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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

V-HAMSTeR v1.0.0

V-HAMSTeR is a bioinformatics software tool designed to predict the hosts of viruses directly from genomic sequences. It can be used by researchers to predict animal, prokaryotic, plant, protist or fungal viral hosts including viruses that may be fragmented or discovered in environmental metagenomic datasets. Features & Uses: The software employs a novel dual-stream deep learning architecture that dynamically fuses implicit sequence embeddings from a genomic foundation model with 13 explicit, handcrafted biological features (e.g., coding density and strand switch rates). To ensure maximum reliability, V=HAMSTeR deploys a 5-fold deep ensemble calibrated via Joint Temperature Scaling, providing users with statistically rigorous confidence probabilities. It also features an automated sequence chunking and mean-pooling module to seamlessly process variable-length contigs. Advantages Over Similar Technologies: Existing tools (e.g., IPEV, RNAVirHost) typically rely on either basic k-mers or isolated neural networks. V-HAMSTeR's hybrid architecture captures both broad genomic context and specific biological motifs that standalone foundation models often miss. Furthermore, unlike competitor tools that struggle with incomplete data or exhibit extreme overconfidence, V-HAMSTeR is explicitly benchmarked and mathematically calibrated for fragmented assemblies (1kb–10kb). This makes it uniquely robust, accurate, and trustworthy for the messy reality of real-world environmental viromics.

Grigson, Susie [Lawrence Berkeley National Laborat↗
DOE OSTI2020

Osteoporosis Treatments Affect Bone Matrix Maturation in a Rat Model of Induced Cortical Remodeling

ABSTRACT To test how osteoporosis drugs affect bone matrix maturation during cortical bone remodeling, 72 pregnant rats were switched from a 0.4% to a 0.01% calcium diet at parturition for a 23‐day lactation period. At weaning, eight dams were sacrificed to establish baseline values, while the remaining dams were returned to 0.4% calcium and treated with vehicle (saline), sodium fluoride (NaF), zoledronic acid (ZA), or sclerostin antibody (Scl‐Ab) for either 7 or 28 days (eight animals per group per time point). Femora were examined by μCT, dynamic histomorphometry, Fourier transform infrared imaging, and three‐point bending of notched specimens. Cortical porosity decreased in all groups from baseline to day 28. Intracortical mineralizing surface (MS/BS) and mineral apposition rate (MAR), as well as the mineral‐to‐matrix ratio were unaffected by treatment, but intracortical crystallinity was increased in the ZA group at day 10 compared with vehicle. Cortical area increased in all groups over 28 days mainly because of an addition of bone at the endocortical surface. Endocortical MS/BS did not vary among the groups, but endocortical MAR was suppressed in the NaF group at day 2 and elevated in the Scl‐Ab group at day 4 compared with vehicle. Endocortical mineral‐to‐matrix ratio was increased at days 5 and 10 following NaF treatment and endocortical crystallinity was increased at day 5 following ZA treatment compared with vehicle. Fracture toughness did not differ among the groups. Thus, the treatments affected matrix maturation more strongly at the endocortical then intracortical envelope. In this model of induced remodeling, the bone formation phase is synchronized at multiple sites, facilitating study of the effects of drugs or other bone‐targeting agents on matrix maturation independent of their effects on the initiation of remodeling. © 2020 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Improved Water Sound Synthesis using Coupled Bubbles

We introduce a practical framework for synthesizing bubble-based water sounds that captures the rich inter-bubble coupling effects responsible for low-frequency acoustic emissions from bubble clouds. We propose coupled-bubble oscillator models with regularized singularities, and techniques to reduce the computational cost of time stepping with dense, time-varying mass matrices. Airborne acoustic emissions are estimated using finite-difference time-domain (FDTD) methods. We propose a simple, analytical surface-acceleration model, and a sample-and-hold GPU wavesolver that is simple and faster than prior CPU wavesolvers. Sound synthesis results are demonstrated using bubbly flows from incompressible, two-phase simulations, as well as procedurally generated examples using single-phase FLIP fluid animations. Our results demonstrate sound simulations with hundreds of thousands of bubbles, and perceptually significant frequency transformations with fuller low-frequency content.

