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At least 217 records · Page 12

Definition of performance specifications for automated Analytical Electrophoresis Facility (AAEF)

In order to provide specifications for the automated Analytical Electrophoresis Facility (AAEF) that would satisfy the broadest variety of demands of a future user community, a survey was carried out of all those people who were identified as having published papers on cell electrophoresis in the past four years. A computer search was conducted of the relevant literature from which a list of 87 investigators was derived and defined as the user community for purposes of the mailing. A questionnaire was developed covering the areas of performance which required definition which was subsequently circulated to the user community. Based on the response to this survey performance specifications were assembled.

Brooks, D. E.↗

An Integrated Low-Speed Performance and Noise Prediction Methodology for Subsonic Aircraft

An integrated methodology has been assembled to compute the engine performance, takeoff and landing trajectories, and community noise levels for a subsonic commercial aircraft. Where feasible, physics-based noise analysis methods have been used to make the results more applicable to newer, revolutionary designs and to allow for a more direct evaluation of new technologies. The methodology is intended to be used with approximation methods and risk analysis techniques to allow for the analysis of a greater number of variable combinations while retaining the advantages of physics-based analysis. Details of the methodology are described and limited results are presented for a representative subsonic commercial aircraft.

Olson, E. D.↗

Technology Assessments within NASA's Integrated Technology Assessment Center

NASA's Advanced Space Transportation Program (ASTP) founded the Integrated Technology Assessment Center (ITAC) to provide a comprehensive, systematic approach to identify long-term technology needs, to quantify payoffs for technology investments, and to assess the progress of ASTP-sponsored technology programs in the hypersonics/Earth-to-orbit area. To accomplish these goals, the ITAC has assembled an experienced team representing a broad sector of the aerospace community and developed a systematic assessment process complete with supporting tools. In the ITAC approach, concepts for transportation systems are first selected based on relevance to the ASTP. Models of these concepts are then developed and data on advanced technologies are collected. Projections of key technology characteristics with respect to the specific concepts of interest are made. Both the models and technology projections are then fed into the ITAC's probabilistic systems analysis framework. The probabilistic outputs are weighed against metrics of interest to ASTP and a multivariate decision making process is used to provide inputs for technology prioritization within the ASTP. At present, the ITAC program is working to evaluate a variety of technologies for three two-stage hypersonic vehicle concepts. Concepts include an all rocket, vertical take off-horizontal landing (VTHL) system, a horizontal take-off-horizontal landing (HTHL) RBCC-propelled first stage/all rocket second stage system, and an HTHL turbine-based first stage/all rocket second stage system. This paper will provide a status update of the ITAC program including current results and plans.

Taylor, J. L.↗

Technology Assessments within NASA's Integrated Technology Assessment Center

NASA's Advanced Space Transportation Program (ASTP) founded the Integrated Technology Assessment Center (ITAC) to provide a comprehensive, systematic approach to identify long-term technology needs, to quantify payoffs for technology investments, and to assess the progress of ASTP-sponsored technology programs in the hypersonics/Earth-to-orbit area. To accomplish these goals, the ITAC has assembled an experienced team representing a broad sector of the aerospace community and developed a systematic assessment process complete with supporting tools. In the ITAC approach, concepts for transportation systems are first selected based on relevance to the ASTP. Models of these concepts are then developed and data on advanced technologies are collected. Projections of key technology characteristics with respect to the specific concepts of interest are made. Both the models and technology projections are then fed into the ITAC's probabilistic systems analysis framework. The probabilistic outputs are weighed against metrics of interest to ASTP and a multivariate decision making process is used to provide inputs for technology prioritization within the ASTP. At present, the ITAC program is working to evaluate a variety of technologies for three two-stage hypersonic vehicle concepts. Concepts include an all rocket, vertical take off-horizontal landing (VTHL) system, a horizontal takeoff-horizontal landing (HTHL) RBCC-propelled first stage/all rocket second stage system, and an HTHL turbine-based first stage/all rocket second stage system. This paper will provide a status update of the ITAC program including current results and plans.

