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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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At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Improving tolerance of yeast to lignocellulosic-derived feedstocks and products

Combined substrate-product toxicity remains one of the main obstacles hampering the scale-up and cost-effectiveness of bioprocesses harnessing lignocellulosic feedstocks, the most abundant, renewable terrestrial resource. Hydrolytic pretreatments release numerous inhibitors impinging on cell viability: the three most acute to yeast S. cerevisiae (the industry dominant biocatalyst) — and universal to all plant sources — are furfural, hydroxymethylfurfural (HMF), and acetic acid. Likewise, desired fermentation products, such as fuel ethanol or commodity organic acids, are toxic to microbes, typically via unknown biological mechanisms. Here, we have engineered both hydrolysate and end-product tolerance in yeast by combining previously-shown alcohol protective modifications with evolved genetic activities targeting the major pretreatment inhibitors. When tested on a wide sampling of genuine lignocellulosic feedstocks, ethanol production increased by >30% on average to titers >100 g/L, achieving parity with clean-sugar equivalents where conditions permit. Furthermore, we designed the tolerance capability to be fully transferable to pre-existing metabolic chassis strains. As such, we “drop-in” hydrolysate competence into one producing lactic acid, demonstrating the first-ever production of a cellulosic plastic at industrial titers. Our advances thus renew the potential of cellulosic biomass utilization for sustainable fuel and non-fuel products at scale.

09 BIOMASS FUELS↗
DOE OSTI2021

The Santorini Volcanic Complex as a Valuable Source of Enzymes for Bioenergy

Marine microbial communities are an untapped reservoir of genetic and metabolic diversity and a valuable source for the discovery of new natural products of biotechnological interest. The newly discovered hydrothermal vent field of Santorini volcanic complex located in the Aegean Sea is gaining increasing interest for potential biotechnological exploitation. The conditions in these environments, i.e., high temperatures, low pH values and high concentration of heavy metals, often resemble harsh industrial settings. Thus, these environments may serve as pools of enzymes of enhanced catalytic properties that may provide benefits to biotechnology. Here, we screened 11 metagenomic libraries previously constructed from microbial mat samples covering the seafloor and the polymetallic chimneys of Kolumbo volcano as well as mat samples from Santorini caldera, to mine, in silico, genes associated with bioenergy applications. We particularly focused on genes encoding biomass hydrolysis enzymes such as cellulases, hemicellulases and lignin-degrading enzymes. A total of 10,417 genes were found for three specific groups of enzymes—i.e., the endoglucanases, the three different beta-glucosidases BGL, bglX and bglB, and the alpha-galactosidases melA, and rafA. Overall, we concluded that the Santorini–Kolumbo volcanic ecosystems constitute a significant resource of novel genes with potential applications in bioenergy that deserve further investigation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

BrainXcan identifies brain features associated with behavioral and psychiatric traits using large-scale genetic and imaging data

Advances in brain MRI have enabled many discoveries in neuroscience. Case-control comparisons of brain MRI features have highlighted potential causes of psychiatric and behavioral disorders. However, due to the cost and difficulty of collecting MRI data, most studies have small sample sizes, limiting their reliability. Furthermore, reverse causality complicates interpretation because many observed brain differences are the result rather than the cause of the disease. Here we propose a method (BrainXcan) that leverages the power of large-scale genomewide association studies (GWAS) and reference brain MRI data to discover new mechanisms of disease etiology and validate existing ones. BrainXcan tests the association with genetic predictors of brain MRI-derived features and complex traits to pinpoint relevant brain-wide and region-specific features. Requiring only genetic data, BrainXcan allows us to test a host of hypotheses on mental illness, across many MRI modalities, using public data resources. For example, our method shows that reduced axonal density across the brain is associated with schizophrenia risk, consistent with the disconnectivity hypothesis. We also find that the hippocampus volume is associated with schizophrenia risk, highlighting the potential of our approach. Taken together, our results show the promise of BrainXcan to provide insights into the biology of GWAS traits.

