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DOE OSTI2023

Breaking the Ice: A Review of Phages in Polar Ecosystems

Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. In this study, understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage–host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.

09 BIOMASS FUELS↗

DOE OSTI2026

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗

DOE OSTI2026

Mutation of active site glutamate in serine hydroxymethyltransferase allows trapping a reactive intermediate: a combined neutron and X-ray crystallography study

Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5′-phosphate (PLP) dependent enzyme that catalyzes a chemical transformation essential for the one-carbon (1C) metabolism. SHMT reversibly converts L-Ser into Gly and transfers a 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF). 5,10-MTHF, a 1C-unit donor, plays a crucial role in the downstream biomolecular syntheses required for the cell homeostasis and proliferation. SHMT is a prominent target for the drug discovery to battle bacterial and parasitic infections, and to treat various types of cancer. SHMT-catalyzed chemistry is governed by the general acid-base catalysis. Knowledge of the catalytic mechanism can aid drug design but can only be achieved when the atomic details of each reaction step are mapped, including accurate determination of hydrogen atom positions. Here we utilized the inactive E53Q mutant of Thermus thermophilus ( Tth ) SHMT to directly determine protonation states with room-temperature neutron crystallography and to capture a reactive intermediate containing the PLP-L-Ser external aldimine and THF in the enzyme active site. We observed protonation of the Schiff base nitrogen (N SB ) in the PLP internal aldimine but no change in the protonation states of other ionizable PLP groups and active site residues compared to wild-type Tth SHMT. X-ray structural analysis of the ternary intermediate complex E53Q-Ser-THF that eluded previous structural characterization shows the strategic positioning of the E53Q side chain in close proximity to the external aldimine and THF and reinforces the proposed role for E53 as the driver of proton transfer events along the reaction pathway.

Drago, Victoria N. [Oak Ridge National Laboratory ↗

NASA NTRS1986

Magnetospheric energetic ions from the earth's ionosphere

In the decade and a half since the initial discovery that the earth's own ionosphere could at times contribute measurably to the hot plasma in the magnetosphere, significant progress has been made in both current knowledge and understanding of this connection. It is now known that ions of ionospheric origin are found in all major regions of the magnetosphere and at its boundaries. The source region in the ionosphere and the acceleration and transport processes involved in coupling the cold ionospheric plasma to the hot magnetospheric plasma are complex and variable. The large scale morphology of the ionospheric outflow and its distribution throughout the magnetosphere is now understood and progress is being made in the understanding of the fundamental physical processes involved. In this paper attention is given to the large scale morphology and current understanding of the sources for ionospheric ions found in various regions of the magnetosphere and their transport.

Shelley, E. G.↗

NASA NTRS1999

Sonoluminescence in Space: The Critical Role of Buoyancy in Stability and Emission Mechanisms

Sonoluminescence is the term used to describe the emission of light from a violently collapsing bubble. Sonoluminescence ("light from sound") is the result of extremely nonlinear pulsations of gas/vapor bubbles in liquids when subject to sufficiently high amplitude acoustic pressures. In a single collapse, a bubble's volume can be compressed more than a thousand-fold in the span of less than a microsecond. Even the simplest consideration of the thermodynamics yields pressures on the order of 10,000 ATM. and temperatures of at least 10,000 K. On the face of things, it is not surprising that light should be emitted from such an extreme process. Since 1990 (the year that Gaitan discovered light from a single bubble) there has been a tremendous amount of experimental and theoretical research in stable, single-bubble sonoluminescence. Yet there remain four fundamental mysteries associated with this phenomenon: 1) the light emission mechanism itself; 2) the mechanism for anomalous mass flux stability; 3) the disappearance of the bubble at some critical acoustic pressure; and 4) the appearance of quasiperiodic and chaotic oscillations in the flash timing. Gravity, in the context of the buoyant force, is implicated in all four of these unexplained phenomena. We are developing microgravity experiments probing the effect of gravity on single bubble sonoluminescence. By determining the stability boundaries experimentally in microgravity, and measuring not only light emission but mechanical bubble response, we will be able to directly test the unambiguous predictions of existing theories. By exploiting the microgravity environment we will gain new knowledge impossible to obtain in earth-based labs which will enable explanations for the above mysteries. We will also be in a position to make new discoveries about bubbles which emit light.

