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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Developing a Process for Collaboration-Based Siting of a Federal Consolidated Interim Storage Facility in the United States: Learning from Communities Living with Legacy Waste

In June of 2023, the U.S. Department of Energy (DOE), Office of Nuclear Energy (NE) announced the selection of its Collaboration-Based Siting (CBS) Consortia, a group of 12 awardees, including the Consortium for Risk Evaluation with Stakeholder Participation (CRESP) (led by Vanderbilt University) to assist DOE-NE with the development of its process for siting a federal consolidated interim storage facility (FCISF) for spent nuclear fuel (SNF) storage. At this time, DOE NE is not soliciting interested host communities, rather the CBS Consortia are tasked with in-depth engagement, mutual learning, and capacity building to provide DOE NE with feedback on the CBS process. CRESP’s objective is to engage communities in two regions (the Pacific Northwest and the Southeast) with sites currently storing defense- and research-related SNF to foster learning concerning the best and worst practices in community participation in risk-informed decision making. This includes learning from existing structures for public input in radioactive waste management decision making [e.g. citizen advisory boards (CABs)] and other local parties about how to build and sustain trust among the parties. CRESP has been working to engage stakeholders and Tribes surrounding two DOE sites historically differing in receptiveness to engaging with DOE and trusting in DOE to accomplish its missions. CRESP’s approach to date has consisted of (1) engaging voluntarily members and former members of the DOE Office of Environmental Management’s CABs to develop a mutual understanding of their perspectives, values, and experiences related to risk and participatory decision making; (2) engaging members of those communities that would likely be part of any radioactive waste management discussions and who may provide valuable feedback for the development of the CBS process; and in the longer term, (3) engaging communities to foster knowledge sharing on understanding and definitions of risk and how risk is factored into community decision making. Our emphasis is to identify opportunities for improving risk communication frameworks, strategies, and decision making. The selection of a future FCISF site is likely to result in the creation of a structure similar to a CAB composed of members of the local community. We anticipate that these insights can help DOE NE learn from existing participatory risk communication structures in place at sites storing defenseor research-related SNF to understand best practices for fostering enduring and participatory relationships with future CABs. Within this paper, we (1) describe CRESP’s overall approach to assisting DOE NE with maturing the CBS process; (2) present a summary of preliminary phase 1 project results, including the development of a body of knowledge (describing available resources to support community engagement, risk communica tion, and participatory decision making) and community ecosystem information (leveraging demographic, social, economic, and environmental attribute mapping and advanced sentiment analysis of social media data); and (3) based on these results, provide observations for future research opportunities to support the development of CBS processes for radioactive waste management facilities, generally.

collaboration-based siting↗
DOE OSTI2023

$\mathrm{EBR-II MOX}$ Fuel Characterization Enabling ARES Phase I Testing

Pretransient characterization was performed for the Experimental Breeder Reactor II (EBR-II) mixed-oxide (MOX) fuel pellets from the SPA-2/-2B Operational Reliability Testing collaboration between Japan and the United States. Continued collaboration under the Advanced Reactor Experiments for Sodium Fast Reactor Fuels project will investigate the transient performance of these rods in the Transient Reactor Test facility at Idaho National Laboratory in the MOXTOP-THOR experiment. The results will fill a gap in existing transient performance data for MOX as these rods have a peak burnup of 14.3 at. % (~134.4 GWd/t) in the EBR-II. Fuel pellet properties were gathered from available resources and their irradiation and decay history evaluated. Further reactor physics calculations were performed to support the experiment design, reactor operations, and safety analyses necessary to enable the programmatic success of this effort. Of the three irradiated fuel pins, two will undergo transient testing, and all three will undergo post-irradiation examination. The methodology development and analysis activities utilized we report enable current experiment design work and provide the pathway through which measured data of this type can be further evaluated.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Modeling and analysis of the tritium fuel cycle for ARC- and STEP-class D-T fusion power plants

