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Angiotensin-(1-7) antagonist [D-Ala7-Ang-(1-7);A-779] attenuates post-suspension hypotension in Sprague-Dawley rats

Cardiovascular deconditioning manifested by reduction in mean arterial pressure (MAP) and cardioaccleration are usually observed in astronauts during standing postflight. The head-down tilt (HDT) rat model with "unloaded" hindlimbs has been extensively studied because some of the observed responses mimic observations made during exposure to microgravity. Angiotensin-(1-7) is a biologically active component of the renin-angiotensin system that acts to oppose the pressor and proliferative actions of Angiotensin II. It produces a hypotensive response by either stimulating production of vasodilator prostaglandins (i.e., prostacyclin), increasing nitric oxide or both. In the present study, we have evaluated the role of a specific inhibitor of Ang-(1-7), D-Ala7-Ang-(1-7)[A-779], as a countermeasure against post-suspension hypotension.

Hindlimb Suspension↗

Biological Research and Space Health Enabled by Machine Learning to Support Deep Space Missions

A key science goal of the NASA “Moon to Mars” campaign is to understand how biology responds to the Lunar, Martian, and deep space environments in order to advance fundamental knowledge, reduce risk, and support safe, productive human space missions. Through the powerful emerging approaches of artificial intelligence (AI) and machine learning (ML), a paradigm shift has begun in biomedical science and engineered astronaut health systems, to enable Earth independence and autonomy of mission operations. Here we present an overview of AI/ML architecture to support deep space mission goals, developed with leaders in the field. First, we focus on the fundamental biological research that supports our understanding of physiological responses to spaceflight, and we describe current efforts to support AI/ML research including data standardization and data engineering through maximally open and FAIR (findable, accessible, interoperable, reusable) databases and the generation of AI-ready datasets for reuse and analysis. We also discuss remote data management frameworks for research data as well as environmental and health data that are generated during deep space missions. We highlight several research projects that leverage data standardization and management for fundamental biological discovery to uncover the complex effects of space travel on living systems. Next, we provide an overview of cutting-edge AI/ML approaches that can be integrated to support remote monitoring and analysis during deep space missions, including generative models and large language models to learn the underlying biomedical patterns and predict outcomes or answer questions during off world medical scenarios. We also describe current AI/ML methods to support this research and monitoring through automated cloud-based labs which enable limited human intervention and closed-loop experimentation in remote settings. These labs could support mission autonomy by analyzing environmental data streams, and would be facilitated through in situ analytics capabilities to avoid sending large raw data files through low bandwidth communications. Finally, in the context of deep space missions with limited communications or access to medical advice from Earth, we describe a solution for integrated, real-time mission biomonitoring across hierarchical levels from continuous environmental monitoring, to wearables and point-of-care devices, to molecular and physiological monitoring. We introduce a precision space health system that will ensure that the future of space health is predictive, preventative, participatory and personalized.

artificial intelligence↗

The RBE-LET relationship for rodent intestinal crypt cell survival, testes weight loss, and multicellular spheroid cell survival after heavy-ion irradiation

This report presents data for survival of mouse intestinal crypt cells, mouse testes weight loss as an indicator of survival of spermatogonial stem cells, and survival of rat 9L spheroid cells after irradiation in the plateau region of unmodified particle beams ranging in mass from 4He to 139La. The LET values range from 1.6 to 953 keV/microns. These studies examine the RBE-LET relationship for two normal tissues and for an in vitro tissue model, multicellular spheroids. When the RBE values are plotted as a function of LET, the resulting curve is characterized by a region in which RBE increases with LET, a peak RBE at an LET value of 100 keV/microns, and a region of decreasing RBE at LETs greater than 100 keV/microns. Inactivation cross sections (sigma) for these three biological systems have been calculated from the exponential terminal slope of the dose-response relationship for each ion. For this determination the dose is expressed as particle fluence and the parameter sigma indicates effect per particle. A plot of sigma versus LET shows that the curve for testes weight loss is shifted to the left, indicating greater radiosensitivity at lower LETs than for crypt cell and spheroid cell survival. The curves for cross section versus LET for all three model systems show similar characteristics with a relatively linear portion below 100 keV/microns and a region of lessened slope in the LET range above 100 keV/microns for testes and spheroids. The data indicate that the effectiveness per particle increases as a function of LET and, to a limited extent, Z, at LET values greater than 100 keV/microns. Previously published results for spread Bragg peaks are also summarized, and they suggest that RBE is dependent on both the LET and the Z of the particle.