Holt, R. Glynn↗

NASA NTRS2004

New Analyses of Diverse Hadean Zircon Inclusions from Jack Hills, Western Australia

The geological record is the only direct source of information regarding physical/chemical processes that may have ultimately been responsible for the origin of life. Known terrestrial rocks have ages that span from present day to approx. 4.0 Ga. This leaves a time gap of more than 500 Myr between lunar formation, and preservation of the oldest terrestrial crust. What were planetary conditions like wherein the prebiotic chemistry leading to life took place? The recent discovery of up to 4.37 Ga detrital zircons from Western Australia represents the only tangible record of the time period termed the Hadean Eon (4.5-4.0 Ga). Knowledge of the paragenesis of the oldest zircons potentially contributes information regarding the origin of the atmosphere, hydrosphere, continental lithosphere and the potential for life on the Hadean Earth.

D Trail↗

NASA NTRS2004

Precursor Science for the Terrestrial Planet Finder

This document outlines a path for the development of the field of extrasolar planet research, with a particular emphasis on the goals of the Terrestrial Planet Finder (TPF). Over the past decade, a new field of research has developed, the study of extrasolar planetary systems, driven by the discovery of massive planets around nearby stars. The planet count now stands at over 130. Are there Earth-like planets around nearby stars? Might any of those planets be conducive to the formation and maintenance of life? These arc the questions that TPF seeks to answer. TPF will be implemented as a suite of two space observatories, a 6-m class optical coronagraph, to be launched around 20 14, and a formation flying mid-infrared interferometer, to be launched sometime prior to 2020. These facilities will survey up to 165 or more nearby stars and detect planets like Earth should they be present in the 'habitable zone' around each star. With observations over a broad wavelength range, TPF will provide a robust determination of the atmospheric composition of planets to assess habitability and the presence of life. At this early stage of TPF's development, precursor observational and theoretical programs are essential to help define the mission, to aid our understanding of the planets that TPF could discover, and to characterize the stars that TPF will eventually study. This document is necessarily broad in scope because the significance of individual discoveries is greatly enhanced when viewed in thc context of the field as a whole. This document has the ambitious goal of taking us from our limited knowledge today, in 2004, to the era of TPF observations in the middle of the next decade. We must use the intervening years wisely. This document will be reviewed annually and updated as needed. The most recent edition is available online at http://tpf.jpl.nasa.gov/ or by email request to lawson@hucy.jpl.nasa.gov

Lawson, P. R.↗

NASA NTRS2006

Exploring the Possibilities: Earth and Space Science Missions in the Context of Exploration

According to Dr. Edward J. Weiler, Director of the Goddard Space Flight Center, "Exploration without science is tourism". At the American Astronautical Society's 43rd Annual Robert H. Goddard Memorial Symposium it was quite apparent to all that NASA's current Exploration Initiative is tightly coupled to multiple scientific initiatives: exploration will enable new science and science will enable exploration. NASA's Science Mission Directorate plans to develop priority science missions that deliver science that is vital, compelling and urgent. This paper will discuss the theme of the Goddard Memorial Symposium that science plays a key role in exploration. It will summarize the key scientific questions and some of the space and Earth science missions proposed to answer them, including the Mars and Lunar Exploration Programs, the Beyond Einstein and Navigator Programs, and the Earth-Sun System missions. It will also discuss some of the key technologies that will enable these missions, including the latest in instruments and sensors, large space optical system technologies and optical communications, and briefly discuss developments and achievements since the Symposium. Throughout history, humans have made the biggest scientific discoveries by visiting unknown territories; by going to the Moon and other planets and by seeking out habitable words, NASA is continuing humanity's quest for scientific knowledge.

Pfarr, Barbara↗

DOE OSTI2020

The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential

Current research on the prokaryotic low abundance taxa, the prokaryotic rare biosphere, is growing, leading to a greater understanding of the mechanisms underlying organismal rarity and its relevance in ecology. From this emerging knowledge it is possible to envision innovative approaches in biotechnology applicable to several sectors. Bioremediation and bioprospecting are two of the most promising areas where such approaches could find feasible implementation, involving possible new solutions to the decontamination of polluted sites and to the discovery of novel gene variants and pathways based on the attributes of rare microbial communities. Bioremediation can be improved through the realization that diverse rare species can grow abundant and degrade different pollutants or possibly transfer useful genes. Further, most of the prokaryotic diversity found in virtually all environments belongs in the rare biosphere and remains uncultivatable, suggesting great bioprospecting potential within this vast and understudied genetic pool. This Mini Review argues that knowledge of the ecophysiology of rare prokaryotes can aid the development of future, efficient biotechnology-based processes, products and services. However, this promise may only be fulfilled through improvements in (and optimal blending of) advanced microbial culturing and physiology, metagenomics, genome annotation and editing, and synthetic biology, to name a few areas of relevance. In the future, it will be important to understand how activity profiles relate with abundance, as some rare taxa can remain rare and increase activity, whereas other taxa can grow abundant. The metabolic mechanisms behind those patterns can be useful in designing biotechnological processes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Major impacts of widespread structural variation on sorghum

Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in genome-wide selection, is not yet understood. In this study, we built an SV data set based on whole-genome resequencing of diverse sorghum lines (n = 363), validated the correlation of photoperiod sensitivity and variety type, and identified SV hotspots underlying the divergent evolution of cellulosic and sweet sorghum. In addition, we showed the complementary contribution of SVs for heritability of traits related to sorghum adaptation. Importantly, inclusion of SV polymorphisms in association studies revealed genotype–phenotype associations not observed with SNPs alone. Three-way genome-wide association studies (GWAS) based on whole-genome SNP, SV, and integrated SNP + SV data sets showed substantial associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the genome level. Our discovery of the widespread impacts of SVs on heritable gene expression variation could render a plausible mechanism for their disproportionate impact on phenotypic variation. This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2007

Translational Research from an Informatics Perspective

Clinical and translational research (CTR) is an essential part of a sustainable global health system. Informatics is now recognized as an important en-abler of CTR and informaticians are increasingly called upon to help CTR efforts. The US National Institutes of Health mandated biomedical informatics activity as part of its new national CTR grant initiative, the Clinical and Translational Science Award (CTSA). Traditionally, translational re-search was defined as the translation of laboratory discoveries to patient care (bench to bedside). We argue, however, that there are many other kinds of translational research. Indeed, translational re-search requires the translation of knowledge dis-covered in one domain to another domain and is therefore an information-based activity. In this panel, we will expand upon this view of translational research and present three different examples of translation to illustrate the point: 1) bench to bedside, 2) Earth to space and 3) academia to community. We will conclude with a discussion of our local translational research efforts that draw on each of the three examples.

Bernstam, Elmer↗

NASA NTRS2011

An Ontology Driven Information Architecture for Interoperable Disparate Data Sources

The mission of the Planetary Data System is to facilitate achievement of NASA's planetary science goals by efficiently collecting, archiving, and making accessible digital data produced by or relevant to NASA's planetary missions, research programs, and data analysis programs. The vision is: (1) To gather and preserve the data obtained from exploration of the Solar System by the U.S. and other nations (2) To facilitate new and exciting discoveries by providing access to and ensuring usability of those data to the worldwide community (3) To inspire the public through availability and distribution of the body of knowledge reflected in the PDS data collection PDS is a federation of heterogeneous nodes including science and support nodes

planetary data systems↗

DOE OSTI2025

TPCpp-10M: Simulated proton-proton collisions in a time projection chamber for AI foundation models

Scientific foundation models hold great promise for advancing nuclear and particle physics by improving analysis precision and accelerating discovery. Yet, progress in this field is often limited by the lack of openly available large scale datasets, as well as standardized evaluation tasks and metrics. Furthermore, the specialized knowledge and software typically required to process particle physics data pose significant barriers to interdisciplinary collaboration with the broader machine learning community. This work introduces a large, openly accessible dataset of 10 million simulated proton-proton collisions, designed to support self-supervised training of foundation models. To facilitate ease of use, the dataset is provided in a common NumPy format. In addition, it includes 70,000 labeled examples spanning three well defined downstream tasks: track finding, particle identification, and noise tagging, to enable systematic evaluation of the foundation model's adaptability. The simulated data are generated using the Pythia Monte Carlo event generator at a center of mass energy of $\sqrt{s}$ = 200 GeV and processed with Geant4 to include realistic detector conditions and signal emulation in the sPHENIX Time Projection Chamber at the Relativistic Heavy Ion Collider, located at Brookhaven National Laboratory. This dataset resource establishes a common ground for interdisciplinary research, enabling machine learning scientists and physicists alike to explore scaling behaviors, assess transferability, and accelerate progress toward foundation models in nuclear and high energy physics. The complete simulation and reconstruction chain is reproducible with the sPHENIX software stack. All data and code locations are provided under Data Accessibility.

Data Analysis, Statistics and Probability (physics↗

DOE OSTI2026

Neural entropy-stable conservative flux form neural networks for learning hyperbolic conservation laws

We propose a neural entropy-stable conservative flux form neural network (NESCFN) for learning hyperbolic conservation laws and their associated entropy functions directly from solution trajectories, without requiring any predefined numerical discretization. While recent neural network architectures have successfully integrated classical numerical principles into learned models, most rely on prior knowledge of the governing equations or assume a fixed discretization. Our approach removes this dependency by embedding entropy-stable design principles into the learning process itself, enabling the discovery of physically consistent dynamics in a fully data-driven setting. By jointly learning both the flux function and a corresponding entropy, NESCFN promotes conservation and entropy dissipation, which is critical for long-term stability and fidelity in the system of hyperbolic conservation laws. Furthermore, numerical results demonstrate that the method achieves stability and conservation over extended time horizons and accurately captures shock propagation speeds, even without oracle access to future-time solution profiles in the training data.