Association study↗
NASA NTRS2015

Astrobiology, Mars Exploration and Lassen Volcanic National Park

The search for evidence of life beyond Earth illustrates how the charters of NASA and the National Park Service share common ground. The mission of NPS is to preserve unimpaired the natural and cultural resources of the National Park System for the enjoyment, education and inspiration of this and future generations. NASA's Astrobiology program seeks to understand the origins, evolution and distribution of life in the universe, and it abides by the principles of planetary stewardship, public outreach, and education. We cannot subject planetary exploration destinations to Earthly biological contamination both for ethical reasons and to preserve their scientific value for astrobiology. We respond to the public's interest in the mysteries of life and the cosmos by honoring their desire to participate in the process of discovery. We involve youth in order to motivate career choices in science and technology and to perpetuate space exploration. The search for evidence of past life on Mars illustrates how the missions of NASA and NPS can become synergistic. Volcanic activity occurs on all rocky planets in our Solar System and beyond, and it frequently interacts with water to create hydrothermal systems. On Earth these systems are oases for microbial life. The Mars Exploration Rover Spirit has found evidence of extinct hydrothermal system in Gusev crater, Mars. Lassen Volcanic National Park provides a pristine laboratory for investigating how microorganisms can both thrive and leave evidence of their former presence in hydrothermal systems. NASA scientists, NPS interpretation personnel and teachers can collaborate on field-oriented programs that enhance Mars mission planning, engage students and the public in science and technology, and emphasize the ethics of responsible exploration.

Lassen Volcanic National Park↗
DOE OSTI2022

Resource Recovery and Environmental Protection in Wyoming’s Greater Green River Basin Using Selective Nanostructured Membranes (Final Report)

Produced water (PW) represents a sizable waste stream that is co-generated with oil and natural gas production. In 2021 Wyoming ranked 8th and 9th, respectively in domestic oil and natural gas production. In 2017 Wyoming ranked as the 4th highest generator of PW in the U.S, accounting for 7% of the total volume generated. In the context of being the 3rd most arid state in the U.S., the value of water reuse becomes obvious. PW reuse, and resource recovery, in any form requires some level of treatment to remove particulates, residual (free, dispersed) hydrocarbons, organics, and salts. The level of treatment depends on the requirements of the reuse, or resource recovery, application. PW management systems in Wyoming employ in order of volume of PW managed the following management strategies: reinjection for enhanced oil recovery, surface discharge, deep well injection, evaporation ponds (impoundments), and commercial management/treatment. Complicating treatment efforts are the relatively high concentrations of organics (natural and synthetic), dispersed/free hydrocarbons, benzene-toluene-ethylbenzene, and xylenes (BTEX) compounds, biologicals, salts, and minerals. Hydrocarbons (dispersed/dissolved crude oils) and BTEX compounds, as well as synthetic organics, present economic and environmental concerns. The former represents lost revenue, while the latter results in negative environmental impacts like emissions from surface impoundments. The overall objective of this proposal was to synthesize superhydrophilic/oleophobic and superhydrophobic/oleophilic membranes for selectively concentrating and then separating BTEX compounds and oil and grease (O&G) from PW originating from the Greater Green River Basin (GGRB) in Wyoming. Three specific research aims were pursued to accomplish this overall objective. This final report details the development of the superhydrophobic and superhydrophilic membranes, as well as the design of the membrane module prototypes specifically. The technoeconomic assessment is separately reported in another document. 1. Aim #1 – Material optimization and performance evaluation of superhydrophilic/oleophobic and superhydrophobic/oleophilic membranes made by electrospinning/spraying. 2. Aim #2 – Design and construction of cross-flow membrane modules for selectively concentrating and then separating BTEX/oil from GGRB produced water. 3. Aim #3 – Techno-economic assessment of BTEX/oil recovery, and clean water production, using superhydrophilic/oleophobic and superhydrophobic/oleophilic membrane separation for GGRB PW. Superhydrophobic membranes were synthesized by electrospinning poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) nanofibers onto polyester (PET) substrates and electrospraying nano-carbon black/PVDF-HFP onto the nanofibrous layer. These membranes were characterized by high (>8000 liters per square meter per hour per bar (LMH/bar)) permeance values for pure hydrocarbon phases and a high hydrocarbon selectivity (>96%) when treating GGRB PW. All results were obtained when operating the membrane in a crossflow configuration representative of actual field operating conditions. Solvent/oil properties, specifically viscosity and total surface energy/tension, affected permeance across the membrane, which resulted in light mineral oil (394 LMH/bar) and o-xylene (1834 LMH/bar) being characterized by lower permeance values in the pure phase tests. Mixed phase fluxes between 40 to 80 LMH were obtained for the PW when operating the membrane at a feed pressure of 0.3 bar. Flux decreased as the mixed phase concentration in the feed decreased pointing to the importance of maximizing the collision efficiency between the emulsion and the membrane surface and maximizing the emulsion concentration in the feed and the turbulence within the feed channel. These tests demonstrated that the superhydrophobic membranes developed here are a viable hydrocarbon recovery method for GGRB PWs and should be pursued for testing in pilot-scale trials. Superhydrophilic membranes were successfully synthesized via electrospinning/spraying using polyacrylonitrile (PAN) nanofibers as a base nanofibrous matrix. Integration of polyaniline (PANI) into the nanofibrous matrix produced a superior membrane, for water filtration applications, relative to PAN alone and reduced graphene oxide (RGO) when integrated into the nanofibrous matrix. This conclusion was based on the PANI-PAN resistance to flux loss (fouling) when treating model solvent/oil solutions representative of GGRB PWs and field collected PW from the GGRB. The synthesized PAN membranes outperformed a commercially available PAN membrane designed for oil/water separation. This finding indicates that the surface chemical and physical characteristics of the electrospun membranes presents improved properties for filtration of challenging waters like GGRB PWs. The electrospun membranes therefore show promise overall as a substitute for conventionally polymerized membranes in PW treatment applications. The PANI-PAN membrane specifically presents superior performance characteristics for concentration O&G prior to treatment by the hydrocarbon recovery membrane and producing high-quality filtrate for reuse and/or additional treatment (desalination).

