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DOE OSTI2023

This St. Patrick’s Day, take a look at “lucky” Lab artifacts from the Manhattan Project

What luck! Tucked inside J. Robert Oppenheimer’s book Bhagavad-Gita is a four-leaf clover. The famed physicist and first Lab director regularly quoted the Hindu scripture, most notably upon witnessing the Trinity test, which was the successful detonation of the first-ever Los Alamos created atomic bomb. Oppenheimer was said to have recalled the line, “Now I am become Death, the destroyer of worlds.” (The quote, though, has been widely misinterpreted.) The clover is taped to what appears to be a calling card from his spouse Kitty and was found inside his copy of the Bhagavad Gita, which was donated to the Lab’s Bradbury Science Museum by private donors Ben and Sara Beck Svetitsky in early 2020. Kitty Oppenheimer was educated as a botanist and biologist, and accompanied her husband to Los Alamos, along with their two children. The family was here in 1943 through the end of World War II in 1945. The book, with the card found inside, makes up one of two of J. Robert Oppenheimer’s personal effects within the Lab’s collections.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2023

Plant Cell Biology International Meeting 2022

There is a strong need to develop the knowledge base that will enable the rational design of improved crop species for sustainable agriculture and biomass production. To attain this goal, researchers must learn how plant cells integrate metabolism and cellular dynamics during growth and in response to environmental challenges. Meeting these goals require data sharing and the development and training of faculty, post-doctoral fellows, graduate and undergraduate students in state-of-the-art quantitative integrative cell biology methods. The inaugural Plant Cell Biology International (PCBI) meeting capitalized on the interaction between two well-established plant cell biology communities across the Atlantic, the Midwest Plant Cell Dynamics (PCD) and the European Network for Plant Endomembrane Research (ENPER) and provided a framework to meet these goals. The conference took place in person successfully during August 1-5th 2022 in Crete, Greece. The conference offered opportunities for undergraduate and graduate students, postdocs, young investigators across the globe to present their results and interact across different disciplines. The conference provided an open and inclusive forum for oral presentations that allowed all labs to share research results. It was attended over 80 % by students, postdocs and young investigators. Workshops on best practices for image acquisition and processing pipelines, publication guidelines by scientific journal editors, professional development and well-being benefited the participants at large. Overall, this was the inaugural joint Plant Cell Biology International conference that for the first time officially brought together plant cell biologists to discuss opportunities and challenges in the field to gain a mechanistic understanding of complex biological processes and advance sustainable agriculture. Due to its success, it was rescheduled for 2025 in Crete, to continue strengthening the plant cell biology community and exchanging knowledge and expertise across the globe.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

2024 Results for Avian Monitoring at the Technical Area 36 Minie Site, Technical Area 39 Point 6, Technical Area 16 Burn Ground, and DARHT at Los Alamos National Laboratory