Non-NASA Center↗

Theoretical evidence that root penetration ability interacts with soil compaction regimes to affect nitrate capture

Abstract Background and Aims Although root penetration of strong soils has been intensively studied at the scale of individual root axes, interactions between soil physical properties and soil foraging by whole plants are less clear. Here we investigate how variation in the penetration ability of distinct root classes and bulk density profiles common to real-world soils interact to affect soil foraging strategies. Methods We utilize the functional–structural plant model ‘OpenSimRoot’ to simulate the growth of maize (Zea mays) root systems with variable penetration ability of axial and lateral roots in soils with (1) uniform bulk density, (2) plow pans and (3) increasing bulk density with depth. We also modify the availability and leaching of nitrate to uncover reciprocal interactions between these factors and the capture of mobile resources. Key Results Soils with plow pans and bulk density gradients affected overall size, distribution and carbon costs of the root system. Soils with high bulk density at depth impeded rooting depth and reduced leaching of nitrate, thereby improving the coincidence of nitrogen and root length. While increasing penetration ability of either axial or lateral root classes produced root systems of comparable net length, improved penetration of axial roots increased allocation of root length in deeper soil, thereby amplifying N acquisition and shoot biomass. Although enhanced penetration ability of both root classes was associated with greater root system carbon costs, the benefit to plant fitness from improved soil exploration and resource capture offset these. Conclusions While lateral roots comprise the bulk of root length, axial roots function as a scaffold determining the distribution of these laterals. In soils with high soil strength and leaching, root systems with enhanced penetration ability of axial roots have greater distribution of root length at depth, thereby improving capture of mobile resources.

59 BASIC BIOLOGICAL SCIENCES↗

Using Complex Probability Amplitudes to Simulate Solute Transport in Composite Porous Media

Probability amplitudes are fundamental to quantum mechanics and offer robust descriptions of complicated systems, which have allowed physicists to explain behaviors inaccessible to classical physics. This article ponders how some of the same conceptual underpinnings of the mathematics used for modeling quantum systems might be applied to subsurface water resources problems and speculates how these tools could facilitate applications on quantum computers. A probability amplitude-based model for describing advective-dispersive transport in porous media using linear operators is investigated. The proposed complex valued model decomposes spreading into two “sub-continuum partial dispersion” coefficients, and this recovers classical spreading when the sum of these coefficients is the Fickian dispersion coefficient. However, the probability amplitudes have a manyto-one relationship to a probability distribution, so it embeds a level of heterogeneity into seemingly equivalent functions. Two propagators with different sub-continuum coefficients may have the same macroscopic behavior when either is considered in isolation, but when they act on the other the system’s behavior changes. Additionally, differences in the amplitudes cause a reduction in spreading as velocity correlations are disrupted, despite both propagators having identical dispersion coefficients, and this cannot be achieved using classical methods without changing the dispersion coefficient. The main point is that these amplitude-based models offer a way to embed information about the system into the propagators, instead of just “averaging it out” when making an upscaled model.

54 ENVIRONMENTAL SCIENCES↗

Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures

Bacterial mRNA sequencing is inefficient due to the abundance of ribosomal RNA that is challenging to deplete. While commercial kits target rRNA from common bacterial species, they are frequently inefficient when applied to divergent species, including those from environmental isolates. Similarly, other methods typically employ large probe sets that tile the entire length of rRNAs; however, such approaches are infeasible when applied to many species. Therefore, we present EMBR-seq+, which requires fewer than 10 oligonucleotides per rRNA by combining rRNA blocking primers with RNase H-mediated depletion to achieve rRNA removal efficiencies of up to 99% in diverse bacterial species. Furthermore, in more complex microbial co-cultures between Fibrobacter succinogenes strain UWB7 and anaerobic fungi, EMBR-seq+ depleted both bacterial and fungal rRNA, with a fourfold improvement in bacterial rRNA depletion compared with a commercial kit, thereby demonstrating that the method can be applied to non-model microbial mixtures. Notably, for microbes with unknown rRNA sequences, EMBR-seq+ enables rapid iterations in probe design without requiring to start experiments from total RNA. Finally, efficient depletion of rRNA enabled systematic quantification of the reprogramming of the bacterial transcriptome when cultured in the presence of the anaerobic fungi Anaeromyces robustus or Caecomyces churrovis. We observed that F. succinogenes strain UWB7 downregulated several lignocellulose-degrading carbohydrate-active enzymes in the presence of anaerobic gut fungi, suggesting close interactions between two cellulolytic species that specialize in different aspects of biomass breakdown. Thus, EMBR-seq+ enables efficient, cost-effective, and rapid quantification of the transcriptome to gain insights into non-model microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗

Efficient genetic code expansion tools enable in vivo study of lysine acetylation in non-model bacteria

Recent proteomic advancements have revealed widespread Nε-lysine acetylation in pathways governing pathogenicity, metabolism, and antibiotic resistance in bacteria. The spontaneous, non-specific nature of this modification in prokaryotes obscures its biological role, necessitating prokaryotic specific in vivo interrogation systems. Genetic Code Expansion (GCE) offers a powerful method to investigate the roles and regulation dynamics of acetyl-lysine in vivo with the precise incorporation of a suite of non-canonical amino acids, including acetyl-lysine analogs. However, its use has been largely restricted to E. coli strains due to challenges associated with implementation and optimization of the technology in more diverse bacterial strains. Here, we present a bacterial host-agnostic, readily optimizable GCE platform designed to site-specifically incorporate non-canonical amino acids into target proteins within living bacteria. We further demonstrate the versatility of this technology by showcasing, for the first time, the successful incorporation of acetyl-lysine in a non- E. coli bacterium.

59 BASIC BIOLOGICAL SCIENCES↗

In Vitro Disease Model of Microgravity Conditioning on Human Energy Metabolism

NASA and its partners are committed to introducing appropriate new technology to enable learning and living safely beyond the Earth for extended periods of time in a sustainable and possibly indefinite manner. In the responsible acquisition of that goal, life sciences is tasked to tune and advance current medical technology to prepare for human health and wellness in the space environment. The space environment affects the condition and function of biological systems from organ level function to shape of individual organelles. The objective of this paper is to study the effect of microgravity on kinetics of drug metabolism. This fundamental characterization is meaningful to (1) scientific understanding of the response of biology to microgravity and (2) clinical dosing requirements and pharmacological thresholds during long term manned space exploration. Metabolism kinetics of the anti-nausea drug promethazine (PMZ) were determined by an in vitro ground model of 3-dimensional aggregates of human hepatocytes conditioned to weightlessness using a rotating wall bioreactor. The authors observed up-regulated PMZ conversion in model microgravity conditions and attribute this to effect to model microgravity conditioning acting on metabolic mechanisms of the cells. Further work is necessary to determine which particular cellular mechanisms are governing the experimental observations, but the authors conclude kinetics of drug metabolism are responsive to gravitational fields and further study of this sensitivity would improve dosing of pharmaceuticals to persons exposed to a microgravity environment.

Snyder, Jessica↗

Detection of "noisy" chaos in a time series

Time series from biological system often displays fluctuations in the measured variables. Much effort has been directed at determining whether this variability reflects deterministic chaos, or whether it is merely "noise". The output from most biological systems is probably the result of both the internal dynamics of the systems, and the input to the system from the surroundings. This implies that the system should be viewed as a mixed system with both stochastic and deterministic components. We present a method that appears to be useful in deciding whether determinism is present in a time series, and if this determinism has chaotic attributes. The method relies on fitting a nonlinear autoregressive model to the time series followed by an estimation of the characteristic exponents of the model over the observed probability distribution of states for the system. The method is tested by computer simulations, and applied to heart rate variability data.