02 PETROLEUM↗
DOE OSTI2021

Integration of evidence across human and model organism studies: A meeting report

The National Institute on Drug Abuse and Joint Institute for Biological Sciences at the Oak Ridge National Laboratory hosted a meeting attended by a diverse group of scientists with expertise in substance use disorders (SUDs), computational biology, and FAIR (Findability, Accessibility, Interoperability, and Reusability) data sharing. The meeting's objective was to discuss and evaluate better strategies to integrate genetic, epigenetic, and 'omics data across human and model organisms to achieve deeper mechanistic insight into SUDs. Specific topics were to (a) evaluate the current state of substance use genetics and genomics research and fundamental gaps, (b) identify opportunities and challenges of integration and sharing across species and data types, (c) identify current tools and resources for integration of genetic, epigenetic, and phenotypic data, (d) discuss steps and impediment related to data integration, and (e) outline future steps to support more effective collaboration—particularly between animal model research communities and human genetics and clinical research teams. This review summarizes key facets of this catalytic discussion with a focus on new opportunities and gaps in resources and knowledge on SUDs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

CamRegBase: a gene regulation database for the biofuel crop, Camelina sativa

Abstract Camelina is an annual oilseed plant from the Brassicaceae family that is gaining momentum as a biofuel winter cover crop. However, a significant limitation in further enhancing its utility as a producer of oils that can be used as biofuels, jet fuels or bio-based products is the absence of a repository for all the gene expression and regulatory information that is being rapidly generated by the community. Here, we provide CamRegBase (https://camregbase.org/) as a one-stop resource to access Camelina information on gene expression and co-expression, transcription factors, lipid associated genes and genome-wide orthologs in the close-relative reference plant Arabidopsis. We envision this as a resource of curated information for users, as well as a repository of new gene regulation information.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Soybean ( Glycine max ) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics

Here, we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1007 Glycine max accessions and yielding 14.9 million variants as well as 4.3 M tag single-nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number of variants and tag SNPs plateaued beyond approximately 800 and 600 accessions, respectively. This suggests extensive coverage of diversity within the cultivated soybean. GmHapMap variants were imputed onto 21 618 previously genotyped accessions with up to 96% success for common alleles. A local association analysis was performed with the imputed data using markers located in a 1-Mb region known to contribute to seed oil content and enabled us to identify a candidate causal SNP residing in the NPC1 gene. We determined gene-centric haplotypes (407 867 GCHs) for the 55 589 genes and showed that such haplotypes can help to identify alleles that differ in the resulting phenotype. Finally, we predicted 18 031 putative loss-of-function (LOF) mutations in 10 662 genes and illustrated how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for applied soybean genomics and breeding.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Amylases in the Human Vagina