Computer Science↗
DOE OSTI2023

Engineering a modular 44 Ti/ 44 Sc generator: eluate evaluation in preclinical models and estimation of human radiation dosimetry

Background: 44 Sc/ 47 Sc is an attractive theranostic pair for targeted in vivo positron emission tomographic (PET) imaging and beta-particle treatment of cancer. The 44 Ti/ 44 Sc generator allows daily onsite production of this diagnostic isotope, which may provide an attractive alternative for PET facilities that lack in-house irradiation capabilities. Early animal and patient studies have demonstrated the utility of 44 Sc. In our current study, we built and evaluated a novel clinical-scale 44 Ti/ 44 Sc generator, explored the pharmacokinetic profiles of 44 ScCl 3 , [ 44 Sc]-citrate and [ 44 Sc]-NODAGA (1,4,7-triazacyclononane,1-glutaric acid-4,7-acetic acid) in naïve mice, and estimated the radiation burden of 44 ScCl 3 in humans. Methods: 44 Ti/ 44 Sc (101.2 MBq) in 6 M HCl solution was utilized to assemble a modular ZR resin containing generator. After assembly, 44 Sc was eluted with 0.05 M HCl for further PET imaging and biodistribution studies in female Swiss Webster mice. Based on the biodistribution data, absorbed doses of 44 / 47 ScCl 3 in human adults were calculated for 18 organs and tissues using the IDAC-Dose software. Results: 44 Ti in 6 M HCl was loaded onto the organic resin generator with a yield of 99.97%. After loading and initial stabilization, 44 ScCl 3 was eluted with 0.05 M HCl in typical yields of 82.9 ± 5.3% (N = 16), which was normalized to the estimated generator capacity. Estimated generator capacity was computed based on elution time interval and the total amount of 44 Ti loaded on the generator. Run in forward and reverse directions, the 44 Sc/ 44 Ti ratio from a primary column was significantly improved from 1038 ± 440 to 3557 ± 680 (Bq/Bq) when a secondary, replaceable, ZR resin cartridge was employed at the flow outlet. In vivo imaging and ex vivo distribution studies of the reversible modular generator for 44 ScCl 3 , [ 44 Sc]-citrate and [ 44 Sc]-NODAGA show that free 44 Sc remained in the circulation significantly longer than the chelated 44 Sc. The dose estimation of 44 ScCl 3 reveals that the radiation burden is 0.146 mSv/MBq for a 70 kg adult male and 0.179 mSv/MBq for a 57 kg adult female. Liver, spleen and heart wall will receive the highest absorbed dose: 0.524, 0.502, and 0.303 mGy/MBq, respectively, for the adult male. Conclusions: A clinical-scale 44 Ti/ 44 Sc generator system with a modular design was developed to supply 44 ScCl 3 in 0.05 M HCl, which is suitable for further radiolabeling and in vivo use. Our data demonstrated that free 44 ScCl 3 remained in the circulation for extended periods, which resulted in approximately 10 times greater radiation burden than stably chelated 44 Sc. Stable 44 Sc/ 47 Sc-complexation will be more favorable for in vivo use and for clinical utility.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2025

Anti-Ebola virus mAb 3A6 protects highly viremic animals from fatal outcome via binding GP(1,2) in a position elevated from the virion membrane

Abstract Monoclonal antibodies (mAbs) against Ebola virus (EBOV) glycoprotein (GP 1,2 ) are the standard of care for Ebola virus disease (EVD). Anti-GP 1,2 mAbs targeting the stalk and membrane proximal external region (MPER) potently neutralize EBOV in vitro and are protective in a mouse model of EVD. However, their neutralization mechanism is poorly understood because they target a GP 1,2 epitope that has evaded structural characterization. Using X-ray crystallography and cryo-electron tomography of mAb 3A6 complexed with its stalk–MPER epitope, we reveal a previously undescribed mechanism in which 3A6 binds to a conformation of GP 1,2 that is lifted from the virion membrane. We further show that in both domestic guinea pig and rhesus monkey EVD models, 3A6 provides therapeutic benefit at high-viremia advanced disease stages and at the lowest dose yet demonstrated for any anti-EBOV mAb-based monotherapy. The findings reported here can guide design of next-generation highly potent anti-EBOV therapeutics and vaccines.