Conservative flux form↗

NASA NTRSDate not supplied

Open-Source Science-led Development of the Atmosphere Observing System (AOS) Mission Science Data System (SDS)

The Earth System Observatory (ESO) Atmosphere Observing System (AOS) mission will provide space-based and suborbital observations of collocated cloud, dynamic, precipitation and aerosol processing leading to improved weather, air quality, and climate predictions. The AOS Science Data System (SDS) will be a system of systems developed within the Cloud to manage the research and operational processing of AOS mission orbital and suborbital sensors and curate these data for reprocessing (e.g., in near real-time or by collection) and transfer them to a NASA Distributed Active Archive Center (DAAC) for long-term storage. Further, AOS SDS will follow guidelines provided by NASA Earth Science Data Systems (ESDS) program including standard conventions for data file formats, naming, and metadata to improve data interoperability, interpretability, usability, discovery, provenance, and spatiotemporal representativeness. The AOS mission follows NASA’s lead in making a commitment to Open-Source Science (OSS) including the sharing of data, software, and knowledge in an open and timely manner. Each of the AOS SDS system components will be developed with open-source concepts including components of SDS itself as well as AOS mission algorithms. Further, the AOS SDS assumes the role to lead and facilitate OSS activities for the AOS mission. This presentation describes the framework of the AOS SDS and its integral part in facilitating OSS within the AOS mission.

David Giles↗

NASA NTRSDate not supplied

Open-Source Science-led Development of the AOS Mission Science Data System (SDS)

David M. Giles↗

DOE OSTI2023

Neutrino self-interactions: A white paper

Neutrinos are the Standard Model (SM) particles which we understand the least, often due to how weakly they interact with the other SM particles. Beyond this, very little is known about interactions among the neutrinos, i.e., their self-interactions. The SM predicts neutrino self-interactions at a level beyond any current experimental capabilities, leaving open the possibility for beyond-the-SM interactions across many energy scales. In this white paper, we review the current knowledge of neutrino self-interactions from a vast array of probes, from cosmology, to astrophysics, to the laboratory. Furthermore, we also discuss theoretical motivations for such self-interactions, including neutrino masses and possible connections to dark matter. Looking forward, we discuss the capabilities of searches in the next generation and beyond, highlighting the possibility of future discovery of this beyond-the-SM physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRSDate not supplied

New developments in space radiation research at NASA: Annotating data using a novel radiation biology ontology

Like many interdisciplinary sciences, data producers and consumers in the field of radiation biology often use a wide variety of terminology to describe their experiments and data. Furthermore, space systems and technologies are rapidly evolving, and a shared understanding and common terminology for these is also lacking. The efficiency of research organizations can be enhanced by standardizing metadata through the use of knowledge resources like ontologies. Employing a sophisticated model such as a formal ontology to standardize metadata enables automated data acquisition processes and supports more complete, accurate meta-analysis through more efficient and complete data discovery and retrieval, particularly when using multiple data sources. Thus, we developed the Radiation Biology Ontology (RBO) in order to improved radiation biology metadata uniformity and transparency. We used open-source software (the Ontology Development Kit, Protégé and WebProtégé) and worked within the OBO Foundry framework, which includes a set of ontology development principles and practices for ontology consistency, uniformity, and accountability. The RBO has now been incorporated into two radiation research data repositories, NASA’s GeneLab omics database (https://genelab.nasa.gov), and the European Commission STORE database (https://www.storedb.org/). Continuous build integration tools allowed our international RBO collaboration to be more efficient and focus its efforts on semantic model design. Currently, the RBO contains over 300 annotated classes and individuals specific to the study of radiation on biological systems, as well as imports of many additional classes from other OBO Foundry ontologies that relate to and/or provide context for these RBO entities. We publish the RBO through the OBO Foundry, so that it is available for browsing, download, and querying through NCBI Bioportal web site and application programming interface. The NASA Ames Life Science Data Archive (ALSDA) is also in the process of adopting use of the RBO, taking NASA one step closer to a knowledge-based system for space biology data. It is our hope that the global communities of radiation research Investigators, data curators and data analysts can similarly leverage the RBO and will contribute to its further development.

radiation↗