Abstract The limited tritium resources available for the first fusion power plants (FPPs) make fuel self-sufficiency and tritium inventory minimization leading issues in FPP design. This work builds on the model proposed by Abdou et al (2020 Nucl. Fusion 61 013001), which analyzed the fuel cycle (FC) of a DEMOnstration nuclear FPP-class FPP with a time-dependent system-level model. Here, we use a modified version of their model to analyze the FC of an Affordable, Robust, Compact (ARC)-class tokamak and two versions of a Spherical Tokamak for Energy Production (STEP)-class tokamak. The ARC-class tokamak breeds tritium in a 2LiF + BeF 2 liquid immersion blanket, while the STEP-class tokamak breeds tritium utilizing either a liquid-lithium blanket design or an encapsulated breeding blanket. A time-dependent system-level model is developed in Matlab Simulink ® to simulate the evolution of tritium flows and tritium inventories in the FC. The main goals of this work are to assess tritium self-sufficiency of the ARC- and STEP-class designs and to determine quantitative design requirements that can be used to analyze the adequacy of a proposed FC system. These design requirements are aimed at achieving a low tritium inventory doubling time ( t d ) and a low start-up inventory ( I s t a r t u p ) while keeping the required tritium breeding ratio (TBR r ) as low as possible. We also consider how improvements in FC technology and POs affect TBR r and I s t a r t u p . The model results show that TBR r for ARC- and STEP-class FPPs should be achievable if the tritium burn efficiency (TBE) reaches 0.5%–1% (TBR r < 1.2). This assumes significant, but attainable, improvements over current abilities. However, the model results indicate that an FPP must achieve ambitious performance targets, including FPP availability > 70%, tritium processing time < 4 h, and the implementation of direct internal recycling (DIR). If future research yields major improvements to achievable TBE, it may be possible to achieve tritium self-sufficiency while operating at lower availability and without implementing DIR.

Physics↗
DOE OSTI2023

LiDAR Measurements to Investigate Farm-to-Farm Interactions at the AWAKEN Experiment

The exponential growth of wind energy and the need to exploit wind resources over areas with higher energy potential have led to the construction of neighboring wind turbines and farms with relatively small separation distances. As a result, for specific wind and atmospheric conditions, the wakes generated by an upstream wind farm may affect wind resources available for a downstream wind farm resulting in detrimental impacts on energy harvesting and structural loads for the downwind wind turbines. Distances between neighboring wind farms are typically larger than those associated with intra-wind-farm wake interactions, generating cumulative wakes whose characteristics might differ from those predicted through classical engineering wake models. These phenomena are referred to as farm-to-farm interactions. A better understanding and characterization of farm-to-farm interactions is one of the science goals tackled by the ongoing American WAKE experimeNt (AWAKEN). The site under investigation for this field campaign comprises two large wind farms in northern Oklahoma, USA, which are spaced roughly 5km apart along the prevailing South-North wind direction. To investigate possible interactions between these two wind farms, the WindFluX mobile LiDAR station has been deployed mainly to perform volumetric scans over their gap region. In this paper, preliminary results from these LiDAR volumetric scans will be discussed, specifically for a case with multiple wind turbine wakes evolving during the occurrence of a low-level jet.

17 WIND ENERGY↗
DOE OSTI2015

Data preservation at the Fermilab Tevatron

The Fermilab Tevatron collider's data-taking run ended in September 2011, yielding a dataset with rich scientific potential. The CDF and DO experiments each have nearly 9 PB of collider and simulated data stored on tape. A large computing infrastructure consisting of tape storage, disk cache, and distributed grid computing for physics analysis with the Tevatron data is present at Fermilab. The Fermilab Run II data preservation project intends to keep this analysis capability sustained through the year 2020 or beyond. To achieve this, we are implementing a system that utilizes virtualization, automated validation, and migration to new standards in both software and data storage technology as well as leveraging resources available from currently-running experiments at Fermilab. Furthermore, these efforts will provide useful lessons in ensuring long-term data access for numerous experiments throughout high-energy physics, and provide a roadmap for high-quality scientific output for years to come.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