Science & Technology - Other Topics↗
DOE OSTI2023

Impaired cardiac glycolysis and glycogen depletion are linked to poor myocardial outcomes in juvenile male swine with metabolic syndrome and ischemia

Abstract Obesity continues to rise in the juveniles and obese children are more likely to develop metabolic syndrome (MetS) and related cardiovascular disease. Unfortunately, effective prevention and long‐term treatment options remain limited. We determined the juvenile cardiac response to MetS in a swine model. Juvenile male swine were fed either an obesogenic diet, to induce MetS, or a lean diet, as a control (LD). Myocardial ischemia was induced with surgically placed ameroid constrictor on the left circumflex artery. Physiological data were recorded and at 22 weeks of age the animals underwent a terminal harvest procedure and myocardial tissue was extracted for total metabolic and proteomic LC/MS–MS, RNA‐seq analysis, and data underwent nonnegative matrix factorization for metabolic signatures. Significantly altered in MetS versus. LD were the glycolysis‐related metabolites and enzymes. In MetS compared with LD Glycogen synthase 1 (GYS1)‐glycogen phosphorylases (PYGM/PYGL) expression disbalance resulted in a loss of myocardial glycogen. Our findings are consistent with the concept that transcriptionally driven myocardial changes in glycogen and glucose metabolism‐related enzymes lead to a deficiency of their metabolite products in MetS. This abnormal energy metabolism provides insight into the pathogenesis of the juvenile heart in MetS. This study reveals that MetS and ischemia diminishes ATP availability in the myocardium via altering the glucose‐G6P‐pyruvate axis at the level of metabolites and gene expression of related enzymes. The observed severe glycogen depletion in MetS coincides with disbalance in expression of GYS1 and both PYGM and PYGL. This altered energy substrate metabolism is a potential target of pharmacological agents for improving juvenile myocardial function in MetS and ischemia.

Broadwin, Mark↗
DOE OSTI2022

Towards replacement of animal tests with in vitro assays: a gene expression biomarker predicts in vitro and in vivo estrogen receptor activity

High-throughput transcriptomics (HTTr) has the potential to support efforts to reduce or replace some animal tests. In past studies, we described a computational approach utilizing a gene expression biomarker consisting of 46 genes to predict estrogen receptor (ER) activity after chemical exposure in ER-positive human breast cancer cells including the MCF-7 cell line. We hypothesized that the biomarker model could identify ER activities of chemicals examined by Endocrine Disruptor Screening Program (EDSP) Tier 1 screening assays in which transcript profiles of the same chemicals were examined in MCF-7 cells. For the 62 chemicals examined including 5 chemicals examined in this study using RNA-Seq, the ER biomarker model accuracy was 1) 97% for in vitro reference chemicals, 2) 76–85% for guideline uterotrophic assays, and 3) 87–88% for guideline and nonguideline uterotrophic assays. For the same chemicals, these accuracies were similar or slightly better than those of the ToxCast ER model based on 18 in vitro assays. The performance of the ER biomarker model indicates that HTTr interpreted using the ER biomarker correctly identifies active and inactive ER reference chemicals. Finally, as part of the HTTr screening program the approach could rapidly identify chemicals with potential ER bioactivities for additional screening and testing.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Optimization of a Lethal, Combat-Relevant Model of Sterile Inflammation in Mice for Drug Candidate Screening