Non-NASA Center↗

Spatial modeling algorithms for reactions and transport in biological cells

Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate, particularly in realistic cell geometries. Here we present Spatial Modeling Algorithms for Reactions and Transport (SMART), a software package that takes in high-level user specifications about cell signaling networks and then assembles and solves the associated mathematical systems. SMART uses state-of-the-art finite element analysis, via the FEniCS Project software, to efficiently and accurately resolve cell signaling events over discretized cellular and subcellular geometries. We demonstrate its application to several different biological systems, including yes-associated protein (YAP)/PDZ-binding motif (TAZ) mechanotransduction, calcium signaling in neurons and cardiomyocytes, and ATP generation in mitochondria. Throughout, we utilize experimentally derived realistic cellular geometries represented by well-conditioned tetrahedral meshes. These scenarios demonstrate the applicability, flexibility, accuracy and efficiency of SMART across a range of temporal and spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗

Time of Emergence and Large Ensemble Intercomparison for Ocean Biogeochemical Trends

Anthropogenically forced changes in ocean biogeochemistry are underway and critical for the ocean carbon sink and marine habitat. Detecting such changes in ocean biogeochemistry will require quantification of the magnitude of the change (anthropogenic signal) and the natural variability inherent to the climate system (noise). Here we use Large Ensemble (LE) experiments from four Earth system models (ESMs) with multiple emissions scenarios to estimate Time of Emergence (ToE) and partition projection uncertainty for anthropogenic signals in five biogeochemically important upper-ocean variables. We find ToEs are robust across ESMs for sea surface temperature and the invasion of anthropogenic carbon; emergence time scales are 20–30 yr. For the biological carbon pump, and sea surface chlorophyll and salinity, emergence time scales are longer (50+ yr), less robust across the ESMs, and more sensitive to the forcing scenario considered. We find internal variability uncertainty, and model differences in the internal variability uncertainty, can be consequential sources of uncertainty for projecting regional changes in ocean biogeochemistry over the coming decades. In combining structural, scenario, and internal variability uncertainty, this study represents the most comprehensive characterization of biogeochemical emergence time scales and uncertainty to date. Our findings delineate critical spatial and duration requirements for marine observing systems to robustly detect anthropogenic change.

54 ENVIRONMENTAL SCIENCES↗

Modeling Global Carbon Costs of Plant Nitrogen and Phosphorus Acquisition

Abstract Most Earth system models (ESMs) do not explicitly represent the carbon (C) costs of plant nutrient acquisition, which leads to uncertainty in predictions of the current and future constraints to the land C sink. We integrate a plant productivity‐optimizing nitrogen (N) and phosphorus (P) acquisition model (fixation & uptake of nutrients, FUN) into the energy exascale Earth system (E3SM) land model (ELM). Global plant N and P uptake are dynamically simulated by ELM‐FUN based on the C costs of nutrient acquisition from mycorrhizae, direct root uptake, retranslocation from senescing leaves, and biological N fixation. We benchmarked ELM‐FUN with three classes of products: ILAMB, a remotely sensed nutrient limitation product, and CMIP6 models; we found significant improvements in C cycle variables, although the lack of more observed nutrient data prevents a comprehensive level of benchmarking. Overall, we found N and P co‐limitation for 80% of land area, with the remaining 20% being either predominantly N or P limited. Globally, the new model predicts that plants invested 4.1 Pg C yr −1 to acquire 841.8 Tg N yr −1 and 48.1 Tg P yr −1 (1994–2005), leading to significant downregulation of global net primary production (NPP). Global NPP is reduced by 20% with C costs of N and 50% with C costs of NP. Modeled and observed nutrient limitation agreement increases when N and P are considered together ( r 2 from 0.73 to 0.83).

54 ENVIRONMENTAL SCIENCES↗

Gaussian processes meet NeuralODEs: a Bayesian framework for learning the dynamics of partially observed systems from scarce and noisy data

We present a machine learning framework (GP-NODE) for Bayesian model discovery from partial, noisy and irregular observations of nonlinear dynamical systems. The proposed method takes advantage of differentiable programming to propagate gradient information through ordinary differential equation solvers and perform Bayesian inference with respect to unknown model parameters using Hamiltonian Monte Carlo sampling and Gaussian Process priors over the observed system states. This allows us to exploit temporal correlations in the observed data, and efficiently infer posterior distributions over plausible models with quantified uncertainty. The use of the Finnish Horseshoe as a sparsity-promoting prior for free model parameters also enables the discovery of parsimonious representations for the latent dynamics. A series of numerical studies is presented to demonstrate the effectiveness of the proposed GP-NODE method including predator–prey systems, systems biology and a 50-dimensional human motion dynamical system. This article is part of the theme issue ‘Data-driven prediction in dynamical systems’.