Los Alamos National Laboratory (LANL) biological subject matter experts in the Environmental Protection and Compliance Division initiated a multi-year program in 2013 to monitor avifauna (birds) at two open detonation sites and one open burn site on LANL property. Additional monitoring began in 2017 at a third firing site, the Dual-Axis Radiographic Hydrodynamic Test (DARHT) Facility. In this annual report, we compare monitoring results from these efforts among years to identify and evaluate firing and open burn site impacts on the local bird community. The objectives of this study are • to determine whether LANL operations impact bird abundance, species richness, or diversity; • to examine occupancy and nest success of secondary-cavity nesting birds that use nest boxes; and • to examine chemical concentrations (such as radionuclides, inorganic elements, and/or organic compounds) in nonviable eggs and deceased nestlings that are collected opportunistically with the upper-level bounds of background concentrations, when available. During May through July 2024, LANL biologists completed multiple avian point count surveys at each of the following treatment sites: • Technical Area (TA) 36 Minie Site, • TA-39 Point 6, • TA-16 Burn Ground, and • DARHT. We recorded a total of 1,088 birds that represented 65 species at the four treatment sites and compared these results with data from their associated control sites. In 2024, abundance and species richness at treatment and control sites continued to trend similarly from year to year, with minor random deviations expected from bird communities. Species richness at firing sites differed little from the previous year’s values. Two new bird species were observed at the firing sites—cedar waxwing (Bombycilla cedrorum) and pinyon jay (Gymnorhinus cyanocephalus). Shannon diversity values at TA-36 Minie Site, TA-39, and DARHT were statistically higher than one or more of their associated controls. Annual species diversity at treatment sites was high in 2024 across all firing sites relative to similar habitat control sites. We also monitored avian nest boxes to compare occupancy and nest success data from nest boxes at treatment sites with the overall avian nest box monitoring network and against a subset of relevant control sites. Nest box success has decreased at both treatment and control sites since monitoring began, suggesting that overlapping climatic factors are responsible for patterns of declining nest success. In 2024, nonviable avian eggs and one nestling were opportunistically collected at Bandelier National Monument, TA-16 Burn Ground, TA-36 Minie, TA-39 Point 6, and DARHT. All egg samples and the one nestling sample were evaluated for per- and polyfluoroalkyl substances, which were detected from all locations, including the control site at Bandelier National Monument. Overall results from 2024 continue to suggest that operations at the four treatment sites are not negatively impacting bird populations. This long-term project will continue to monitor for any changes over time.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

CRCNS US-France Research Proposal: Collaborative Research: Encoding reward expectation in Drosophilia

The fruit fly Drosophila melanogaster has been a valuable model for investigating the genetic and neural bases that underlie learning and memory. Early and most current studies use basic behavior conditioning protocols to study learning in controlled laboratory settings. More recently, the ability to transgenically manipulate many of the brain neurons in the fruit fly with exquisite specificity, and the recent knowledge of the synaptic ‘connectome’ of the fruit fly brain, makes these animals almost unique as a comprehensive model for studies of learning, memory and motivated behavior. In fact, the connectome has revealed many types of new connections that had until now been overlooked. Within this context, the thesis of this proposal is that studies of learning and memory will be greatly enhanced by using more sophisticated means for evaluating memory representations, such as have been developed in vertebrates, and combining those studies with information from the connectome guided by computational modelling. We propose to push beyond the boundaries of existing conditioning protocols for fruit flies to investigate more complex memory representations. In particular, we will investigate the function of reinforcement pathways in relation to the absence of expected reinforcement. More specifically, we propose a series of experiments designed to investigate the memory representations in fruit flies when an expected consequence of a Conditioned Stimulus (CS) fails to occur. Although studies have evaluated how this failure can establish extinction memory for the CS, our studies will go beyond studying extinction. Specifically, we predict that in Drosophila when a CS is associated with a failed expectation of an appetitive food reinforcement it will acquire aversive value, and vice versa for a failed expectation of an aversive reinforcer. We combine these studies with manipulations of reinforcement pathways in the CNS inspired from the connectome, iteratively knitted in with established computational models. Intellectual Merit: The concept of reinforcement expectation and incentive contrast have been influential in the development of studies of associative learning in mammals. These questions are particularly challenging to answer in vertebrates because they require exquisite cellular, temporal, and genetic specificity of experimental manipulations. The recent development of work with identified neurons and their connectomes makes the larval and adult fly brains ripe as models for pushing our understanding of neural bases for these higher- order conditioning phenomena. Broader Impacts: Public health: These analyses and the conceptual framework of prediction error processing underlying them have a profound impact on our understanding of reinforcement-related behavior in humans, including monetary rewards and the mnemonic consequences of traumatic experiences, and for pathologies of the dopamine reinforcement system. Educational: This project will provide interdisciplinary training for postdoctoral researchers, Ph.D. and undergraduate students. The PIs will act as co-supervisors or mentors of students working in the different labs via face-to-face and internet-based technologies. We will also work with ASU’s award-winning Ask- A-Biologist program. This is an online science program designed to enrich the learning experiences of students of all ages and to provide classroom material for use by K-12 teachers. We will develop an extension of a game developed under a prior NSF award, and the new game will include modules to teach K-12 students about how insects learn. We will also integrate into the AAB site a program developed by a collaborator (B Gerber) at the Leibniz Institut für Neurobiologie, Magdeburg, and now in use in schools in Germany, to teach K-12 students how to train animals using the fruit fly larval learning paradigm. Underrepresented groups: All PIs will work with their university offices of Academic Diversity and Equal Opportunity for reaching underrepresented students.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