ABSTRACT Introduction Extensive trauma, commonly seen in wounded military Service Members, often leads to a severe sterile inflammation termed systemic inflammatory response syndrome (SIRS), which can progress to multiple organ dysfunction syndrome (MODS) and death. MODS is a serious threat to wounded Service Members, historically causing 10% of all deaths in trauma admissions at a forward deployed combat hospital. The importance of this problem will be exacerbated in large-scale combat operations, in which evacuation will be delayed and care of complex injuries at lower echelons of care may be prolonged. The main goal of this study was to optimize an existing mouse model of lethal SIRS/MODS as a therapeutic screening platform for the evaluation of immunomodulatory drugs. Materials and Methods Male C57BL/6 mice were euthanized, and the bones and muscles were collected and blended into a paste termed tissue–bone matrix (TBX). The TBX at 12.5%–20% relative to body weight of each recipient mouse was implanted into subcutaneous pouches created on the dorsum of anesthetized animals. Mice were observed for clinical scores for up to 48 hours postimplantation and euthanized at the preset point of moribundity. To test effects of anesthetics on TBX-induced mortality, animals received isoflurane or ketamine/xylazine (K/X). In a separate set of studies, mice received TBX followed by intraperitoneal injection with 20 mg/kg or 40 mg/kg Eritoran or a placebo carrier. All Eritoran studies were performed in a blinded fashion. Results We observed that K/X anesthesia significantly increased the lethality of the implanted TBX in comparison to inhaled anesthetics. Although all the mice anesthetized with isoflurane and implanted with 12.5% TBX survived for 24 hours, 60% of mice anesthetized with K/X were moribund by 24 hours postimplantation. To mimic more closely the timing of lethal SIRS/MODS following polytrauma in human patients, we extended observation to 48 hours. We performed TBX dose–response studies and found that as low as 15%, 17.5%, and 20% TBX caused moribundity/mortality in 50%, 80%, and 100% mice, respectively, over a 48-hour time period. With 17.5% TBX, we tested if moribundity/mortality could be rescued by anti-inflammatory drug Eritoran, a toll-like receptor 4 antagonist. Neither 20 mg/kg nor 40 mg/kg doses of Eritoran were found to be effective in this model. Conclusions We optimized a TBX mouse model of SIRS/MODS for the purpose of evaluating novel therapeutic interventions to prevent trauma-related pathophysiologies in wounded Service Members. Negative effects of K/X on lethality of TBX should be further evaluated, particularly in the light of widespread use of ketamine in treatment of pain. By mimicking muscle crush, bone fracture, and necrosis, the TBX model has pleiotropic effects on physiology and immunology that make it uniquely valuable as a screening tool for the evaluation of novel therapeutics against trauma-induced SIRS/MODS.

General & Internal Medicine↗
DOE OSTI2025

A Multi-Sensor Approach for Measuring Bird and Bat Collisions with Offshore Wind Turbines (Final Technical Report)

Collision of birds and bats with wind turbines is a conservation concern for both land-based and offshore wind projects. The fatality rates of birds and bats at land-based turbines are well documented. The measurement strategies on land focus on finding carcasses following collision, estimating the number of carcasses missed through searcher efficiency, carcass persistence trials and carcass fall distributions, and modeling statistically robust fatality rates. Few technologies have been developed to monitor offshore bird and bat collisions, and many that have been developed focused on detecting collisions with large birds. The few studies that have attempted to document collisions at offshore turbines do not account for smaller bodied animals or for collisions that might be missed, which prevents the calculation of statistically robust fatality rates. The overall goal of this report, A Multi-Sensor Approach for Measuring Bird and Bat Collisions with Offshore Wind Turbines (Project), was to develop an effective multi-sensor system for quantifying bird and bat collision rates, specifically for offshore wind facilities. The Project goal and resulting automated collision detection system was achieved through two major technological advancements: 1) refining The Netherlands Organisation for Applied Scientific Research’s (TNO’s) existing WT-Bird® vibration sensing system, that had successfully detected large bird collisions during daytime, to allow for improved detection of smaller birds and bats during both daytime and nighttime hours and 2) improving image processing systems and developing and integrating machine learning algorithms to automatically detect and classify small and large bird and bat collisions with offshore turbines. This final technical report (FTR) summarizes Methods , Results , Conclusions , and Lessons Learned during each of the five Tasks identified for this research and development effort. This FTR includes summaries of the following: Task 1. Initial Engineering Tests to Improve WT-Bird® Task 2. Installation of WT‐Bird® on a Utility-scale Turbine at the National Wind Technology Center – National Renewable Energy Laboratory Task 3. Field Tests and Refinement of the Object Detection System Task 4. Validation of WT-Bird® on a Land-based Turbine Task 5. Preparation for the Implementation of WT-Bird® on an Offshore Turbine. This research and development effort documented successful improvement of the WT Bird® collision detection system to detect small birds and bats, and WT-Bird® is the first collision detection system to validate results compared to land-based post-construction monitoring. The collision trials provide estimates of missed targets that can be used to estimate fatality rates, a significant improvement relative to other offshore collision monitoring systems. Advances were made in developing an edge-processing solution to reduce data storage requirements, which is important if the system is deployed for long periods of time at offshore turbines. The improved WT-Bird® system also provides an important option for wind operators on land or offshore who need to document specific details about when collisions occur, particularly efforts to further research on bat impact minimization, or when standard fatality searches are impractical (e.g. offshore) or inadequate (e.g. challenging locations on land).

