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At least 721 records · Page 40

Does Collection Time Bias the Ecology of Cleanroom Air Samples?

Microbial monitoring of astromaterials collections has taken on increased importance with the return of biologically sensitive samples from the asteroids Ryugu and Bennu and the initiation of the Mars Sample Return Program. Terrestrial bacteria and fungi can alter the mineralogy and organic composition of our collections causing irreversible contamination of pristine samples and increasing the risk of false positives for life detection measurements. NASA has conducted routine microbial monitoring of its existing collections since 20181. Initial monitoring focused on surface samples collected with foam swabs. Although, airborne microbiology is often decoupled from surface microbiology in the built environment2 culture-based air sampling techniques like impactors were not compliant with existing contamination control requirements. Bringing organic rich media, gelatin or liquids into curation cleanrooms presents an unacceptable risk to pristine samples. In 2022 NASA purchased a materials complaint air sampler and began collecting air samples from the cleanrooms in addition to surface samples3. The new instrument uses an electret filter to collect samples that are suitable for cultivating organisms or for direct DNA sequencing. Preliminary DNA sequencing results appeared to indicate that longer sampling times biased the microbial community in favor of hearty, spore-forming bacteria3. We present the results of a study comparing overnight sampling (17 hours) to short (1 hour) sampling of unoccupied curation cleanrooms. The results will help us optimize our monitoring protocols and develop a more detailed inventory of the ecology of astromaterials curation cleanrooms. Methods: We analyzed 72 paired air samples from six different cleanrooms including the meteorite processing lab (ISO 7 equivalent, 16 samples), the lunar lab (ISO 6 equivalent, 10 samples), the stardust lab (ISO 5 equivalent 14 samples), the OSIRIS-REx lab (ISO 5 equivalent, 12 samples), the Hayabusa2 lab (ISO 5 equivalent, 14 samples), and the Genesis lab (ISO 4 equivalent, 6 samples). All the samples were collected with an InnovaPrep Bobcat air sampler operating at a sampling rate of 200 L/min. The sampler operates for 5 minutes out of every 20 minute period. Half of the samples were collected by filtering 3,000L (15 min. of active sampling) of air across an electret filter for one hour. The rest of the samples were collected by filtering approximately 51,000 L air across the filter overnight (~17 hours, 255 min. of active sampling). Cells were eluted from the filter using 6-7 ml of pressurized 0.15% tween 20 in PBS (phosphate buffered saline). This liquid was used to cultivate bacteria according to previously published methods1,4,5 and for DNA extraction and next generation sequencing. DNA was extracted with a Qiagen MagAttract PowerMicrobiome kit6. To identify bacteria and archaea, the 16S rRNA gene was amplified using Earth Microbiome primers for the V4 region 7. The amplified DNA was sequenced on an Illumina MiSeq using a V3 reagent kit. The resulting sequences were processed using DADA2 and QIIME2 as implemented on the EDGE bioinformatics platform8–10. Results: Only two of the 72 samples had no amplifiable DNA. Amplified DNA concentrations ranged from 2.67 – 0.272 ng/µl. The median concentration of amplified DNA for the 1 hour samples was 0.770 ± 0.368 ng/µl. The