MITRE Domain Specific Language (DSL) for synthetic biology workflows (CRADA Final Report)

MITRE is currently developing BioNet, a network designed to facilitate the work of biologist collaborators that are distributed across multiple organizations. BioNet is envisaged to break down traditional barriers in biology, allowing for an integrated, service-based approach to projects which can utilize expertise from any participating entity. This disaggregation fosters innovation by enabling contributions from multiple sources. The public will benefit from the development of the BioNet (to which this project contributes), in that this fostered innovation could positively contribute to our economy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Neutrons in Structural Biology: Challenges and Opportunities (Workshop Report)

Gaining a thorough understanding of biological systems requires building our knowledge about biological processes from the level of atoms and electrons, and up to whole organisms. Such comprehensive knowledge will allow for a predictive understanding of complex biological systems behavior. It will guide us in the design and development of novel therapeutics and vaccines to tackle existing health threats and to prepare for future pandemics, and it will provide information necessary to create new biomaterials and bio-inspired technologies through manipulation of biological macromolecules, their assemblies, single cells and even microorganisms. Reaching these goals will require a synergistic combination of multiple experimental techniques with molecular calculations and predictive simulations, and the design and development of new techniques and capabilities that bridge current knowledge and technology gaps. Neutron scattering provides unique information about the biomacromolecular structure and function and can play a major role in achieving these goals. A workshop was held to engage the scientific community in identifying pressing challenges in biochemistry, structural biology, enzymology and structure-guided drug design not solved with the current neutron scattering technologies or utilizing other structural biology techniques such as X-ray crystallography, NMR, and cryo-EM. The workshop brought together structural biology, biochemistry and computational experts, as well as early career researchers and students, creating a forum for discussing scientific advancement and collaboration. The workshop included a one-day satellite training workshop where graduate students and postdoctoral researchers were educated in the application of neutron crystallography and small-angle scattering in structural biology. Furthermore, the Instrument Scientific Advisory Board (ISAB) for the development of a macromolecular neutron diffractometer at ORNL’s Second Target Station was introduced at the workshop. The major outcome was that neutrons can provide atomic-level understanding of biomacromolecular structure, function and dynamics which is of paramount importance for addressing the identified challenges. Neutron crystallography, in particular, can resolve long-standing biochemical issues regarding enzyme function by delineating the underlying chemistry and can have a major impact on the design of small-molecule therapeutics, especially in combination with molecular computation (quantum chemistry and molecular dynamics simulations) and the emerging artificial intelligence (AI)-assisted drug design technologies. The unique properties of neutrons, including their high sensitivity to hydrogen and their non-destructive nature, make them ideal probes of biological matter. There is a palpable need in the scientific community to expand and enhance the impact of neutron sciences on biology. Neutron crystallography is the only structural biology method capable of determining positions of all hydrogen atoms in proteins, nucleic acids and their complexes at near-physiological temperatures and of unstable species at cryogenic temperatures. Moreover, neutron analysis is non-ionizing, non-destructive and does not perturb the structure or redox chemistry of active site metal centers and clusters in proteins, which can be invaluable for studying radiation-sensitive metalloprotein complexes. Further, neutron energies used in scattering applications are similar to atomic motions, permitting neutron spectroscopies to characterize the dynamics of biomacromolecules on the picosecond to microsecond timescales. The different sensitivities of neutrons to protium (H) and deuterium (D) isotopes of hydrogen allow enhanced visibility of specific parts of biological complexes through isotopic labeling. The impact of neutrons will be most powerful when neutron scattering is combined with complementary experimental techniques that use photons and electrons, and with high-performance computing. The interconnection and mutuality of the experimental and theoretical capabilities will drive discoveries in biological and health sciences to generate more complete picture of complex biological systems. The major limitation in the field of biological neutron crystallography has been signal-to-noise, demanding large samples that are difficult to produce for the majority of biomacromolecules and limiting the applicability of this technique in biological sciences. A neutron crystallography instrument at the Second Target Station will revolutionize biological science with neutrons by engaging a large scientific community of structural biologists, enabling successful neutron diffraction experiments from radically smaller biomacromolecular crystals, resolving unanswered biochemical questions, and meaningfully contributing to rational drug design. The meeting highlighted 10 grand challenges that will be addressed with this advanced capability over the next decade and beyond, and the recommendations required to help address them are given below.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Status of Federally Listed Threatened and Endangered Species at Los Alamos National Laboratory