17 WIND ENERGY↗
DOE OSTI2021

National Virtual Biotechnology Laboratory: Report on Rapid R&D Solutions to the COVID-19 Crisis

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply short ages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. Within months, NVBL teams produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment (PPE), creating nearly 1,000 new jobs. They used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported U.S. Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDC), and U.S. Department of Defense (DoD) efforts to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. NVBL teams also studied how to control indoor virus movement to minimize uptake and protect human health. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development (R&D) solutions. As the fight against COVID continues, sustained efforts are needed to confront this pandemic as well as future threats. Examples include: 1) Establishing “supply chains on demand” to meet emergency production needs by leveraging the materials and manufacturing expertise of DOE national laboratories and developing advances in electronics, sensing, robotics, and automation capabilities; 2) Improving the speed and robustness of drug discovery by integrating experimental platforms with DOE’s computational and experimental user facilities, which provide unique resources to support the discovery of high-potential therapeutic agents; 3) Protecting public, environmental, and animal health by developing new testing protocols and instrumentation adaptable to diverse sample types (both physiological and environmental) to quickly detect a wide range of pathogens and monitor other biorisks; 4) Supporting near-real-time data needs of decision-makers at the local, regional, state, and national levels by advancing data curation, analysis, and modeling using artificial intelligence and new data science tools for managing and evaluating large diverse datasets; 5) Harnessing DOE’s expertise in environmental modeling to design rooms and air handling for offices, classrooms, restaurants, and other structures to minimize biorisk transmissions. Going forward, NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, the Office of Science will continue to be an integral component of agency wide efforts to prepare for and respond to biorisks and other crises.

42 ENGINEERING↗
DOE OSTI2024

Radionuclide-specific Parameters Dataset

The radionuclide-specific parameters dataset is searchable for radiological information for multiple isotopes simultaneously. After selecting radionuclides of interest and the desired parameters, the RAIS will generate a table containing the values, chosen according to an established hierarchy. Results can be downloaded in Excel format. 50 parameters are available, including atomic number, soil to animal transfer coefficients, plant uptake coefficients, half-life, specific activity, and water solubility. Seven primary sources are used to populate the dataset of radiological-specific parameters. These values should be used in cancer risk assessments for the calculation of preliminary remediation goals (PRGs), hazard characterization, and transport modeling. Users can select up to 1000 radionuclides per query. The dataset supports environmental risk assessments, regulatory decision-making, and environmental planning with tools for benchmarking against risk-based standards. This structured approach ensures a robust evaluation of environmental risks tailored to regulatory needs.

