 medical conditions currently built into the IMPACT suite were categorized into systems, and these diagnoses were used as keywords for our literature search. Using PubMed and Google Scholar, we performed a literature survey of AI tools applicable to these conditions. Article inclusion criteria included publication between the years 2017-2023, as the sentinel paper discussing the “selective attention” driving ChatGPT and other generative transformer models was published in June 2017. Where applicable, we reviewed only the top 1000 research articles (based on relevance) for each of the keywords/phrases. AI tools whose training sets were exclusive to a pediatric patient population were excluded. We also excluded any medical diagnostic tools (such as CT, MRI, mass spectrometry) or procedures (such as endoscopy, surgery) that are unlikely to be available during LDEMs due to mass and volume constraints, CMO knowledge, skills, and abilities, and/or inherent procedural risks. RESULTS Our survey highlighted several AI-driven tools for the triage, diagnosis, and management of those medical conditions highlighted by IMPACT. Selected publications for each medical condition were then screened for inclusion within ten systems-based categories including: general diagnostic tools (25), tools to diagnose and manage respiratory (40), dermatologic (34), neurologic (28), auditory and vestibular (30), ophthalmic (34), musculoskeletal (104), infection-associated (92), and gynecologic (19) conditions, as well as tools that could be deployed in the setting of trauma and emergency (34). CONCLUSIONS Numerous AI-driven tools were highlighted within this literature survey, ranging from chatbot assistants that triage knee pain to vision transformer models for diagnosis of ophthalmic conditions using ocular surface images captured with a mobile phone. Remaining challenges include optimizing connectivity and integration of existing and developing systems into the vehicles or habitats. Notably, findings from this survey could help guide the initial design of an all-encompassing, onboard medical AI assistant for use during future LDEMs.

R A Lacinski↗

Human Spaceflight Applications of Novel Miniature X-Ray Technologies

INTRODUCTION: Radiography (XR) has long been a cornerstone of terrestrial medical imaging, though it has not yet been used in the spaceflight environment. Medical systems for human spaceflight missions are constrained by mass, volume, and power, and until recently, XR systems have been considered too large and power-consuming for spaceflight diagnostic and therapeutic applications. However, the rise of commercial spaceflight and NASA’s refocused efforts on returning crews to the Moon for long-duration missions have introduced a higher degree of medical risk to human spaceflight and require a re-evaluation when optimizing medical system design. Over the last decade, XR devices have miniaturized while maintaining good diagnostic and therapeutic sensitivity and specificity, making new in-flight medical and non-medical XR applications a possibility. Initial research identified several medical conditions where miniature XR would be beneficial for the diagnosis and/or management of medical conditions arising in space, though a more in-depth analysis is required to identify whether XR may add value to the management of such conditions. With this presentation, we aim to introduce the potential utility of miniature XR, review prior work highlighting where XR may be beneficial, and evaluate how miniature XR may reduce medical risk in human spaceflight missions. METHODS: IMPACT (Informing Mission Planning via Analysis of Complex Tradespaces) is a risk assessment tool developed by NASA to advance exploration mission medical system design by quantitatively estimating mission medical risk. IMPACT v1.0 includes a novel evidence library baselined to exploration environments, an expanded list of 119 medical conditions, medical capabilities and resources critical for management of these medical conditions, and the ability for rapid and iterative analysis in the setting of modifiable design reference missions (DRMs). Our first analysis identified which of the 119 medical conditions XR had diagnostic or therapeutic utility for. Subject matter experts (SMEs) recorded which XR views would be performed under ideal terrestrial circumstances for diagnosis/management of each condition, as well as which views are pragmatic for spaceflight limitations. A second analysis utilized IMPACT to identify significant conditions that contribute greatest to medical risk during a notional long-duration Lunar orbit and Lunar surface DRM. Medical system risk estimates include loss of crew life (LOCL), need for return to definitive care (RTDC; medical evacuation), and an estimate of crew task time affected (TTA). Using a standardized semi-quantitative scoring methodology, a deeper evaluation of each of the most significant medical conditions was performed. Data from both of these separate analyses were used to hypothesize what ideal and pragmatic XR studies may impact clinical management of the most significant conditions predicted to lead to medical risk. RESULTS: Approximately 1/3 of the IMPACT conditions were identified as being more effectively or comprehensively assessed or treated with the addition of miniature XR technology. The resulting conditions benefitting diagnostically and therapeutically from XR are revealed, as well as the ideal and pragmatic XR views and medical procedures benefitting from XR. The conditions of clinical significance and those most contributing to risk are also displayed. Among the conditions that contribute greatest to LOCL, four conditions for which XR may improve the diagnosis and management of include: decompression sickness, traumatic shock, dental abscess, and respiratory failure. Among conditions that contributed to RTDC, the evaluation and management of wrist fracture is likely improved by XR. For conditions leading to crew TTA, evaluation and management of EVA shoulder injuries, upper and lower extremity strains, back strains, and EVA hand injuries are likely improved by XR. DISCUSSION: Miniature XR in spaceflight has the potential to improve the evaluation and management of a substantial portion of conditions that most contribute to medical risk. This presentation is an introduction to the possibilities miniature XR provides for future human spaceflight missions and subsequent presenters will expand on potential applications in more detail. LEARNING OBJECTIVES: 1) Understand the previous limitations of using radiography in the management of spaceflight medical conditions; 2) Evaluate the findings from the IMPACT tool analysis, which allows quantification of the benefit miniature XR could provide for managing high-risk medical conditions in long-duration lunar orbit and surface missions, focusing on improvements in crew health outcomes; 3) Analyze case studies where miniature XR technology could reduce the medical risks associated with spaceflight missions, specifically in diagnosing and managing conditions such as decompression sickness, traumatic shock, and EVA-related injuries.