Los Alamos National Laboratory (LANL) contains suitable habitat for three species protected under the Endangered Species Act (ESA): Mexican spotted owl ( Strix occidentalis lucida ), Jemez Mountains salamander ( Plethodon neomexicanus ), and southwestern willow flycatcher ( Empidonax traillii extimus ). LANL biologists have documented two other species nearby and manage them for any potential impacts. These species are the western distinct population segment of the yellow-billed cuckoo ( Coccyzus americanus ) and the New Mexico meadow jumping mouse ( Zapus hudsonius luteus ).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Evaluating Movement Patterns of the Rattlesnake Hills Elk Herd on Hanford for Calendar Years 2019-2024

Biologists first documented elk on the Hanford Site in 1972; since then, the elk herd known as the Rattlesnake Hills Elk Herd (RHEH) has grown substantially (PNNL-13331, Population Characteristics and Seasonal Movement Patterns of the Rattlesnake Hills Elk Herd: Status Report 2000). Through the 1990s, the core range of the RHEH was focused on the portion of the Hanford Reach National Monument known as the Fitzner-Eberhardt Arid Lands Ecology (ALE) Reserve. More recently, larger numbers of elk have been occupying the U.S. Department of Energy (DOE), Hanford Field Office (HFO), formerly the DOE, Richland Operations Office managed portion- of the Hanford Site, known as central Hanford (Figure 1-1). This began with bachelor groups of bulls occupying the site intermittently, and the herd has grown to resident herds, including bulls, cows, and calves. The Washington Department of Fish and Wildlife (WDFW) established a target herd size for the RHEH of less than 350 animals to minimize damages on adjacent private agricultural lands (Washington State Elk Herd Plan–Yakima Elk Herd [WDFW 2002]). Attempts to control the RHEH population through hunting on private lands and a relocation effort during 2000 have failed to limit growth of the population toward the WDFW target, and the herd exceeds 1,600 according to recent counts (PNNL-13331; DOE/RL- 2023-20, Hanford Annual Site Environmental Report for Calendar Year 2022). Although elk are present on central Hanford year-round, they continue to move between areas offsite, the ALE Reserve, and central Hanford throughout the year, and it is these movements that result in many of the elk-vehicle collisions (EVC) that occur along Hanford Site roads and on the Washington State highways bordering the site. In addition, changes in management strategies on the ALE Reserve, including recent and potential future tribal elk hunts, may alter herd behavior and result in additional animals transiting onto and off central Hanford.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Summer Bat Monitoring Report for Calendar Year 2023