ABSTRACT Dominance of Lactobacillus species in vaginal communities is a hallmark of healthy conditions in the female genital tract. Key nutrients for lactobacilli include sugars produced when glycogen is degraded by α-amylase in the vagina. While α-amylase activity has been demonstrated in vaginal fluids, it is unclear whether α-amylases are produced solely by the host, bacteria in the vagina, or both. We screened cervicovaginal mucus from 23 reproductive-age women, characterized the species composition of vaginal communities, measured vaginal pH, and determined levels of amylase activity, glycogen, and lactic acid. Based on differences in these measured variables, one sample from each of four individual donors was selected for metagenomic and proteomic analyses. Of eight putative bacterial amylases identified in the assembled bacterial metagenomes, we detected four in vaginal fluids. These amylases were produced by various bacteria in different vaginal communities. Moreover, no two communities were the same in terms of which bacteria were producing amylases. Although we detected bacterial amylases in vaginal fluids, there was no clear association between the bacterial species that was dominant in a community and the level of amylase activity. This association was likely masked by the presence of human α-amylase, which was also detected in vaginal fluids. Finally, the levels of amylase activity and glycogen were only weakly associated. Our findings show, for the first time, that multiple amylases from both bacterial and human origins can be present simultaneously in the vagina. This work also suggests that the link between glycogen, amylase, and Lactobacillus in the vagina is complex. IMPORTANCE In this study, we show that multiple bacteria in the vaginal community produce amylases that hydrolyze glycogen into simpler sugars (i.e., maltose and maltotriose). These sugars serve as “common goods” that sustain bacterial populations in vaginal communities. Given the temporal changes that are observed in the human vaginal microbiome, we expect the kinds of bacterial amylases produced will also vary over time. These differences influence the pool of resources that are broadly shared and shape the species composition of the vaginal bacterial community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Coupling a recurrent neural network to SPAD TCSPC systems for real-time fluorescence lifetime imaging

Fluorescence lifetime imaging (FLI) has been receiving increased attention in recent years as a powerful diagnostic technique in biological and medical research. However, existing FLI systems often suffer from a tradeoff between processing speed, accuracy, and robustness. Inspired by the concept of Edge Artificial Intelligence (Edge AI), we propose a robust approach that enables fast FLI with no degradation of accuracy. This approach couples a recurrent neural network (RNN), which is trained to estimate the fluorescence lifetime directly from raw timestamps without building histograms, to SPAD TCSPC systems, thereby drastically reducing transfer data volumes and hardware resource utilization, and enabling real-time FLI acquisition. We train two variants of the RNN on a synthetic dataset and compare the results to those obtained using center-of-mass method (CMM) and least squares fitting (LS fitting). Results demonstrate that two RNN variants, gated recurrent unit (GRU) and long short-term memory (LSTM), are comparable to CMM and LS fitting in terms of accuracy, while outperforming them in the presence of background noise by a large margin. To explore the ultimate limits of the approach, we derive the Cramer-Rao lower bound of the measurement, showing that RNN yields lifetime estimations with near-optimal precision. To demonstrate real-time operation, we build a FLI microscope based on an existing SPAD TCSPC system comprising a 32 x 32 SPAD sensor named Piccolo. Four quantized GRU cores, capable of processing up to 4 million photons per second, are deployed on the Xilinx Kintex-7 FPGA that controls the Piccolo. Powered by the GRU, the FLI setup can retrieve real-time fluorescence lifetime images at up to 10 frames per second. The proposed FLI system is promising and ideally suited for biomedical applications, including biological imaging, biomedical diagnostics, and fluorescence-assisted surgery, etc.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Microbial production of fuels, commodity chemicals, and materials from sustainable sources of carbon and energy

Anthropogenic carbon emissions are driving rapid changes to the earth's climate, disrupting whole ecosystems and endangering the stability of human society. Innovations in engineered microbial fermentation enable the fossil resource-free production of fuels, commodity chemicals, and materials, thereby reducing the carbon emissions associated with these products. Microorganisms have been engineered to catabolize sustainable sources of carbon and energy (i.e., plant biomass, plastic waste, and one-carbon feedstocks) and biosynthesize carbon-neutral or carbon-negative products. These engineering efforts exploit and optimize natural biological pathways or generate unnatural pathways which can biosynthesize chemicals that have not yet been accessed using synthetic chemistry. Further, recent advances in microbial fermentation seek not only to maximize the titer, rate, and yield of desired products, but also to tailor microbial catabolism to utilize inexpensive feedstocks. Ultimately, these advances aim to lower the cost of bioproduction so that microorganism-derived chemicals can be economically competitive with fossil-derived chemicals.