Science & Technology - Other Topics↗

Systems Engineering of Rhodococcus opacus to Enable Production of Drop-in Fuels from Lignocellulose

Production of drop-in fuels from lignocellulose using Rhodococcus opacus PD630 (hereafter R. opacus) is a challenging goal. During the grant period we have pushed the field forward significantly in several areas of research. Towards the end goal of accelerating the adoption of R. opacus in biofuel production, during the grant period we have expanded the phenotypic characterization of R. opacus grown in single aromatic (model lignocellulosic) compounds or their mixtures, modeling the growth conditions in lignocellulosic biomass. Harnessing the power of adaptive evolution, we produced evolved R. opacus isolates with superior lignin valorization capabilities and identified differentially expressed genes and pathways after adaptation. We used next generation multi-omic techniques such as genomic, transcriptomic, and metabolomic analyses, to identify the catabolic pathways used by R. opacus to degrade aromatic compounds and funnel these degradation products into central metabolism, as well as the aromatic transport genes required for increased tolerance and utilization. Taking this information one step further, we identified endogenous transcription factors and regulatory mechanisms important for degradation of five model aromatic compounds. To accurately estimate R. opacus growth and consumption on model lignin compounds we pioneered the use of novel extraction procedures prior to GC-MS analysis. Alongside 13 C-metabolic flux analysis, we have elucidated the metabolic routes preferred by Rhodococcus opacus during aromatic compound degradation. Finally, we used in tandem lipidomics and high-resolution mass spectrometry to identify the modulation of mycolic acids and phospholipid membrane composition modification as a strategy for aromatic tolerance in R. opacus. Being a non-model organism, R. opacus lacks the breadth of tools and technical foundation which drive biofuel research in more well-understood microbes such as Escherichia coli. To reduce this burden for use, we designed and produced new tools for genomic manipulation and engineering in R. opacus. These engineering breakthroughs support efficient genomic editing, enabling gene overexpression, repression, and genetic alteration. Using these tools, we have generated synthetically engineered strains with increased lipogenesis and growth, both positive traits required for increased lignin valorization. Optimizing engineered strains for biofuel production from lignocellulose requires extremely sophisticated synthetic rewiring of metabolism. To facilitate systems-level reorganization of metabolism in R. opacus, we created a genome-scale model that accurately predicts metabolic flux and growth rates on the aromatic compound phenol. Lignin requires extensive pre-treatment before biological degradation by R. opacus. Towards an eventual goal of degrading real-world lignin, we developed new depolymerization processes to generate lignin breakdown products (LBP). We optimized LBP storage and composition analysis techniques, enabling accurate prediction of specific LBP compound integration into cell wall components. Overall, through the work funded by this grant we generated 20 manuscripts (17 published, 3 in review/preparation), methods for increased accuracy in metabolomics of aromatic compounds, multiple genetic tools for altering the R. opacus genome, genome scale models for predicting flux through metabolic pathways, as well as multi-omic data for community use. The work funded by this grant has increased the knowledge of aromatic degradation in bacteria and advanced our efforts to optimize R. opacus for lignin valorization.

09 BIOMASS FUELS↗

Shock waves and shock tubes; Proceedings of the Fifteenth International Symposium, Berkeley, CA, July 28-August 2, 1985

A detailed survey is presented of shock tube experiments, theoretical developments, and applications being carried out worldwide. The discussions explore shock tube physics and the related chemical, physical and biological science and technology. Extensive attention is devoted to shock wave phenomena in dusty gases and other multiphase and heterogeneous systems, including chemically reactive mixtures. Consideration is given to techniques for measuring, visualizing and theoretically modeling flowfield, shock wave and rarefaction wave characteristics. Numerical modeling is explored in terms of the application of computational fluid dynamics techniques to describing flowfields in shock tubes. Shock interactions and propagation, in both solids, fluids, gases and mixed media are investigated, along with the behavior of shocks in condensed matter. Finally, chemical reactions that are initiated as the result of passage of a shock wave are discussed, together with methods of controlling the evolution of laminar separated flows at concave corners on advanced reentry vehicles.