Bats are mammals belonging to the order Chiroptera, which means “hand-wing.” They use a thin membrane of skin stretched between their fingers to fly. All bat species known in the state of Washington are insectivorous and each bat can consume 600-1,000 insects per hour while feeding. Bats typically give birth once per year to a single pup, making bat populations vulnerable to impacts and slow to recover. Several species of bats have been documented on the Hanford Site, with nine species identified during The Nature Conservancy surveys in 1997 and 1998, and an additional seven species listed as potentially present as documented in Biodiversity Inventory and Analysis of the Hanford Site. Final Report 1994-1999 (Soll et al., 1999). Ongoing U.S. Department of Energy (DOE), Richland Operations Office (RL) acoustic surveys, including HNF-53759, Summer Bat Monitoring Report for Calendar Year 2012, have also confirmed the presence of the same nine species documented by Soll et al. (1999). An additional species, the spotted bat (Euderma maculatum), was observed roosting on the exterior of a facility by Hanford Site personnel in 2021; the species was confirmed by Hanford Site biologists via photograph (Table 1-1).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Summer Bat Monitoring Report for Calendar Year 2022

Bats belong to the order Chiroptera, which means “hand-wing.” They use a thin membrane of skin stretched between their fingers to fly. All bat species known in the state of Washington are insectivorous and each bat can consume 600-1000 insects per hour while feeding. Bats typically give birth once per year to only one pup, making bat populations vulnerable to impacts and slow to recover. Several species of bats have been documented on the Hanford Site, with nine species identified during the Nature Conservancy surveys in 1997 and 1998, and an additional seven species listed as potentially present (Soll et al. 1999). Previous U.S. Department of Energy, Richland Operations Office (DOE-RL) acoustic surveys conducted in 2012 also confirmed the presence of the same nine species documented by Soll et al. (HNF-53759). In 2021, an additional species, the spotted bat, was observed roosting on the exterior of a facility by Hanford Site personnel; the species was confirmed via photograph by site biologists (Table 1).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Summer Bat Monitoring Report for Calendar Year 2021

Bats belong to the order Chiroptera, which means “hand-wing.” They use a thin membrane of skin stretched between their fingers to fly. All bat species known in the state of Washington are insectivorous, and each bat can consume 600-1000 insects per hour while feeding. Unlike rodents, who give birth to multiple litters of several young each year, bats typically give birth once per year to only one pup, making bat populations more vulnerable to impacts and slower to recover. Several species of bats have been documented on the Hanford Site, with nine species identified during The Nature Conservancy surveys in 1997 and 1998, and an additional seven species listed as potentially present (Soll et al. 1999). Previous U.S. Department of Energy, Richland Operations Office (DOE-RL) acoustic surveys conducted in 2012 also confirmed the presence of the same nine species documented by Soll et al. (HNF-53759). In 2021, an additional species, the spotted bat, was observed roosting on the exterior of a facility by Hanford Site personnel; the species was confirmed via photograph by site biologists (Table 1).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Burrowing Owl Survey Report for Sandia National Laboratories: 2025

The Burrowing Owl Survey Report for Sandia National Laboratories: 2025 provides data and analysis on occupancy surveys that were conducted during the 2025 survey season. The surveys were conducted in partnership with Kirtland Air Force Base’s Natural Resource Program and the United States Fish and Wildlife Service to maintain and expand on the long-term dataset on burrowing owls on base. Ecology Program biologists conducted roadside census surveys at survey areas previously identified by Kirtland Air Force Base along with several additional survey areas deemed suitable for occupancy. Remote sensor camera monitoring was also conducted on three nest burrows. In total, 12 breeding pairs of burrowing owls were confirmed in 2025. Several owls were confirmed to have leg bands, indicating previous captures and recurrence of these specific individuals on base. Occupancy surveys on burrowing owls continue to provide valuable information on ecosystem health and can serve to inform future management direction and decisions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Evaluation of Howard A. Hanson Dam Juvenile Fish Passage and Survival Study Live Fish Injury Assessment, Sensor Fish, and BioPA Modeling Tasks