Status and future plans for C 3 R&D

C 3 is an opportunity to realize an e + e - collider for the study of the Higgs boson at √s = 250 GeV, with a well defined upgrade path to 550 GeV while staying on the same short facility footprint. C 3 is based on a fundamentally new approach to normal conducting linear accelerators that achieves both high gradient and high efficiency at relatively low cost. Given the advanced state of linear collider designs, the key system that requires technical maturation for C 3 is the main linac. This paper presents the staged approach towards a facility to demonstrate C 3 technology with both Direct (source and main linac) and Parallel (beam delivery, damping ring, ancillary component) R&D. The primary goal of the C 3 Demonstration R&D Plan is to reduce technical and cost risk by building and operating the key components of C 3 at an adequate scale. This R&D plan starts with the engineering design, and demonstration of one cryomodule and will culminate in the construction of a 3 cryomodule linac with pre-production prototypes. This R&D program would also demonstrate the linac rf fundamentals including achievable gradient and gradient stability over a full electron bunch train and breakdown rates. It will also investigate beam dynamics including energy spread, wakefields, and emittance growth. This work will be critical to confirm the suitability of the C 3 beam parameters for the physics reach and detector performance in preparation for a Conceptual Design Report (CDR), as well as for follow-on technology development and industrialization. The C 3 Demonstration R&D Plan will open up significant new scientific and technical opportunities based on development of high-gradient and high-efficiency accelerator technology. It will push this technology to operate both at the GeV scale and mature the technology to be reliable and provide high-brightness electron beams. The timeline for progressing with C 3 technology development will be governed by practical limitations on both the technical progress and resource availability. It consists of four stages: Stage 0) Ongoing fundamental R&D on structure prototypes, damping and vibrations. Stage 1) Advancing the engineering maturity of the design and developing start-to-end simulations including space-charge and wakefield effects. This stage will include testing of strucutres operating at cryogenic temperatures. Beam tests would be performed with high beam current to test full beam loading. Stage 2) Production and testing of the first cryomodule at cryogenic temperatures. This would provide sufficient experimental data to compile a CDR and it is anticipated for Stage 2 to last 3 years and to culminate with the transport of photo-electrons through the first cryomodule. Stage 3) Updates to the engineering design of the cryomodules, production of the second and third cryomodule and their installation. Lower charge and lower emittance beams will be used to investigate emittance growth. The successful full demonstration of the 3 cryomodules to deliver up to a 3 GeV beam and achieve the C 3 five gradient will allow a comprehensive and robust evaluation of the technical design of C 3 as well as mitigate technical, schedule, and cost risks required to proceed with a Technical Design Report (TDR).

radiation hardened magnets↗
DOE OSTI2025

A 28 nm multiply-accumulate ASIC architecture for on-chip data compression in MHz frame rate X-ray and electron pixel detectors

Modern X-ray detector systems urgently require compact, efficient, and fast data compression schemes to handle the transmission of big data from pixel arrays, enabling frame rates in the MHz regime. Here, in this work, a data compression ASIC that implements a streaming fixed-length lossy compression scheme is introduced and analyzed, proving the feasibility and benefits of on-chip compression. The compression scheme utilizes a vector matrix product logic, which performs a number of floating-point multiplications, additions, and accumulations. The logic is verified, synthesized, and shown to fit in the area resource available for the X-ray detector under study, which comprises 192 × 168 pixels each of 12-bit width, and having a total area of 20 mm× 20 mm, about 2 mm× 20 mm of which are available for the digital logic. Several system architectures, precisions, and compression ratios ranging from 100 to 250 were analyzed to pave the way for on-chip fixed-length compression (e.g., principal component analysis, singular value decomposition) and data reduction (e.g., azimuthal integration) for X-ray and electron detectors.

Data compression↗
DOE OSTI2025

Examining future changes in coastal low-level jet properties offshore California through dynamical downscaling

The coastal low-level jet, or coastal low-level jet (CLLJ), is a synoptically-forced meteorological feature frequently present offshore the western United States (U.S.). Characterized by a wind speed maximum that resides at the top of the marine boundary layer, the CLLJ is largely controlled by the location and strength of the North Pacific High (NPH) as well as the coastal geometry. Considering the rich wind resource available in this offshore region, the Bureau of Ocean Energy Management identified wind energy lease areas offshore California and supported the deployment of two U.S. Department of Energy wind lidar buoys near Morro Bay and Humboldt. Despite our relatively good understanding of the fundamental mechanisms responsible for large-scale CLLJ properties offshore the western U.S., future changes in CLLJ characteristics are less clear. To address this research challenge, and ultimately to better inform future wind turbine deployments, we use simulations driven by three global climate models (GCMs). We apply self-organizing maps to the model outputs for a historical and two future climate periods to show the range of NPH regimes that support CLLJ conditions during the warm seasons, as well as the subtle contribution from land-falling cyclones approaching the mainland during the cold seasons. Compared to the historical period, the three GCM-driven simulations agree that CLLJ conditions will become more (less) prevalent from central California northward (southward). They agree less with respect to future changes in maximum CLLJ wind speeds and CLLJ heights. However, after considering model biases present during the historical period, wind speeds between the models are actually more similar during the 2070–2095 period than during the historical period. The potential combination of more frequent CLLJ conditions characterized by relatively consistent wind speeds occurring at lower heights across northern California suggests that the Humboldt lease area may be ideal for a long-term wind turbine deployment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Life-cycle carbon footprint and total production potential of cross-laminated timber from California’s wildland-urban interface