Taylor, J. L.↗

Integrated Technology Assessment Center (ITAC) Update

The Integrated Technology Assessment Center (ITAC) has developed a flexible systems analysis framework to identify long-term technology needs, quantify payoffs for technology investments, and assess the progress of ASTP-sponsored technology programs in the hypersonics area. For this, ITAC has assembled an experienced team representing a broad sector of the aerospace community and developed a systematic assessment process complete with supporting tools. Concepts for transportation systems are selected based on relevance to the ASTP and integrated concept models (ICM) of these concepts are developed. Key technologies of interest are identified and projections are made of their characteristics with respect to their impacts on key aspects of the specific concepts of interest. Both the models and technology projections are then fed into the ITAC's probabilistic systems analysis framework in ModelCenter. This framework permits rapid sensitivity analysis, single point design assessment, and a full probabilistic assessment of each concept with respect to both embedded and enhancing technologies. Probabilistic outputs are weighed against metrics of interest to ASTP using a multivariate decision making process to provide inputs for technology prioritization within the ASTP. ITAC program is currently finishing the assessment of a two-stage-to-orbit (TSTO), rocket-based combined cycle (RBCC) concept and a TSTO turbine-based combined cycle (TBCC) concept developed by the team with inputs from NASA. A baseline all rocket TSTO concept is also being developed for comparison. Boeing has recently submitted a performance model for their Flexible Aerospace System Solution for Tomorrow (FASST) concept and the ISAT program will provide inputs for a single-stage-to-orbit (SSTO) TBCC based concept in the near-term. Both of these latter concepts will be analyzed within the ITAC framework over the summer. This paper provides a status update of the ITAC program.

Taylor, J. L.↗

Data management for community research projects: A JGOFS case study

Since the mid 1980s, much of the marine science research effort in the United Kingdom has been focused into large scale collaborative projects involving public sector laboratories and university departments, termed Community Research Projects. Two of these, the Biogeochemical Ocean Flux Study (BOFS) and the North Sea Project incorporated large scale data collection to underpin multidisciplinary modeling efforts. The challenge of providing project data sets to support the science was met by a small team within the British Oceanographic Data Centre (BODC) operating as a topical data center. The role of the data center was to both work up the data from the ship's sensors and to combine these data with sample measurements into online databases. The working up of the data was achieved by a unique symbiosis between data center staff and project scientists. The project management, programming and data processing skills of the data center were combined with the oceanographic experience of the project communities to develop a system which has produced quality controlled, calibrated data sets from 49 research cruises in 3.5 years of operation. The data center resources required to achieve this were modest and far outweighed by the time liberated in the scientific community by the removal of the data processing burden. Two online project databases have been assembled containing a very high proportion of the data collected. As these are under the control of BODC their long term availability as part of the UK national data archive is assured. The success of the topical data center model for UK Community Research Project data management has been founded upon the strong working relationships forged between the data center and project scientists. These can only be established by frequent personal contact and hence the relatively small size of the UK has been a critical factor. However, projects covering a larger, even international scale could be successfully supported by a network of topical data centers managing online databases which are interconnected by object oriented distributed data management systems over wide area networks.

Lowry, Roy K.↗

Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost

Permafrost underlies a large portion of the land in the Northern Hemisphere. It is proposed to be an extreme habitat and home for cold-adaptive microbial communities. Upon thaw permafrost is predicted to exacerbate increasing global temperature trend, where awakening microbes decompose millennia old carbon stocks. Yet our knowledge on composition, functional potential and variance of permafrost microbiome remains limited. In this study, we conducted a deep comparative metagenomic analysis through a 2 m permafrost core from Svalbard, Norway to determine key permafrost microbiome in this climate sensitive island ecosystem. To do so, we developed comparative metagenomics methods on metagenomic-assembled genomes (MAG). We found that community composition in Svalbard soil horizons shifted markedly with depth: the dominant phylum switched from Acidobacteria and Proteobacteria in top soils (active layer) to Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria in permafrost layers. Key metabolic potential propagated through permafrost depths revealed aerobic respiration and soil organic matter decomposition as key metabolic traits. We also found that Svalbard MAGs were enriched in genes involved in regulation of ammonium, sulfur and phosphate. Here, we provide a new perspective on how permafrost microbiome is shaped to acquire resources in competitive and limited resource conditions of deep Svalbard soils.

59 BASIC BIOLOGICAL SCIENCES↗

Non-additive microbial community responses to environmental complexity

Environmental composition is a major, though poorly understood, determinant of microbiome dynamics. Here we ask whether general principles govern how microbial community growth yield and diversity scale with an increasing number of environmental molecules. By assembling hundreds of synthetic consortia in vitro, we find that growth yield can remain constant or increase in a non-additive manner with environmental complexity. Conversely, taxonomic diversity is often much lower than expected. To better understand these deviations, we formulate metrics for epistatic interactions between environments and use them to compare our results to communities simulated with experimentally-parametrized consumer resource models. We find that key metabolic and ecological factors, including species similarity, degree of specialization, and metabolic interactions, modulate the observed non-additivity and govern the response of communities to combinations of resource pools. Our results demonstrate that environmental complexity alone is not sufficient for maintaining community diversity, and provide practical guidance for designing and controlling microbial ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

Metagenome-assembled genomes from topsoils along a hillslope water gradient across early snowmelt to late summer in East River, CO