Bershader, D.↗

Calculation of Heavy Ion Inactivation and Mutation Rates in Radial Dose Model of Track Structure

In the track structure model, the inactivation cross section is found by summing an inactivation probability over all impact parameters from the ion to the sensitive sites within the cell nucleus. The inactivation probability is evaluated by using the dose response of the system to gamma rays and the radial dose of the ions and may be equal to unity at small impact parameters. We apply the track structure model to recent data with heavy ion beams irradiating biological samples of E. Coli, B. Subtilis spores, and Chinese hamster (V79) cells. Heavy ions have observed cross sections for inactivation that approach and sometimes exceed the geometric size of the cell nucleus. We show how the effects of inactivation may be taken into account in the evaluation of the mutation cross sections in the track structure model through correlation of sites for gene mutation and cell inactivation. The model is fit to available data for HPRT (hypoxanthine guanine phosphoribosyl transferase) mutations in V79 cells, and good agreement is found. Calculations show the high probability for mutation by relativistic ions due to the radial extension of ions track from delta rays. The effects of inactivation on mutation rates make it very unlikely that a single parameter such as LET (linear energy transfer) can be used to specify radiation quality for heavy ion bombardment.

Cucinotta, Francis A.↗

Radiation Effects: Core Project

The risks to personnel in space from the naturally occurring radiations are generally considered to be one of the most serious limitations to human space missions, as noted in two recent reports of the National Research Council/National Academy of Sciences. The Core Project of the Radiation Effects Team for the National Space Biomedical Research Institute is the consequences of radiations in space in order to develop countermeasure, both physical and pharmaceutical, to reduce the risks of cancer and other diseases associated with such exposures. During interplanetary missions, personnel in space will be exposed to galactic cosmic rays, including high-energy protons and energetic ions with atomic masses of iron or higher. In addition, solar events will produce radiation fields of high intensity for short but irregular durations. The level of intensity of these radiations is considerably higher than that on Earth's surface, and the biological risks to astronauts is consequently increased, including increased risks of carcinogenesis and other diseases. This group is examining the risk of cancers resulting from low-dose, low-dose rate exposures of model systems to photons, protons, and iron by using ground-based accelerators which are capable of producing beams of protons, iron, and other heavy ions at energies comparable to those encountered in space. They have begun the first series of experiments using a 1-GeV iron beam at the Brookhaven National Laboratory and 250-MeV protons at Loma Linda University Medical Center's proton synchrotron facility. As part of these studies, this group will be investigating the potential for the pharmaceutical, Tamoxifen, to reduce the risk of breast cancer in astronauts exposed to the level of doses and particle types expected in space. Theoretical studies are being carried out in a collaboration between scientists at NASA's Johnson Space Center and Johns Hopkins University in parallel with the experimental program have provided methods and predictions which are being used to assess the levels of risks to be encountered and to evaluate appropriate strategies for countermeasures. Although the work in this project is primarily directed toward problems associated with space travel, the problem of protracted exposures to low-levels of radiation is one of national interest in our energy and defense programs, and the results may suggest new paradigms for addressing such risks.

Dicello, John F.↗

A Unified Data Infrastructure for Biological and Environmental Research: A Report from the BER Advisory Committee

The Biological and Environmental Research (BER) program within the U.S. Department of Energy (DOE) Office of Science supports large-scale data generation efforts across its two divisions: Biological Systems Science and Earth and Environmental Systems Sciences. These efforts include user facilities in atmospheric radiation measurements, genomics, metabolomics, proteomics, compute, and imaging. In addition, BER supports the development of plant-based fuels; research in biosystems design, environmental microbiomes, and atmospheric systems; energy flux monitoring; climate-based ecosystem experiments; pathogen biopreparedness; and modeling of climate, urban interfaces, and interactions between people and energy resources. For data access, BER supports community data services at its user facilities, along with specialized data initiatives for Earth and environmental science, climate modeling, genomic and microbial analysis, and multisector dynamics modeling.

54 ENVIRONMENTAL SCIENCES↗