median concentration of amplified DNA for the overnight samples was 0.877 ± 0.434 ng/µl. On average the overnight samples had slightly more sequences (58,960 vs. 59,456) and ASV’s (amplicon sequence variants) (60 vs 64.5) than the one hour samples, but these differences are not statistically significant. The most abundant ASV in every sample mapped to the genus Cupravidus. ASV’s mapping to the genuses Bacillus, Schlegelella, Thermus, and Staphylococcus were also common. Discussion and Future Work: Alpha diversity statistics like Shannon Entropy and Faith Phylogenetic Diversity are used to describe the diversity of organisms in a single sample. If a longer sampling time was biasing the data, we would expect to see a change in these diversity statistics vs. sample time. However, we did not observe this in our data. The median Shannon entropy was slightly higher for the overnight samples (3.773 vs 3.611) as was the Faith Phylogenetic Diversity (4.042 vs 3.596), but both values were within a standard deviation of each other for the two sampling times (Fig. 1). It is unlikely, that the longer sampling time is introducing bias into our data. We do observe a significant decrease in diversity when comparing the air samples by lab. The Genesis lab (ISO 4 equivalent) has a lower median number of ASV’s (45.5) than the other labs (62). Median values for Shannon Entropy (3.717 vs. 3.430) and Faith Phylogenetic Diversity (3.796 vs. 3.548) are also lower for Genesis, but those values are with one standard deviation of each other for the different sampling times. This is consistent with previous culture-based results suggesting that the environment in cleanrooms tends to select for a core group of organisms capable of surviving under dry, low nutrient, conditions. The presence of the ASV’s mapping to Cupravidus and Thermus in our sequencing blanks and controls suggests that several of the most common organisms in our samples represent contaminants from the reagents used to perform the DNA extractions and sequencing. Further work is needed to identify these contaminants, remove them from our data and recalculate the diversity statistics. This is a systematic error. Therefore, we do not expect removing the sequencing contaminants to change our conclusions. Longer air sample collection times appear to result in slightly higher diversity and do not bias the results towards “hardy” bacteria like spore-formers. Based on these preliminary results we conclude that sampling at least 3,000 liters of air is sufficient to capture the microbial diversity of cleanrooms, and that air samples can also be collected overnight without negatively impacting diversity. These results allow us to be flexible when designing microbial monitoring plans so that they do not interfere with routine lab activity. References: 1. Regberg, A. B. et al. 49th Lunar and Planetary Science Conference (2018). 2. The United States Pharmacopeial Convention. USP General Chapter <1116> (2013). 3. Regberg, A. B., et al. 54th Lunar and Planetary Science Conference (2023). 4. Regberg, A. B. et al. 53rd Lunar and Planetary Science Conference ( 2022). 5. Davis, R. E.,et al. 50th Lunar and Planetary Science Conference (2019). 6. Qiagen. MagAttract® PowerMicrobiome® DNA/RNA EP Kit Handbook. (2018). 7. Walters, W. et al. mSystems 1, (2015). 8. Callahan, B. J. et al. Nat. Methods 13, 581–583 (2016). 9. Hall, M. & Beiko, R. G. Microbiome Analysis: Methods and Protocols113–129 (Springer, 2018). 10. Philipson, C. et al. Bio-Protoc. 7, e2622 (2017).