Drought is changing the American Mountain West at unprecedented rates with unknown consequences to soil microbiome composition and function. As a part of LBNL Watershed Science Focus Area (SFA), we investigated shifts in microbial community and transcriptional activity on a subalpine conifer-meadow transition zone throughout the summer of 2023 as soil dried down. This work took place in Crested Butte, CO on Snodgrass mountain, using a proxy for drought conditions.Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal community at 0-10cm from three sites along a hillslope water gradient across five timepoints from early snowmelt to late summer. 42 metagenomes were sequenced at Joint Genome Institute (JGI) and can be found under the JGI GOLD (Genomes Online Database) sequencing project Gs0166660. Metagenomes were assembled through an inhouse pipeline (see methods), binned using four autobinners (concoct, maxbin2, metabat2, and vamb) and consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>70%) and contamination (<10%), and dereplicated at 95% ANI using drep. This dataset (1) a zip file of 157 MAGs (as fasta files, Gs0166660_bins_tar.gz), (2) sample metadata file with sample IGSNs (International Generic Sample Numbers) (samples.csv), (3) bounding box coordinates for the sampled locations (Gs0166660.kml), (4) metagenome assembly and coassembly metadata file listing IMG/M (Integrated Microbial Genomes/Metagenomes) metagenome accessions linking samples to metagenomes (EastRiver_Drought_ESSDive_Metadata.csv), (5) location metadata file (locations.csv), (6) file-level metadata file (flmd.csv) and (7) data dictionary (dd.csv) file.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗

Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily

Abstract Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.

54 ENVIRONMENTAL SCIENCES↗

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA): Integrating Metabolomics into Environmental Systems Biology

Our research endeavors entail ambitious objectives to explore the communities of microorganisms and quantify their chemical input and output to determine specific biochemical activity. To achieve these scientific aims, we are creating advanced algorithms to scrutinize extensive experimental data produced through high-throughput technologies, enabling us to elucidate how biological functions are influenced by environmental factors on various scales, and how microbial systems alter their surroundings. By studying the metabolic interdependence of bacterial communities for their survival and reproductive prosperity, we can gain insights into their biochemical capabilities. To accomplish this, we employed cutting-edge mass spectrometry-based techniques and metabolic fingerprinting methods, which offer high chemical specificity and sensitivity. As our efforts progressed, the project evolved into ENIGMA, encompassing a broader range of technology development, including untargeted metabolomics and its implementation for system-level organism analysis.

54 ENVIRONMENTAL SCIENCES↗

Enabling Innovation and Collaboration Across Geography and Culture: A Case Study of NASA's Systems Engineering Community of Practice

In 2004, NASA faced major knowledge sharing challenges due to geographically isolated field centers that inhibited personnel from sharing experiences and ideas. Mission failures and new directions for the agency demanded better collaborative tools. In addition, with the push to send astronauts back to the moon and to Mars, NASA recognized that systems engineering would have to improve across the agency. Of the ten field centers, seven had not built a spacecraft in over 30 years, and had lost systems engineering expertise. The Systems Engineering Community of Practice came together to capture the knowledge of its members using the suite of collaborative tools provided by the NASA Engineering Network (NEN.) The NEN provided a secure collaboration space for over 60 practitioners across the agency to assemble and review a NASA systems engineering handbook. Once the handbook was complete, they used the open community area to disseminate it. This case study explores both the technology and the social networking that made the community possible, describes technological approaches that facilitated rapid setup and low maintenance, provides best practices that other organizations could adopt, and discusses the vision for how this community will continue to collaborate across the field centers to benefit the agency as it continues exploring the solar system.

NEN↗

Thermodynamic equilibrium and kinetic fundamentals of oxide dissolution in aqueous solution

Dissolution of oxides in aqueous solutions is fundamentally important for a range of applications and a critical process that determines the chemical durability of industrial ceramics, the performance of nuclear waste forms, and the chemical weathering of minerals. The thermodynamic equilibrium and kinetics of dissolution reactions are key to determining the rate at which oxides dissolve. The increase in collaborative research across disciplines in materials research necessitates a common background to tackle shared scientific problems across different fields. This review selectively examines the fundamentals of dissolution theories that have been developed in chemistry, geochemistry, and materials science, and assembles them into a single collective document for the broader materials science community. Applications of the theories are highlighted using examples from specific areas, but can be similarly applied to other areas. Challenges and future research needs for a predictive-level understanding are discussed in light of the current literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep Green: Structural and Functional Genomic Characterization of Conserved Unannotated Green Lineage Proteins

Our overall objective is to improve and increase functional and structural predictions for a growing number of plant proteins of unknown structure and function (the Deep Green proteins), and to make our predictive data useful and accessible to the larger research community. The project is divided into five major objectives which include 1) Assembly and curation of Deep Green candidate protein sets; 2) in silico structural and functional predictions and network analyses; 3) assembly and validation of reverse genetic resources in Chlamydomonas reinhardtii (Chlamydomonas); 4) high throughput functional genomics characterization and prioritization in Chlamydomonas; and 5) structural validation of selected candidates and functional validation in two important reference plant species, Arabidopsis thaliana (Arabidopsis) and Setaria viridis (Setaria).