The live fish injury assessment, Sensor Fish, and BioPA modeling study tasks were conducted by researchers from Pacific Northwest National Laboratory (PNNL). The four tasks were part of the larger Evaluation of Howard A. Hanson Dam (HAHD) Juvenile Fish Passage and Survival study, which had six total tasks. To achieve study objectives for each of the four tasks, field work occurred at Green Peter Dam (GPR) to evaluate the highest elevation steep slope bypass pipe, at HAHD to evaluate baseline conditions of the horseshoe tunnel, and at PNNL’s Aquatic Research Laboratory (ARL) to evaluate simulated dam passage conditions (i.e., shear forces and collision). Each of these evaluations utilized live fish injury assessment, Sensor Fish, and BioPA modeling. Live fish injury assessment and survival (tagged with and without balloon or passive integrated transponder [PIT] tags) was correlated with Sensor Fish to determine thresholds. The CFD analyses were then performed, and the computed values were compared to the corresponding measured values of Sensor Fish data. The results of the overall injury and survival of fish was also used in the validation of the CFD modeling method. Collectively, the results will aid in future modeling of fish passage at HAHD. Results from these tasks can be used by biologists, engineers, resource managers, and regional decision-makers to inform baseline conditions under current operations and the engineering design of the new FPF at HAHD. This draft report contains initial data and results from the four tasks. Table 8 1, Table 8 2, and Table 8 3, and Figure 8 1, Figure 8 2, and Figure 8 3 depict the CFD modeling findings for the GPR steep slope bypass, HAHD horseshoe tunnel, and laboratory testing. Table 8 4, Table 8 5, and Table 8 6 depict the Sensor Fish findings for the GPR steep slope bypass and HAHD horseshoe tunnel testing. The Mv values observed in the HAHD were significantly lower compared to the laboratory experiments conducted at PNNL. Currently, investigations are underway to understand the reasons for this disparity and to establish an appropriate threshold value for Mv. Survival predictions presented in the tables below should be considered preliminary and should not be used until further analyses and adjustments are completed. The next steps for modeling will include the flow regime, (i.e., density of flow regimes due to water and air mixing ) to continue to improve on the threshold value for Mv.

13 HYDRO ENERGY↗
DOE OSTI2025

Evaluation of Howard A. Hanson Dam Juvenile Fish Passage and Survival Study: Downstream Passage and Survival (Acoustic Telemetry) (Task Final Report)

The Downstream Passage and Survival (Acoustic Telemetry) task was one of several tasks for the Evaluation of Howard A. Hanson Dam (HAHD) Juvenile Fish Passage and Survival study. For this task, a juvenile fish passage and survival study was conducted at HAHD from March 10, 2024 through June 27, 2024 for arrays in the HAHD Reservoir and Green River, and through July 9, 2024 for the arrays in the Duwamish River. Fish releases occurred over four times from March through May. Active tag (acoustic telemetry) technology was used to provide biological baseline information for the passage and survival of juvenile Puget Sound (PS) Chinook salmon (Oncorhynchus tshawytscha). Results will be used by biologists, engineers, resource managers, and regional decision-makers to inform the engineering design of the new fish passage facility (FPF) at HAHD. However, hatchery sub-yearling PS Chinook salmon of the appropriate size for tag implantation during the study period (> 95 mm in fork length, Geist et al. 2018) were unavailable. Therefore, yearling Coho salmon (O. kisutch) were used as a surrogate species for this acoustic telemetry study.

13 HYDRO ENERGY↗
DOE OSTI2026

CRADA Number NFE-24-10495 with Algaeo, LLC (CRADA Final Report)

This study investigated the potential for a synthetic consortium of mutualistic terrestrial microbes— comprising the fungi Laccaria bicolor and Serendipita indica alongside bacterial Pseudomonas strains—to influence the growth and productivity of the freshwater microalgae Chlorella vulgaris. The project aimed to determine if microbial complexes engineered to enhance terrestrial plant growth could provide similar growth-promoting benefits or pathogen resistance within an aquatic algal system. Using a quantitative experimental design, C. vulgaris was co-cultured with the microbial mix under controlled laboratory conditions, with growth rates, biomass density, and metabolic activity monitored over a standard cultivation period. The results demonstrated no significant symbiotic relationship or growth enhancement between these terrestrial microbes and the microalgae, as the C. vulgaris maintained independent growth trajectories unaffected by the fungal or bacterial inoculants. We conclude that the specialized mutualisms of these fungi and bacteria are likely niche-specific to vascular plants and do not readily translate to the phycosphere of C. vulgaris. These findings are valuable to synthetic biologists and bioenergy researchers, as they define the functional boundaries of inter-kingdom microbial engineering and underscore the necessity of selecting niche-compatible species when designing consortia for industrial algal cultivation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Overview of Fish Passage Facilities at Hydropower Developments across the Conterminous United States