A. B. Regberg↗

Coordinated Analysis of Phosphates in Samples From Asteroid (101955) Bennu

Asteroid (101955) Bennu is a B-type asteroid and a prime candidate for investigating the remnants of planet formation and enhancing our understanding of potential sources of crucial bio-essential elements for the early Earth. Remote observations of the surface of Bennu unveiled a terrain of boulders primarily composed of hydrated phyllosilicates, organic molecules, and carbonates. The hydrated nature of Bennu, the abundance of carbonates, and the presence of cm-scale carbonate veins provide clues to the nature of the building blocks of Bennu’s parent body and to its complex geological history. Here we present the first mineralogical, chemical, and isotopic results of analysis of phosphates in samples returned from Bennu by NASA’s OSIRIS-REx mission. We seek to test the hypothesis that heating of Bennu’s parent asteroid resulted in hydrothermal alteration in which melted ice reacted with the initial constituents.

J. J. Barnes↗

Spectral Correlation in MODIS Water-Leaving Reflectance Retrieval Uncertainty

Spectral remote sensing reflectance, Rrs(λ) (sr−1), is the fundamental quantity used to derive a host of bio-optical and biogeochemical properties of the water column from satellite ocean color measurements. Estimation of uncertainty in those derived geophysical products is therefore dependent on knowledge of the uncertainty in satellite-retrieved R rs . Furthermore, since the associated algorithms require R rs at multiple spectral bands, the spectral (i.e., band-to-band)error covariance in R rs is needed to accurately estimate the uncertainty in those derived properties. This study establishes a derivative-based approach for propagating instrument random noise, instrument systematic uncertainty, and forward model uncertainty into R rs as retrieved using NASA’s multiple-scattering epsilon (MSEPS) atmospheric correction algorithm, to generate pixel-level error covariance in R rs . The approach is applied to measurements from Moderate Resolution Imaging Spectroradiometer (MODIS) on the Aqua satellite and verified using Monte Carlo (MC) analysis. We also make use of this full spectral error covariance in R rs to calculate uncertainty in phytoplankton pigment chlorophyll-a concentration (chl a , mg/m 3 ) and diffuse attenuation coefficient of downwelling irradiance at 490 nm (K d (490), m -1 ). Accounting for the error covariance in R rs generally reduces the estimated relative uncertainty in chl a by ∼1-2% (absolute value) in waters with chl a < 0.25 mg/m 3 where the color index (CI) algorithm is used. The reduction is ∼5-10% in waters with chl a > 0.35 mg/m 3 where the blue-green ratio (OCX) algorithm is used. Such reduction can be higher than 30% in some regions. For K d (490), the reduction by error covariance is generally ∼2%, but can be higher than 20% in some regions. The error covariance in R rs is further verified through forward-calculating chl a from MODIS-retrieved and in situ R rs and comparing estimated uncertainty with observed differences. An 8-day global composite of propagated uncertainty shows that the goal of 35% uncertainty in chl a can be achieved over deep ocean waters (chl a ≤ 0.1 mg/m3). While the derivative-based approach generates reasonable error covariance in R rs some assumptions should be updated as our knowledge improves. These include the inter-band error correlation in top-of-atmosphere reflectance, and uncertainties in the calibration of MODIS 869 nm band, in ancillary data, and in the in situ data used for system vicarious calibration.

Ocean color↗

Retrieval-Augmented Generation and LLM Agents for Biomimicry Design Solutions

We present BIDARA, a Bio-Inspired Design And Research Assistant, to address the complexity of biomimicry – the practice of designing modern-day engineering solutions inspired by biological phenomena. Large Language Models (LLMs) have been shown to act as sufficient general purpose task solvers, but they often hallucinate and fail in regimes that require domain-specific and up-to-date knowledge. We integrate Retrieval-Augmented Generation (RAG) and Reasoning-and-Action agents to aid LLMs in avoiding hallucination and utilizing updated knowledge during generation of biomimetic design solutions. We find that incorporating RAG increases the feasibility of the design solutions in both prompting and agent settings, and we use these findings to guide our ongoing work. To the extent of our knowledge, this is the first work that integrates and evaluates Retrieval-Augmented Generation within LLM-generated biomimetic design solutions.

biomimicry↗

Retrieval-Augmented Generation and LLM Agents for Biomimicry Design Solutions

We present BIDARA, a Bio-Inspired Design And Research Assistant, to address the complexity of biomimicry – the practice of designing modern-day engineering solutions inspired by biological phenomena. Large Language Models (LLMs) have been shown to act as sufficient general purpose task solvers, but they often hallucinate and fail in regimes that require domain-specific and up-to-date knowledge. We integrate Retrieval-Augmented Generation (RAG) and Reasoning-and-Action agents to aid LLMs in avoiding hallucination and utilizing updated knowledge during generation of biomimetic design solutions. We find that incorporating RAG increases the feasibility of the design solutions in both prompting and agent settings, and we use these findings to guide our ongoing work. To the extent of our knowledge, this is the first work that integrates and evaluates Retrieval-Augmented Generation within LLM-generated biomimetic design solutions.

biomimicry↗

Emulating Nature: The Future of Sustainable Design with BIDARA

BIDARA (Bio-inspired Design and Research Assistant) is a GPT-4o chatbot that was instructed to help scientists and engineers understand, learn from, and emulate the strategies used by living things to create sustainable designs and technologies. BIDARA can guide users through the Biomimicry Institute’s Design Process, a step-by-step method to propose biomimetic solutions to challenges. This process includes defining the problem, biologizing the challenge, discovering natural models, abstracting design strategies, and emulating nature's lessons.