09 BIOMASS FUELS↗
DOE OSTI2024

Dynamics of ER stress-induced gene regulation in plants

Endoplasmic reticulum (ER) stress is a potentially lethal condition that is induced by the abnormal accumulation of unfolded or misfolded secretory proteins in the ER. In eukaryotes, ER stress is managed by the unfolded protein response (UPR) through a tightly regulated, yet highly dynamic, reprogramming of gene transcription. Although the core principles of the UPR are similar across eukaryotes, unique features of the plant UPR reflect the adaptability of plants to their ever-changing environments and the need to balance the demands of growth and development with the response to environmental stressors. Here, the past decades have seen notable progress in understanding the mechanisms underlying ER stress sensing and signaling transduction pathways, implicating the UPR in the effects of physiological and induced ER stress on plant growth and crop yield. Facilitated by sequencing technologies and advances in genetic and genomic resources, recent efforts have driven the discovery of transcriptional regulators and elucidated the mechanisms that mediate the dynamic and precise gene regulation in response to ER stress at the systems level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Final Scientific/Technical Report: Real Time Particle Size and Settling Velocity for In-Situ Monitoring of Deep-Sea Polymetallic Nodule Mining

In the coming decade, it is anticipated that deep-sea mining activities will commence throughout the deep ocean, at depths around 4000-6000m where vast deposits of baseball-sized rocks called polymetallic nodules lay on the seabed. These nodules contain resources such as cobalt, copper and nickel which are needed to produce batteries for electric vehicles. Collector machines driving on the seabed and gathering these nodules will stir up clouds of sediment, and there is concern about how the resulting concentration of sediment in the near-bottom ocean water will affect deep and mid-ocean biology. There is currently no technology capable of comprehensively monitoring the concentrations and properties of stirred up sediment in the deep. This project addressed this critical gap by developing a deep-sea particle measurement system (Real-Time Size and Settling Velocity, RTSSV) that uses a multi-camera high-resolution video imaging system, with accompanying image processing, to measure the concentration, size distribution and settling speed of sediment. Importantly, these measurements are made in-situ, so that delicate sediment aggregates will not be disturbed, as is the case when collecting samples at depth to be measured in the lab. The instrument can be mounted on a variety of established deep-sea platforms such as moorings, AUVs and ROVs, providing data in near real time, where the key measurements need to be made—from the source of the sediment disturbance and throughout the resulting plume—vital for determining if deep-sea mining can be done in an environmentally responsible manner. The developed system (RTSSV) will possess the only such capability worldwide, giving a US-based group a substantial competitive advantage as this newly evolving global industry develops. As added value, the technology will also have widespread application to the offshore oil and gas industry, dredging industry, and to sediment science research.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