This dataset contains geo-referenced information on the presence and types of fish passage facilities at hydropower developments across the conterminous United States (CONUS) presented in the ORNL Hydropower Fish Passage Database Webmap (https://www.ornl.gov/project/quantifying-national-fish-passage-data/webmap). It was developed through collaborative partnerships with fish passage engineers and biologists at both the US Fish and Wildlife Service (USFWS) and the National Marine Fisheries Service (NMFS), and hydropower experts at the Low Impact Hydropower Institute (LIHI). Information contained within this dataset has been provided by many different sources, including State and Federal resource management agencies, non-governmental organizations, hydropower industry members, and published datasets=. This dataset is intended to provide a high-level overview of the distribution of fish passage infrastructure at hydropower developments across CONUS; a more comprehensive database is anticipated to be released later in 2025. This dataset contains one data file in comma-separate (*.csv) format and the information within it was last updated on 24 March 2025.

13 HYDRO ENERGY↗
DOE OSTI2025

Hydropower Fish Passage Webmap

The National Fish Passage Webmap application provides an environment that allows users to visualize information information on fish passage facility existence, type, and direction at hydropower developments across the conterminous United States. It was developed through collaborative partnerships with fish passage engineers and biologists at both the US Fish and Wildlife Service (USFWS) and the National Marine Fisheries Service (NMFS), and hydropower experts at the Low Impact Hydropower Institute (LIHI). Data on fish passage facilities at hydropower features were compiled from numerous sources including published and non-published datasets, published reports, email communications with federal and state resource managers and hydropower operators, and by extracting information from regulatory documents within the FERC eLibrary. The number of sources for a given feature varied, which occasionally resulted in conflicting information regarding the existence of fish passage facilities or in the type or sub-type of passage technologies. Such discrepancies were reviewed and resolved individually, based on the weight of evidence or, when available, on direct observations from information providers or aerial imagery.

13 HYDRO ENERGY↗
DOE OSTI2021

A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum

A better understanding of the genetic and metabolic mechanisms that confer stress resistance and tolerance in plants is key to engineering new crops through advanced breeding technologies. This requires a systems biology approach that builds on a genome-wide understanding of the regulation of gene expression, plant metabolism, physiology and growth. In this study, we examine the response to drought stress in Sorghum, as we leverage the tools for transcriptomics and plant metabolic modeling we have implemented at the U.S. Department of Energy Systems Biology Knowledgebase (KBase). KBase enables researchers worldwide to collaborate and advance research by allowing them to upload private or public data into the KBase Narrative Interface, empowering them to analyze this data using a rich, extensible array of computational and data-analytics tools, and allows them to securely share scientific workflows and conclusions. We demonstrate how to use the current RNA-seq tools in KBase, applicable to both plants and microbes, to assemble and quantify long transcripts and identify differentially expressed genes effectively. More specifically, we demonstrate the utility of the platform by identifying key genes that are differentially expressed during drought-stress in Sorghum bicolor, which is an important sustainable production crop plant. We then show how to use KBase tools to predict the membership of genes in metabolic pathways and examine expression data in the context of metabolic subsystems. We demonstrate the power of the platform by making the data analysis and interpretation available to the biologists in the reproducible, re-usable, point-and-click format of a KBase Narrative thus promoting FAIR (Findable, Accessible, Interoperable and Reusable) guiding principles for scientific data management and stewardship.

59 BASIC BIOLOGICAL SCIENCES↗