The frequency, scale, and severity of wildfires are steadily increasing in the Western United States. Sustainable forest management practices through forest thinning could reduce the impact of wildfires and provide lumber for wood-based, long-lived, and low-carbon building materials. This study explores the potential for harvesting biomass in California (CA) to mitigate wildfire risk and provide multi-decade carbon storage in the form of cross-laminated timber (CLT) for use in buildings. First, we assessed biomass resource availability, finding that the total live hardwood and live softwood available in the wildland-urban interfaces (WUIs) across CA sums to 14.1 million metric tons (MMT) and 34.9 MMT, respectively, which contains the equivalent of 90 MMT of atmospheric carbon dioxide. Then, we conducted a life cycle assessment of CLT considering softwood and hardwood sources to provide insights into emissions and energy demand associated with utilization of the wood removed for wildfire risk management. We found that the net life cycle carbon footprint of live hardwood and softwood when including biogenic carbon storage/emissions is 414 and 317 kg CO2e/m3 CLT, respectively. To incorporate the timing of these emissions and uptake, we have also conducted a cradle-to-grave time-dependent global warming potential (GWP) analysis. The time-adjusted GWP for live hardwood and live softwood is −227 and −104 kg CO2e/m3 CLT, respectively. In terms of total CLT production potential, 0.03 and 0.005 million m3 CLT can be sourced from live softwood and hardwood, respectively, in WUI on gentle slopes in CA. The resulting insights and approaches from this study are broadly applicable to other forested regions and WUIs across the US and the world, and provide a holistic approach to use forest thinning as a wildfire mitigation strategy in combination with a novel approach for life cycle assessment of building materials with a limited dataset.

Bose, Baishakhi↗
DOE OSTI2022

Real-time semantic segmentation on FPGAs for autonomous vehicles with hls4ml

In this paper, we investigate how field programmable gate arrays can serve as hardware accelerators for real-time semantic segmentation tasks relevant for autonomous driving. Considering compressed versions of the ENet convolutional neural network architecture, we demonstrate a fully-on-chip deployment with a latency of 4.9 ms per image, using less than 30% of the available resources on a Xilinx ZCU102 evaluation board. The latency is reduced to 3 ms per image when increasing the batch size to ten, corresponding to the use case where the autonomous vehicle receives inputs from multiple cameras simultaneously. We show, through aggressive filter reduction and heterogeneous quantization-aware training, and an optimized implementation of convolutional layers, that the power consumption and resource utilization can be significantly reduced while maintaining accuracy on the Cityscapes dataset.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2017

Warming and elevated CO 2 alter the suberin chemistry in roots of photosynthetically divergent grass species

A majority of soil carbon (C) is either directly or indirectly derived from fine roots, yet roots remain the least understood component of the terrestrial carbon cycle. The decomposability of fine roots and their potential to contribute to soil C is partly regulated by their tissue chemical composition. Roots rely heavily on heteropolymers such as suberins, lignins and tannins to adapt to various environmental pressures and to maximize their resource uptake functions. Since the chemical construction of roots is partly shaped by their immediate biotic/abiotic soil environments, global changes that perturb soil resource availability and plant growth could potentially alter root chemistry, and hence the decomposability of roots. However, the effect of global change on the quantity and composition of root heteropolymers are seldom investigated. We examined the effects of elevated CO 2 and warming on the quantity and composition of suberin in roots of Bouteloua gracilis (C4) and Hesperostipa comata (C3) grass species at the Prairie Heating and CO 2 Enrichment (PHACE) experiment at Wyoming, USA. Roots of B. gracilis exposed to elevated CO 2 and warming had higher abundances of suberin and lignin than those exposed to ambient climate treatments. In addition to changes in their abundance, roots exposed to warming and elevated CO 2 had higher ω-hydroxy acids compared to plants grown under ambient conditions. The suberin content and composition in roots of H. comata was less responsive to climate treatments. In H. comata, α,ω-dioic acids increased with the main effect of elevated CO 2 , whereas the total quantity of suberin exhibited an increasing trend with the main effect of warming and elevated CO 2 . The increase in suberin content and altered composition could lower root decomposition rates with implications for root-derived soil carbon under global change. Our study also suggests that the climate change induced alterations in species composition will further mediate potential suberin contributions to soil carbon pools.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics

Abstract Summary Although advances in untargeted metabolomics have made it possible to gather data on thousands of cellular metabolites in parallel, identification of novel metabolites from these datasets remains challenging. To address this need, Metabolic in silico Network Expansions (MINEs) were developed. A MINE is an expansion of known biochemistry which can be used as a list of potential structures for unannotated metabolomics peaks. Here, we present MINE 2.0, which utilizes a new set of biochemical transformation rules that covers 93% of MetaCyc reactions (compared to 25% in MINE 1.0). This results in a 17-fold increase in database size and a 40% increase in MINE database compounds matching unannotated peaks from an untargeted metabolomics dataset. MINE 2.0 is thus a significant improvement to this community resource. Availability and implementation The MINE 2.0 website can be accessed at https://minedatabase.ci.northwestern.edu. The MINE 2.0 web API documentation can be accessed at https://mine-api.readthedocs.io/en/latest/. The data and code underlying this article are available in the MINE-2.0-Paper repository at https://github.com/tyo-nu/MINE-2.0-Paper. MINE 2.0 source code can be accessed at https://github.com/tyo-nu/MINE-Database (MINE construction), https://github.com/tyo-nu/MINE-Server (backend web API) and https://github.com/tyo-nu/MINE-app (web app). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow ( Salix spp.)

Many studies have highlighted the complex and diverse basis for heterosis in inbred crops. Despite the lack of a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, heterozygous, and polyploid species, such as willow (Salix spp.). Shrub willow is a dedicated energy crop bred to be fast-growing and high yielding on marginal land without competing with food crops. A trend in willow breeding is the consistent pattern of heterosis in triploids produced from crosses between diploid and tetraploid species. Here, we test whether differentially expressed genes are associated with heterosis in triploid families derived from diploid Salix purpurea, diploid Salix viminalis, and tetraploid Salix miyabeana parents. Three biological replicates of shoot tips from all family progeny and parents were collected after 12 weeks in the greenhouse and RNA extracted for RNA-Seq analysis. This study provides evidence that nonadditive patterns of gene expression are correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow. Expression-level dominance was most correlated with heterosis for biomass yield traits and was highly enriched for processes involved in starch and sucrose metabolism. In addition, there was a global dosage effect of parent alleles in triploid hybrids, with expression proportional to copy number variation. Importantly, differentially expressed genes between family parents were most predictive of heterosis for both field and greenhouse collected traits. Altogether, these data will be used to progress models of heterosis to complement the growing genomic resources available for the improvement of heterozygous perennial bioenergy crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Seismic moment tensor classification using elliptical distribution functions on the hypersphere

Discrimination of underground explosions from naturally occurring earthquakes and other anthropogenic sources is one of the fundamental challenges of nuclear explosion monitoring. In an operational setting, the number of events that can be thoroughly investigated by analysts is limited by available resources. The capability to rapidly screen out events that can be robustly identified as not being explosions is, therefore, of great potential benefit. Nevertheless, possible mis-classification of explosions as earthquakes currently limits the use of screening methods for verification of test-ban treaties. Moment tensors provide a physics-based classification tool for the characterization of different seismic sources and have enabled the advent of new techniques for discriminating between earthquakes and explosions. Following normalization and projection of their six-degree vectors onto the hypersphere, existing screening approaches use spherically symmetric metrics to determine whether any new moment tensor may have been an explosion. Here, we show that populations of moment tensors for both earthquakes and explosions are anisotropically distributed on the hypersphere. Distributions possessing elliptical symmetry, such as the scaled von Mises–Fisher distribution, therefore provide a better description of these populations than the existing spherically symmetric models. We describe a method that uses these elliptical distributions in combination with a Bayesian classifier to achieve successful classification rates of 99 per cent for explosions and 98 per cent for earthquakes using existing catalogues of events from the western United States. The 1983 May 5 Crowdie underground nuclear test and 2018 July 20 DAG-1 deep-borehole chemical explosion are the only two explosions out of 140 that are incorrectly classified. Application of the method to the 2006–2017 nuclear tests in the Democratic People’s Republic of Korea yields 100 per cent identification rates and we provide a simple routine MTid for general usage. The approach provides a means to rapidly assess the likelihood of an event being an explosion and can be built into monitoring workflows that rely on simultaneously assessing multiple different discrimination metrics.

