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In the original article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) were mistakenly omitted from the ENCODE Project Consortium author list. The original Article has been corrected online.
In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) are now included in the author list. These errors have been corrected in the online version of the article.
Regular exercise promotes whole-body health and prevents disease, but the underlying molecular mechanisms are incompletely understood. Here, the Molecular Transducers of Physical Activity Consortium profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome and immunome in whole blood, plasma and 18 solid tissues in male and female Rattus norvegicus over eight weeks of endurance exercise training. The resulting data compendium encompasses 9,466 assays across 19 tissues, 25 molecular platforms and 4 training time points. Thousands of shared and tissue-specific molecular alterations were identified, with sex differences found in multiple tissues. Temporal multi-omic and multi-tissue analyses revealed expansive biological insights into the adaptive responses to endurance training, including widespread regulation of immune, metabolic, stress response and mitochondrial pathways. Many changes were relevant to human health, including non-alcoholic fatty liver disease, inflammatory bowel disease, cardiovascular health and tissue injury and recovery. The data and analyses presented in this study will serve as valuable resources for understanding and exploring the multi-tissue molecular effects of endurance training and are provided in a public repository (https://motrpac-data.org/).
A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating a structured body of information about gene functions, which now includes experimental findings reported in more than 175,000 publications for human genes and genes in experimentally tractable model organisms 1,2 . Here, we describe the results of a large, international effort to integrate all of these findings to create a representation of human gene functions that is as complete and accurate as possible. Specifically, we apply an expert-curated, explicit evolutionary modelling approach to all human protein-coding genes. This approach integrates available experimental information across families of related genes into models that reconstruct the gain and loss of functional characteristics over evolutionary time. The models and the resulting set of 68,667 integrated gene functions cover approximately 82% of human protein-coding genes. The functional repertoire reveals a marked preponderance of molecular regulatory functions, and the models provide insights into the evolutionary origins of human gene functions. We show that our set of descriptions of functions can improve the widely used genomic technique of Gene Ontology enrichment analysis. The experimental evidence for each functional characteristic is recorded, thereby enabling the scientific community to help review and improve the resource, which we have made publicly available.
Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, the ENCODE consortium mapped biochemical signals across hundreds of cell types and tissues and integrated these data to develop a registry containing 0.9 million human and 300,000 mouse candidate cis-regulatory elements (cCREs) annotated with potential functions. Here we have expanded the registry to include 2.37 million human and 967,000 mouse cCREs, leveraging new ENCODE datasets and enhanced computational methods. This expanded registry covers hundreds of unique cell and tissue types, providing a comprehensive understanding of gene regulation. Functional characterization data from assays such as STARR-seq, massively parallel reporter assay, CRISPR perturbation and transgenic mouse assays have profiled more than 90% of human cCREs, revealing complex regulatory functions. We identified thousands of novel silencer cCREs and demonstrated their dual enhancer and silencer roles in different cellular contexts. Integrating the registry with other ENCODE annotations facilitates genetic variation interpretation and trait-associated gene identification, exemplified by the identification of KLF1 as a novel causal gene for red blood cell traits. This expanded registry is a valuable resource for studying the regulatory genome and its impact on health and disease.
New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.
In the version of this article initially published, four people were missing from the alphabetical list of IMG/M Data Consortium members: Lauren V. Alteio of the Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria; Jeffrey L. Blanchard of the Biology Department, University of Massachusetts Amherst, Amherst, MA, USA; Kristen M. DeAngelis of the Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA; and William Rodriguez-Reillo of the Research Computing Division, Harvard Medical School, Boston, MA, USA. The error has been corrected in the PDF and HTML versions of the article.
Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. Further, to address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories. Here we report the summary of the outcomes to provide robust benchmarks and a valuable entry point for the scientific community.
Efficient response to the pandemic through the mobilization of the larger scientific community is challenged by the limited reusability of the available primary genomic data. Here, the Genomic Standards Consortium board highlights the essential need for contextual genomic data FAIRness, for empowering key data-driven biological questions.
Abstract The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification.
Abstract There is an urgent need for new, better instrumentation and techniques for detecting and characterizing special nuclear material (SNM), i.e., highly enriched uranium and plutonium. The development of improved instruments and techniques requires experiments performed with the SNM itself, which is of limited availability. This paper describes the findings of experiments performed at the National Criticality Experiments Research Center conducted using new instruments and techniques on unclassified, kg-quantity SNM objects. These experiments, performed in the framework of the Department of Energy, National Nuclear Security Administration Consortium for Monitoring, Technology, and Verification, focused on detecting, characterizing, and localizing SNM samples with masses ranging from 3.3 to 13.8 kg, including plutonium and highly enriched uranium using prototype detectors and techniques. The work demonstrates SNM detection and characterization using recently-developed prototype detection systems. Specifically, we present new results in passive detection and imaging of plutonium and uranium objects using gamma-ray and dual particle (fast neutron and gamma-ray) imaging. We also present a new analysis of the delayed neutron emissions during active interrogation of uranium using a neutron generator.