59 BASIC BIOLOGICAL SCIENCES↗

Intelligent Computer-Aided Training (ICAT)

The Software Technology Branch has developed and demonstrated a number of ICAT System for a variety of complex procedural tasks in the NASA operational environment. A general ICAT architecture was developed and shown to be adaptable across this spectrum of tasks. Currently underway is the assembly of a suite of software tools that will permit the training community to rapidly develop and deploy ICAT systems for a variety of Space Station training tasks. The use of ICAT technology for selected training applications within the Space Station Freedom program can significantly reduce the costs of training system development. Once developed ICAT systems can be more readily and efficiently evolved and maintained than many conventional training systems. ICAT systems can be delivered for both ground based and on-orbit training. The availability of sophisticated on-orbit training will serve to reduce EVA time and can be especially useful in preparing crew for the performance on infrequent, mission critical tasks. ICAT systems can deliver uniform but individualized training to large numbers of personnel in a workstation environment.

Savely, Robert T.↗

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.

59 BASIC BIOLOGICAL SCIENCES↗

Mesoporous Thin Film Architectures: Addressing Material Demands through Molecular Self-Assembly

Mesoporous thin films spark interest across a wide range of disciplines due to their tunable nanostructures, large internal surface areas, and strong compatibility with planar optical, electronic, and microfluidic devices. While attention in the porous materials community has shifted toward macroporous or disordered nanoporous systems, a resurgence in mesoporous thin film research is underway, driven by new molecular self-assembly methods, advanced materials chemistry, and improved characterization techniques. The integration of high-χN block copolymer design, kinetically persistent micelle templating, and postdeposition processing protocols now allows control over structural parameters such as pore size, wall thickness, porosity, and connectivity. These advances have overcome many of the thermodynamic and processing constraints that previously limited widespread adoption. Rather than serving only as high-surface-area supports, mesoporous thin films are engineered as active interfaces where responsive chemistries and nanoscale confinement act in tandem. Embedding switchable ligands, thermoresponsive polymers, redox mediators, or ion-selective groups directly within the pore walls enables real-time control over transport, optical, and electrochemical properties. These capabilities open up new directions in adaptive coatings, gated membranes, and fast-response biosensors. To further expand their functional scope, mesoporous films are integrated into hierarchical and multicomponent architectures. Techniques such as triblock terpolymer templating, crack-directed assembly, and nanoimprint lithography allow for control over spatial organization on the micron and submicron scale and pore system orientation. This enables programmable anisotropy, enhanced molecular diffusion, and wavelength-selective photonic behavior, essential for next-generation sensing, catalysis, and energy applications. Such structural and functional complexity requires equally sophisticated characterization. Multimodal and in situ techniques can track material dynamics under operational conditions. Recent progress includes extended-range ellipsometric porosimetry (EP) for hierarchical architectures, vacuum EP for interface energetics, time-resolved EP for diffusion kinetics, and correlative AFM-SAXS mapping. The introduction of advanced neutron-based spectroscopies, particularly quasielastic neutron scattering (QENS), promises to provide real-time access to ion transport dynamics and segmental motion under nanoscale confinement, offering a path toward deeper mechanistic understanding of structure-performance correlations in mesoporous systems. This Account reflects the technical advances made and the interdisciplinary collaborations that have shaped our collective vision. The particular dimensions of mesopores enable us to subtly tune interactions at the molecular, interfacial, and mesoscopic levels that permit us to harness nanoconfinement. What emerges is a versatile, modular platform capable of chemical gating, energy transduction, and sensing with a level of tunability unmatched by other porous materials. We highlight critical challenges including the need for more robust large-area processing, a deeper understanding of dynamic behavior under cycling, and better integration with device-level architectures. Our strategies support the transition of mesoporous thin films into active high-performance components in next-generation energy, environmental, and biomedical systems.

oxides↗

Engineering microbial consortia with rationally designed cellular interactions

Synthetic microbial consortia represent a frontier of synthetic biology that promises versatile engineering of cellular functions. They are primarily developed through the design and construction of cellular interactions that coordinate individual dynamics and generate collective behaviors. Here we review recent advances in the engineering of synthetic communities through cellular-interaction programming. We first examine fundamental building blocks for intercellular communication and unidirectional positive and negative interactions. Here, we then recap the assembly of the building blocks for creating bidirectional interactions in two-species ecosystems, which is followed by the discussion of engineering toward complex communities with increasing species numbers, under spatial contexts, and via model-guided design. We conclude by summarizing major challenges and future opportunities of engineered microbial ecosystems.

42 ENGINEERING↗