DOE BSSD Performance Management Metrics Report Q1

Microbes play key roles in our biosphere, from driving global nutrient cycling to impacting plant, animal and human health and disease. Complex data from microbial genomes, proteins, and metabolites provide a window into these tiny engines that drive life on our planet. Yet these data are dispersed among researchers’ laboratories and various repositories, making it difficult to access. This calls for new ways of managing data, improving data interoperability, advancing community standards, and creating an infrastructure where data are shared efficiently. We have built the National Microbiome Data Collaborative (NMDC) to advance how scientists create, use, and reuse data to redefine the way we understand and harness the power of microbes. The vision of the National Microbiome Data Collaborative (NMDC) is to drive a microbiome data sharing network connecting data, people, and ideas to advance microbiome innovation and discovery. The NMDC was launched in 2019 and brought together DOE National Laboratories to collaborate across resources, capabilities, and expertise. The NMDC team was strategically assembled to include software developers, microbial researchers, metadata experts, and multi-omics specialists. The diversity of the NMDC team reflects the inherently interdisciplinary nature of microbiome science, and we leverage the strengths of the DOE National Laboratory system. Towards BER’s goal of advancing an iterative systems biology approach to the understanding of microbial genomes, the NMDC serves as a foundation for infrastructure, data standards, and community building. Together with the flagship DOE User Facilities, the Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL), we are developing core capabilities in metadata standards for environmental descriptors and sample handling and processing; standardized bioinformatic workflows; an interface for data search and access; and robust community engagement activities. The NMDC production platform supports long-term data infrastructure and community building for BER’s bioenergy and environmental research goals. Our approach leverages lessons learned and an ambitious framework for collaborative, interdisciplinary data infrastructure to support microbiome research. The NMDC supports data, information, and knowledge access through three defined software tools – the Submission Portal, NMDC EDGE, and the Data Portal – driven by community needs. Herein, we describe the value proposition for the microbiome research community, our overarching strategy, and challenges and opportunities for developing the NMDC as both an infrastructure and community engagement program.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask)

Metadata are contextual data about your experimental data. Metadata are the who, what, when, where, and why of these data. Metadata puts these data into context. In microbiome research, metadata includes information about the sample: when it was collected, where it was collected from, what kind of sample it is, and what were the properties of the environment or experimental condition from which the sample was taken. Information about sample processing is also metadata: methods used to extract and purify molecules (e.g., DNA) from the sample, type of DNA sequencing or other ’omics analyses done, and where the raw experimental data are located. This documentation includes information on the following topics: What are metadata? What kinds of metadata are there? Why are metadata important? Why should metadata be standardized? Why should metadata be machine readable? What is an ontology? Why are ontologies important? What are some examples of ontologies? The documentation also includes further resources on metadata guides and tools and tips for formatting metadata for maximum utility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An ontology-based knowledge graph for representing interactions involving RNA molecules

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to each patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are constantly produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph (KG) encompassing biological knowledge about RNAs gathered from more than 60 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Genetic Identification of Lamprey Genera and Anadromous Ecotypes in Watersheds of the Northeastern Pacific Ocean

ABSTRACT Nonparasitic, nonmigratory Western Brook Lamprey (WBL; Lampetra ayresii ), and parasitic, anadromous Western River Lamprey (WRL; L. ayresii ) are sympatric lampreys that likely represent different life history variations of a single species. Novel genetic tools are critical for differentiating WBL and WRL, whose larvae preclude morphological identification (ID) and will enable comprehensive assessment of imperiled native lampreys of the Northeastern Pacific (including WBL, WRL, and Pacific Lamprey, Entosphenus tridentatus ). We developed 47 candidate single nucleotide polymorphism (SNP) markers using whole genome resequencing of WBL ( N = 24) and WRL ( N = 15) from Ksi Ts'oohl Ts'ap Creek (Nass River, British Columbia, Canada) which are likely ecotypes distinguished by few divergent SNPs across multiple chromosomes. We used five novel candidate SNPs to perform genetic ID of WBL and WRL ecotypes in collections of mixed native lampreys from lower Columbia River tributaries ( N = 1474), Ksi Ts'oohl Ts'ap Creek ( N = 352), and ocean phase WRL from the Georgia Basin (Salish Sea, British Columbia, Canada; N = 91). Two previously published SNPs were used to ID genera, Entosphenus versus Lampetra . Morphological ID utilized photographs collected from a subset of genotyped lampreys, and high concordance was demonstrated between ID methods for genera (99%) and Lampetra ecotypes (> 98%). We characterized spatial and temporal composition of lamprey genera and ecotypes surveyed across NE Pacific tributaries under the expectation these compositions would be similar across nearby sites and across years at the same site. Proportions of lamprey genera were highly variable within regions and across years; however, Lampetra ecotypic proportions were spatially and temporally stable. WRL were rare in lower Columbia tributaries (~1% average rate among Lampetra ) and common further north (> 40% of Lampetra ). Genetic ID methods are powerful monitoring tools that create the novel ability to ascertain genera and ecotypes regardless of life stage, while increasing the efficiency of surveys by eliminating time‐intensive morphological data collection.

Silver, G. S. [Columbia River Inter‐Tribal Fish Co↗