Manning, Karessa [Oak Ridge National Laboratory (O↗
DOE OSTI2020

Combining Random Mutagenesis and Metabolic Engineering for Enhanced Tryptophan Production in Synechocystis sp. Strain PCC 6803

Tryptophan (Trp) is an essential aromatic amino acid that has value as an animal feed supplement, as the amount found in plant-based sources is insufficient. An alternative to production by engineered microbial fermentation is to have tryptophan biosynthesized by a photosynthetic microorganism that could replace or supplement both the plant and industrially used microbes. We selected Synechocystis sp. strain PCC 6803, a model cyanobacterium, as the host and studied metabolic engineering and random mutagenesis approaches. Previous work on engineering heterotrophic microbes for improved Trp titers has targeted allosteric feedback regulation in enzymes 3-deoxy-d-arabinoheptulosonate 7-phosphate synthase (DAHPS) and anthranilate synthase (AS) as major bottlenecks in the shikimate pathway. In this work, the genes encoding feedback-resistant enzymes from Escherichia coli, aroG fbr and trpE fbr , were overexpressed in the host wild-type (WT) strain. Separately, the WT strain was subjected to random mutagenesis and selection using an amino acid analog to isolate tryptophan-overproducing strains. The randomly mutagenized strains were sequenced in order to identify the mutations that resulted in the desirable phenotypes. Interestingly, the tryptophan overproducers had mutations in the gene encoding chorismate mutase (CM), which catalyzes the conversion of chorismate to prephenate. The best tryptophan overproducer from random mutagenesis was selected as a host for metabolic engineering where aroG fbr and trpE fbr were overexpressed. The best strain developed produced 212 ± 23 mg/liter of tryptophan after 10 days of photoautotrophic growth under 3% (vol/vol) CO2. We demonstrated that a combination of random mutagenesis and metabolic engineering was superior to either individual approach.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome

Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont’s genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Site-wide occupancy assessment using camera traps for seven mammalian species at Los Alamos National Laboratory

Los Alamos National Laboratory (LANL or Laboratory) is committed to solving national security challenges through scientific excellence and has been serving the nation and northern New Mexico for over 70 years. Being located on the Pajarito Plateau in the eastern flanks of the Jemez Mountains, the Laboratory is surrounded by a rich diversity of plants and animals. It is common to see many different species of wildlife on Laboratory property; however, sometimes interactions with wildlife can be negative. Vehicle accidents with wildlife have become a common occurrence. With the current and ongoing expansion of the Laboratory on the Pajarito Plateau, it has the potential to further impact wildlife movement including large game species. Local agencies and tribal Pueblos rely on large game species and do not want these species to be restricted from moving across property boundaries. Temporal and spatial aspects of where wildlife occur on the site is a phenomena that is either not well understood in uncommon species or needs periodic reevaluation for common species. Estimating the distribution of multiple species across the landscape provides wildlife biologists with crucial information for monitoring and conserving animal populations in a particular area. Utilizing motion activated wildlife cameras, also known as camera traps, to monitor wildlife populations has become an essential tool for biologists. Camera traps are non-invasive and cost-effective and can document multiple elusive or uncommon wildlife species, such as carnivores, simultaneously. Occupancy modeling provides a flexible framework for the analysis of the distribution for multiple wildlife species. It explicitly recognizes whether a species is spatially common or rare (occupancy = ψ) and if that species is easy or hard to detect (detection probability = p ). Multispecies and multi-season occupancy models can detect trends in species occupancy because individual species may vary in seasonal movements, detection probability, and transition rates between habitats. In this study, we assessed the site as a whole to ascertain when and where medium and large mammal species are present. Understanding wildlife patterns at the Laboratory will better inform future management decisions regarding land use and development strategies. We placed motion activated wildlife cameras in a random systematic sampling design and used these data to create occupancy models. We tested for differences in single-species occupancy and detection probability by season of mammal species captured on 20 camera traps placed across the Laboratory in a 40 mi² (103 km²) area. We focus the interpretation of our findings on seven mammal species found during this study. They are Rocky Mountain elk ( Cervus canadensis nelsoni ; hereafter “elk”), mule deer ( Odocoileus hemionus ; hereafter “deer”), mountain lion ( Puma concolor ; hereafter “lion”), American black bear ( Ursus americanus ; hereafter “bear”), coyote ( Canis latrans ), bobcat ( Lynx rufus ), and gray fox ( Urocyon cinereoargenteus ; hereafter “fox”).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A framework for challenges and solutions in biodesign research