Brandon Ruffridge↗

Evaluation of Vertical Patterns in Chlorophyll-A Derived From A Data Assimilating Model of Satellite-Based Ocean Color

Satellite-based sensors of ocean color have become the primary tool to infer changes in surface chlorophyll, while BGC-Argo floats are now filling the information gap at depth. Here we use BGC-Argo data to assess depth-resolved information on chlorophyll-a derived from an ocean biogeochemical model constrained by the assimilation of surface ocean color remote sensing. The data-assimilating model replicates well the general seasonality and meridional gradients in surface and depth-resolved chlorophyll-a inferred from the float array in the Southern Ocean. On average, the model tends to overestimate float-based chlorophyll, particularly at times and locations of high productivity such as the beginning of the spring bloom, subtropical deep chlorophyll maxima, and non-iron limited regions of the Southern Ocean. The highest model RMSE in the upper 50 m with respect to the float array is of 0.6 mg Chl m −3 , which should allow the detection of seasonal changes in float-based biomass (varying between 0.01 and >1 mg Chl m −3 ) but might hinder the identification of subtle changes in chlorophyll at narrow local scales. Both model and float profiling data show good agreement with in situ data from station ALOHA, with model estimates showing a slight accuracy edge in inferring depth-resolved observations. Uncertainties in float bio-optical estimates impede their use as a reliable benchmark for validation, but the general qualitative agreement between model and float data provides confidence in the ability of model to replicate biogeochemical features below the surface, where data is not directly constrained by the assimilation of satellite ocean color.

Lionel A Quintero↗

From Research to Reality -- Challenges and Opportunities in Complex System Design

The scope and scale of our interconnected society requires that we view the world through a complex system lens, where numerous parts interact, and emergent behaviors are the norm. Understanding complex systems is critical for decision-making and policy development in domains such as ecological systems, financial markets, supply chains, and global transportation systems, where decision-makers need reliable information to predict the impact of decisions that may play out over decades. Traditional approaches to the research that produces this information are often insufficient, where hypotheses are tested in an isolated environment, and where the results may not carry over to the integrated system. There are a multitude of advancements in system engineering, artificial intelligence, and test and evaluation that are emerging to meet the challenge. Approaches such as agile development, model-based system engineering, design of experiments, large language models, and formal ontologies are providing ways to manage complexity and increase our collective ability to make the changes that we want to see in the world. In this talk I will provide a few examples related to the architecture of the National Airspace System (NAS), where we have investigated the use of large language models, basic formal ontology, and applied category theory to help researchers and system engineers be more effective in this complex design space. Bio: Dr. Ian Levitt’s current research focus is on the complex evolution of the National Airspace System. Prior to joining NASA in 2020, he was with the FAA leading international standards and national laboratory development for the agency. Dr. Levitt earned his PhD in mathematics from Rutgers University in 2009. His mission is to promote a healthy and continuous transformation of society through open information and cooperation.

Ian Levitt↗

Evaluating Crystallinity in Thermoplastic composites

Polymer matrix composites (PMCs) offer many benefits for the aerospace industry due to their potential for weight reduction when compared to metal or ceramic based materials. Most PMCs currently in flight use thermoset matrices, however, thermoplastic resins are being explored as alternatives due to their ability to be remelted, which is of particular interest due to the potential for in-situ repair and manufacturing required in space. Most thermoplastic resins are semicrystalline polymers. The properties of semicrystalline thermoplastics are largely influenced by their crystallinity, which can vary due to many factors including thermal treatments, environmental conditions, and mechanical deformation. Monitoring the crystallinity of thermoplastic composites is key to ensuring these materials reliably meet the high demands required by space exploration. This talk discusses the use of multiple techniques such as Polarized Light Optical Microscopy and Fourier-Transform Infrared Spectroscopy to characterize the crystallinity in various thermoplastic composites, including carbon fiber reinforced PMCs and novel bio-based Martian and Lunar regolith composites designed for in-situ manufacturing. This work aims to provide the fundamental data necessary to understand the effects of crystallinity on thermoplastic PMCs, which is key to advancing their use in space applications.

Thermoplastics↗

Micromechanical Design of Carbon Nanotube Ribbon Reinforced Polymer Composite Materials