58 GEOSCIENCES↗
DOE OSTI2021

The importance of independent replication of treatments in plant science

Among other foci, the Journal of Experimental Botany aims to advance understanding of plant environment interactions, including abiotic stress, mineral nutrition, and the response of plants to global change. Advancing understanding in these areas often requires manipulation of the growth environment. Experiments range in scale and include: growth chambers (Yiotis et al., 2020), glasshouses (Rho et al., 2019), whole plant chambers (Sharwood et al., 2017), and open-air field experiments (Ruiz-Vera et al., 2020). The application of environmental manipulations can be constrained by available resources, operational costs, and time. In designing experiments, researchers attempt to balance logistical challenges with the desire to address scientific questions and maximize statistical power.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias

Marine algae are central to global carbon fixation, and their productivity is dictated largely by resource availability. Reduced nutrient availability is predicted for vast oceanic regions as an outcome of climate change; however, there is much to learn regarding response mechanisms of the tiny picoplankton that thrive in these environments, especially eukaryotic phytoplankton. Here, we investigate responses of the picoeukaryote Micromonas commoda, a green alga found throughout subtropical and tropical oceans. Under shifting phosphate availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA modification enzymes and biased codon usage of transcripts more abundant during phosphate-limiting versus phosphate-replete conditions, consistent with the role of transfer RNA modifications in regulating codon recognition. To associate the observed shift in the expression of the transfer RNA modification enzyme complement with the transfer RNAs encoded by M. commoda, we also determined the transfer RNA repertoire of this alga revealing potential targets of the modification enzymes. Codon usage bias was particularly pronounced in transcripts encoding proteins with direct roles in managing phosphate limitation and photosystem-associated proteins that have ill-characterized putative functions in “light stress.” The observed codon usage bias corresponds to a proposed stress response mechanism in which the interplay between stress-induced changes in transfer RNA modifications and skewed codon usage in certain essential response genes drives preferential translation of the encoded proteins. Collectively, we expose a potential underlying mechanism for achieving growth under enhanced nutrient limitation that extends beyond the catalog of up- or downregulated protein-encoding genes to the cell biological controls that underpin acclimation to changing environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

The BioMart community portal: an innovative alternative to large, centralized data repositories

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria

The Microviridae family represents one of the major clades of single-stranded DNA (ssDNA) phages. Their cultivated members are lytic and infect Proteobacteria, Bacteroidetes, and Chlamydiae. Prophages have been predicted in the genomes from Bacteroidales, Hyphomicrobiales, and Enterobacteriaceae and cluster within the ‘Alpavirinae’, ‘Amoyvirinae’, and Gokushovirinae. We have isolated ‘Ascunsovirus oldenburgi’ ICBM5, a novel phage distantly related to known Microviridae. It infects Sulfitobacter dubius SH24-1b and uses both a lytic and a carrier-state life strategy. Using ICBM5 proteins as a query, we uncovered in publicly available resources sixty-five new Microviridae prophages and episomes in bacterial genomes and retrieved forty-seven environmental viral genomes (EVGs) from various viromes. Genome clustering based on protein content and phylogenetic analysis showed that ICBM5, together with Rhizobium phages, new prophages, episomes, and EVGs cluster within two new phylogenetic clades, here tentatively assigned the rank of subfamily and named ‘Tainavirinae’ and ‘Occultatumvirinae’. They both infect Rhodobacterales. Occultatumviruses also infect Hyphomicrobiales, including nitrogen-fixing endosymbionts from cosmopolitan legumes. A biogeographical assessment showed that tainaviruses and occultatumviruses are spread worldwide, in terrestrial and marine environments. The new phage isolated here sheds light onto new and diverse branches of the Microviridae tree, suggesting that much of the ssDNA phage diversity remains in the dark.

59 BASIC BIOLOGICAL SCIENCES↗