The bioeconomy represents an advanced economic paradigm that builds upon previous agricultural, industrial, and digital economic models. It seeks to tackle critical global challenges such as resource scarcity, escalating healthcare demands, and environmental degradation. At the heart of the bioeconomy is biomanufacturing, which uses natural or engineered enzymes or cell factories built from ​biological components like promoters, terminators, regulatory sequences, reporters, and functional genes into various chassis hosts (including animal, microbial, plant, and de novo systems) to create products such as food, energy, medicine, materials, chemicals, and engineered tissue/organs. An enabler of biomanufacturing is biodesign – also known as biosystems design and closely related to synthetic biology or engineering biology. This interdisciplinary field aims to understand and predictably modify existing life forms or create entirely new biological entities/systems using rational engineering strategies and automated design tools. Through these capabilities, biodesign supports the discovery, optimization, and creation of efficient platforms for biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Feeding state-dependent neuropeptidergic modulation of reciprocally interconnected inhibitory neurons biases sensorimotor decisions in Drosophila

Abstract An animal’s feeding state changes its behavioral priorities and thus influences even nonfeeding-related decisions. How the feeding state information is transmitted to nonfeeding-related circuits and what circuit mechanisms are involved in biasing nonfeeding-related decisions remain open questions. By combining calcium imaging, neuronal manipulations, behavioral analysis and computational modeling, we determined that the competition between different aversive responses to mechanical cues is biased by changes in the feeding state. We found that this effect is achieved by the differential modulation of two different types of reciprocally connected inhibitory neurons promoting opposing actions. This modulation results in a more frequent active type of response and, less frequently, a protective type of response if larvae are fed sugar than when they are fed a balanced diet. Information about the internal state is conveyed to inhibitory neurons through homologs of the vertebrate neuropeptide Y, which is known to be involved in regulating feeding behavior.

Science & Technology - Other Topics↗
DOE OSTI2020

Estimating the Timing of Early Simian-Human Immunodeficiency Virus Infections: a Comparison between Poisson Fitter and BEAST

Many HIV prevention strategies are currently under consideration where it is highly informative to know the study participants’ times of infection. These can be estimated using viral sequence data sampled early in infection. However, there are several scenarios that, if not addressed, can skew timing estimates. These include multiple transmitted/founder (TF) viruses, APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like)-mediated mutational enrichment, and recombination. Here, we suggest a pipeline to identify these problems and resolve the biases that they introduce. We then compare two modeling strategies to obtain timing estimates from sequence data. The first, Poisson Fitter (PF), is based on a Poisson model of random accumulation of mutations relative to the TF virus (or viruses) that established the infection. The second uses a coalescence-based phylogenetic strategy as implemented in BEAST. The comparison is based on timing predictions using plasma viral RNA (cDNA) sequence data from 28 simian-human immunodeficiency virus (SHIV)-infected animals for which the exact day of infection is known. In this particular setting, based on nucleotide sequences from samples obtained in early infection, the Poisson method yielded more accurate, more precise, and unbiased estimates for the time of infection than did the explored implementations of BEAST. The inference of the time of infection is a critical parameter in testing the efficacy of clinical interventions in protecting against HIV-1 infection. For example, in clinical trials evaluating the efficacy of passively delivered antibodies (Abs) for preventing infections, accurate time of infection data are essential for discerning levels of the Abs required to confer protection, given the natural Ab decay rate in the human body. In such trials, genetic sequences from early in the infection are regularly sampled from study participants, generally prior to immune selection, when the viral population is still expanding and genetic diversity is low. In this particular setting of early viral growth, the Poisson method is superior to the alternative approach based on coalescent methods. This approach can also be applied in human vaccine trials, where accurate estimates of infection times help ascertain if vaccine-elicited immune protection wanes over time.

59 BASIC BIOLOGICAL SCIENCES↗