Lightweight materials are an important component of the design of aerospace structures. Carbon nanotube materials have been considered for this purpose due to the strength and stiffness of individual nanotubes, and the commercial availability of bulk formats such as fibers. These fibers can have a ribbon cross section which results in a different design space for their composites relative to traditional reinforcements which have a round cross section. This work applies brick-and-mortar micromechanical models and classical lamination theory with an inverse approach to investigate the design space of these composites. Using this approach, the influences of fiber geometry and axial and transverse mechanical properties are mapped. Finally, a sensitivity study is performed and the relative impacts of ±10% variations in the constituent material and geometric properties are ranked. Lamina axial moduli were found to range from a maximum of 3x to 1x minimum relative to a target quasi-isotropic laminate modulus depending on the anisotropy and shear modulus of the lamina. The fiber targets depended strongly on the fiber volume fraction in the lamina and the fiber axial modulus target was found to range from 4.8x to 3.2x the quasi-isotropic laminate target. The sensitivity analysis found that the largest driver of performance was the volume fraction, followed by the fiber axial modulus. While bio-based brick-and-mortar composites, such as nacre, can benefit from reinforcement aspect ratios above 10, for carbon nanotube ribbon (or carbon fiber)/polymer composites the sensitivity study indicated that the optimal cross-sectional aspect ratio was relatively smaller, potentially less than three.

Micromechanics↗

3D Printing of Advanced Biocomposites on Earth and Beyond

Human exploration off planet is severely limited by the cost of launching materials into space and re-supply. Thus materials brought from earth must be light, stable and reliable at destination. Using traditional approaches a lunar or Mars base would require either transporting a hefty store of metals or heavy manufacturing equipment and construction materials for in situ extraction; both would severely limit any other mission objectives. Long-term human space presence requires periodic replenishment, adding a massive cost overhead. Even robotic missions often sacrifice science goals for heavy radiation and thermal protection. Biology has the potential to solve these problems because it can replicate and repair itself, and do a wide variety of chemical reactions including making food, fuel and materials. Synthetic biology can greatly enhance and expand life's evolved repertoire. Using natural and synthetically altered organisms as the feedstock for additive manufacturing could one day make possible the dream of producing bespoke tools, food, smart fabrics and even replacement organs on demand. To this end our lab has produced a proof-of-concept bioprinter with nearly one-cell resolution. Genetically engineering yeast cells to secrete bioproducts subsequent to printing allows the potential to make biomaterials with a fine microstructure. Imagine a production system that, at a few micron scale resolution, can add mollusk shell for compressive strength per unit mass, spider silk or collagen for tensile strength per unit mass, and potentially biologically-deposited wires. Now imagine what new products can be enabled by such a technology, on earth or beyond.

Biology↗

An Overview of Approaches and Challenges for Retrieving Marine Inherent Optical Properties from Ocean Color Remote Sensing

Ocean color measured from satellites provides daily global, synoptic views of spectral water-leaving reflectances that can be used to generate estimates of marine inherent optical properties (IOPs). These reflectances, namely the ratio of spectral upwelled radiances to spectral downwelled irradiances, describe the light exiting a water mass that defines its color. IOPs are the spectral absorption and scattering characteristics of ocean water and its dissolved and particulate constituents. Because of their dependence on the concentration and composition of marine constituents, IOPs can be used to describe the contents of the upper ocean mixed layer. This information is critical to further our scientific understanding of biogeochemical oceanic processes, such as organic carbon production and export, phytoplankton dynamics, and responses to climatic disturbances. Given their importance, the international ocean color community has invested significant effort in improving the quality of satellite-derived IOP products, both regionally and globally. Recognizing the current influx of data products into the community and the need to improve current algorithms in anticipation of new satellite instruments (e.g., the global, hyperspectral spectroradiometer of the NASA Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission), we present a synopsis of the current state of the art in the retrieval of these core optical properties. Contemporary approaches for obtaining IOPs from satellite ocean color are reviewed and, for clarity, separated based their inversion methodology or the type of IOPs sought. Summaries of known uncertainties associated with each approach are provided, as well as common performance metrics used to evaluate them. We discuss current knowledge gaps and make recommendations for future investment for upcoming missions whose instrument characteristics diverge sufficiently from heritage and existing sensors to warrant reassessing current approaches.