A Anderson↗

Effect of salinity on the preservation of biomarkers in hypersaline microbial mat kerogens

Kerogen is the residue that remains after the minerals and organic compounds have been extracted from a rock using acid and organic solvents, respectively [1]. It is not only the largest organic carbon sink in the geological record but the best-preserved fraction due to its recalcitrance and ability to retain syngenetic source information during deposition [2]. Due to the complex, macromolecular, cross-linked polymeric structure of kerogen, it is difficult to analyse intact, often requiring breakdown into smaller subunits through thermal (pyrolysis) or chemical treatment (chemolysis) [3]. Saline and hypersaline environments host diverse microbial communities, which can trap and bind organic matrices such as cellular components (e.g., extracellular polymeric substances, cell wall, peptidoglycan, sheath material, etc.) with sediments, forming layered, laminated structures called microbial mats. Here we present depth profiles of two hypersaline cores through a microbial mat with differing total salinities. We looked at the composition of organic compounds released from kerogen during high temperature, hydrogen-assisted, pyrolysis to understand the effect of salinity on the composition and timing of their incorporation [4]. Field Site: The Exportadora del Sal S. A. (ESSA) saltern of Guerrero Negro (Baja California Sur, Mexico) lies within a typical sabhka environment adjacent to Laguna Ojo de Liebre. Note the spatial extent of the 13 major ponds of the ESSA system. The GN ponds thrive under well-monitored and stable conditions with steady state accretion and degradation of mat layers (around 0.5–1.4 cm per year). Organic mats typically attain up to 10 cm in thickness, depending on the location, which represents about 60 years of growth since these ponds were established. Sedimentation rate is rapid in these non-lithifying and non-mineralising mats, 1–1.5 cm per year. This environment is ideal for investigating in situ lipid preservation and diagenesis without the influence of constantly changing physical parameters. Methods: P4n5 and P5AB cores were collected as ~9 cm and 6.5 cm fresh cores, respectively, in June 2001 and September 2010, respectively from the ESSA saltern. The P4n5 core (9-9.1% salinity) was taken from Pond 4 near 5 and sub-divided into 10 layers. The P5AB core (11.2% salinity) was taken from Pond 5A near 5B and sub-divided into 8 layers. Lyophilised microbial mat powders were solvent-extracted using a modified Bligh-Dyer method and analysed by gas chromatography-mass spectrometry (GC-MS). Additionally, a subset of layers—layer 4 and layer 7—which represented active biomass and sediment-processed, respectively, were subjected to mild-acid methanolysis. The respective residues from conventional solvent extraction and acid methanolysis were loaded with a molybdenum sulfide catalyst and placed into a stainless-steel reactor. Samples were run on the hydropyrolysis set up (heated to 500 °C with 13-15 MPa of H2 pressure), extracted, and analysed by GC-MS. Results: Molecular profiles from the two ponds were significantly different and reflect the contributions of different photosynthetic and respiratory microbial communities to preserved organic matter. For example, the higher salinity P5AB core showed evidence of greater archaeal inputs (similarly observed in lab culture experiments [5]) as well as potential kerogen-bound carotenoids/carotenoid rearranged products or fragments. A hydrophobic emulsion formed during the acid methanolysis processing of layer 4 from both P4n5 and P5AB and layer 7 of P5AB. Hydropyrolysis of this hydrophobic residues released a greater abundance of polycyclic lipids relative to the pre-extracted control. Implications and Future Work: Catalytic hydropyrolysis of kerogen can rapidly generate abundant saturated pyrolysate products from the bound biomarker pool without altering the structures or stereochemistries of the products [6]. Chemical processing of solvent-extractable residues indicated that cellular matrices such as extracellular polymeric substances (EPS) may play a role in the sequestration of polycyclic lipid biomarkers such as steranes and hopanes. Their higher relative abundance compared to the pre-extracted control in the higher salinity layers and cores preliminarily aligns with this hypothesis, although further experiments are required to confirm this. It has been well-documented that EPS plays an important role in mineralisation, specifically carbonate formation, in microbial ecosystems. EPS can enhance calcium carbonate precipitation by providing diffusion-limited sites that create alkalinity gradients in response to microbial processes [7]. It has been experimentally demonstrated that salinity influences the total amount of EPS (both loosely- and tightly-bound) which increases with increasing salinity [8]. The higher salinity at Guerrero Negro switches the microbial population from filamentous Microcoleus to being dominated by Phormidium, Oscillatoria, and unicellular cyanobacteria. We demonstrated that lipid binding into kerogen via strong covalent linkages occurs at the very earliest stages of sedimentary diagenesis. We are currently investigating the influence of salinity on organic preservation through experimental and modelling approaches. Understanding how key biomarkers transform into preserved organic matter (i.e., from precursor biolipids to bound geolipids) in brine ecosystems will aid the search for organic biosignatures on other planetary bodies, especially Icy Moons and modern Mars.

hypersaline↗