Bio-optics↗

Biocene 2018 - Welcome to the Period of New Life

Biocene is the period of new life. When our descendants look back at this period in time, they will see evidence, in the geologic and electronic record, of anthropic climate change, growing population, and scarcity of resources. But they will also see the rebirth of human ingenuity as we overcame the challenges that faced us through nature-inspired exploration. The Periodic Table of Life (PeTaL) is a proposed tool and open source framework that uses artificial intelligence to aid in the systematic inquiry of biology for its application to human systems. This presentation defines the PeTaL concept and workflow. Biomimicry, biophysics, biomimetics, bionics and numerous other terms refer to the use of biology and biological principles to inform practices in other disciplines. For the most part, the domain of inquiry in these fields have been confined to extant biological models with the proponents of biomimicry often citing the evolutionary success of extant organisms relative to extinct ones. The primary objective of this paper is to expand the domain of inquiry for human processes that seek to model those that are, were or could be found in nature with examples that relate to the field of aerospace and to spur development of tools that can work together to accelerate the use of artificial intelligence in problem solving. Specifically specialized fields such as paleomimesis, anthropomimesis and physioteleology are proposed in conjunction with artificial evolution. Blockchain technology may be vital in allowing open source design tools such as PeTaL to democratize design and yet protect intellectual property. The overarching philosophy outlined here can be thought of as physiomimetics, a holistic and systematic way of learning from natural history. The backbone of PeTaL integrates an unstructured database with an ontological model consisting of function, morphology, environment, state of matter and ecosystem. Tools include text classification, thesaurus, data visualization, and analysis. Applications of PeTaL include guiding human space exploration, understanding human and geological history, and discovering new or extinct life.

Biocene↗

Sensitivity of Inherent Optical Properties from Ocean Reflectance Inversion Models to Satellite Instrument Wavelength Suites

The Earth science community seeks to develop climate data records (CDRs) from satellite measurements of ocean color, a continuous data record that now exceeds 20 years. Space agencies will launch additional instruments in the coming decade that will continue this data record, including the NASA PACE spectrometer. Inherent optical properties (IOPs) quantitatively describe the absorbing and scattering constituents of seawater and can be estimated from satellite-observed spectroradiometric data using semi-analytical algorithms (SAAs). SAAs exploit the contrasting optical signatures of constituent matter at spectral bands observed by satellite sensors. SAA performance, therefore, depends on the spectral resolution of the satellite spectroradiometer. A CDR spanning SeaWiFS, MODIS, OLCI, and PACE, for example, would include IOPs derived using varied wavelength suites if all available wavelengths were considered. Here, we explored differences in derived IOPs that stem simply from the use of (eight) different wavelength suites of input radiometric measurements. Using synthesized data and SeaWiFS Level-3 mission-long composites, we demonstrated equivalent SAA performance for all wavelength suites, but that IOP retrievals vary by several percent across wavelength suites and as a function of water type. The differences equate to roughly ≤ 6, 12, and 7% for a(sub dg)(443), a(sub ph)(443), and b(sub bp)(443), respectively, for waters with C(sub a) ≤ 1 mg -cu m. These values shrink for sensors with similar wavelength suites (e.g., SeaWiFS, MODIS, and MERIS) and rise to substantially larger values for higher C(sub a) waters. Our results also indicate that including 400 nm (in the case of OLCI) influences the derived IOPs, using longer wavelengths (>600 nm) influences the derived IOPs when there is a red signal, and, including additional spectral information shows potential for improved IOP estimation, but not without revisiting SAA parameterizations and execution. While modest in scope, we believe this study contributes to the knowledge base for CDR development. The implication of ignoring such an analysis as CDRs continue to be developed is a prolonged inability to distinguish between algorithmic and environmental contributions to trends and anomalies in the IOP time-series.

ocean color satellites↗

Chlorophyll Algorithms for Ocean Color Sensors - OC4, OC5 and OC6

A high degree of consistency and comparability among chlorophyll algorithms is necessary to meet the goals of merging data from concurrent overlapping ocean color missions for increased coverage of the global ocean and to extend existing time series to encompass data from recently launched missions and those planned for the near future, such as PACE, OLCI, HawkEye, EnMAP and SABIA-MAR. To accomplish these goals, we developed 65 empirical ocean color (OC) chlorophyll algorithms for 25 satellite instruments using the largest available and most globally representative database of coincident in situ chlorophyll a and remote sensing reflectances. Excellent internal consistency was achieved across these OC ‘Version -7’ algorithms, as demonstrated by a median regression slope and coefficient of determination (R (sup 2)) of 0.985 and 0.859, respectively, among 903 pairwise comparisons of OC-modeled chlorophyll. SeaWiFS and MODIS-Aqua satellite-to-in situ match-up results indicated equivalent, and sometimes superior, performance to current heritage chlorophyll algorithms.

ocean color↗