Subcutaneous white adipose tissue (scWAT) is a dynamic storage and secretory organ that regulates systemic homeostasis, yet the impact of endurance exercise training (ExT) and sex on its molecular landscape is not fully established. Utilizing an integrative multi-omics approach, and leveraging data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we show profound sexual dimorphism in the scWAT of sedentary rats and in the dynamic response of this tissue to ExT. Specifically, the scWAT of sedentary females displays -omic signatures related to insulin signaling and adipogenesis, whereas the scWAT of sedentary males is enriched in terms related to aerobic metabolism. These sex-specific -omic signatures are preserved or amplified with ExT. Integration of multi-omic analyses with phenotypic measures identifies molecular hubs predicted to drive sexually distinct responses to training. Overall, this study underscores the powerful impact of sex on adipose tissue biology and provides a rich resource to investigate the scWAT response to ExT.
The Consortium for Advanced Simulation of Light Water Reactors (CASL) has developed the CASL toolset, Virtual Environment for Reactor Analysis (VERA), for pressurized water reactor (PWR) analysis. Recently the CASL VERA was improved for Magnox reactor analysis, which required the development of a new cross section library and new geometrical and thermal feedback capabilities for graphite-moderated Magnoxreactors. The MPACT neutronics module of the CASL core simulator is a 3D whole core transport code, which requires a new cross section library with a different energy group structure due to the different neutronic characteristics of Magnox compared with PWR. A new 69-group structure was developed based on the MPACT 51-group structure to have more thermal energy groups and to be a subset of the SCALE 252-group structure. The ENDF/B-VII.1 MPACT 69-group library was developed for Magnox reactor analysis using the SCALE/AMPX and VERA-XSTools for which a super-homogenization method was applied, and transport cross sections were generated for graphite using a neutron leakage conservation method. Benchmark results show that new MPACT 69-group library works reasonably well for Magnox reactor analysis.
The American WAKE experimeNt (AWAKEN) is a large field campaign focused on gathering observations for improved understanding of atmospheric and wind power plant flow physics, one of the outstanding needs for the wind energy community as described in the Science paper by Veers et al.1 "Grand challenges in wind energy." AWAKEN was planned over several years with an international consortium of numerous stakeholders, including national laboratories, academic researchers, wind turbine manufacturers, and wind farm operators. A highlight of the AWAKEN campaign is the extensive use of remote sensing instrumentation to characterize the atmosphere and its interactions with wind power plants, enabled by recent developments in lidar, radar, and thermodynamic profiling technology. Advanced modeling techniques like mesoscale and large-eddy simulations (LES) also played an important role in the preparation of the experiment and the interpretation of the experimental data collected. This special-topic issue for the Journal of Renewable and Sustainable Energy presents a collection of 12 papers that describe the preparatory work and some initial analyses from the AWAKEN campaign. An overview of the contents of the various papers in this special issue is provided in Sec. II.
Solar-driven bioelectrosynthesis represents a promising approach for converting abundant resources into value-added chemicals with renewable energy. Microorganisms powered by electrochemical reducing equivalents assimilate CO 2 , H 2 O, and N 2 building blocks. However, products from autotrophic whole-cell biocatalysts are limited. Furthermore, biocatalysts tasked with N 2 reduction are constrained by simultaneous energy-intensive autotrophy. To overcome these challenges, we designed a biohybrid coculture for tandem and tunable CO 2 and N 2 fixation to value-added products, allowing the different species to distribute bioconversion steps and reduce the individual metabolic burden. This consortium involves acetogen Sporomusa ovata, which reduces CO 2 to acetate, and diazotrophic Rhodopseudomonas palustris, which uses the acetate both to fuel N 2 fixation and for the generation of a biopolyester. We demonstrate that the coculture platform provides a robust ecosystem for continuous CO 2 and N 2 fixation, and its outputs are directed by substrate gas composition. Moreover, we show the ability to support the coculture on a high–surface area silicon nanowire cathodic platform. The biohybrid coculture achieved peak faradaic efficiencies of 100, 19.1, and 6.3% for acetate, nitrogen in biomass, and ammonia, respectively, while maintaining product tunability. Finally, we established full solar to chemical conversion driven by a photovoltaic device, resulting in solar to chemical efficiencies of 1.78, 0.51, and 0.08% for acetate, nitrogenous biomass, and ammonia, correspondingly. Ultimately, our work demonstrates the ability to employ and electrochemically manipulate bacterial communities on demand to expand the suite of CO 2 and N 2 bioelectrosynthesis products.
The Consortium for Advanced Simulation of Light Water Reactors is developing the Virtual Environment for Reactor Applications (VERA), and the MPACT code, which is the primary deterministic neutron transport solver in VERA, provides sub-pin level flux and power distributions as part of full-scale cycle depletion and analysis. In such calculations, an important aspect is the radial reflector treatment. To improve the fidelity of the radial reflector treatment, MPACT was extended to approximate the modeling of the reactor’s structural components such as the core shroud, barrel, neutron pads, and vessel. This work explores several modeling configurations with varying levels of fidelity and computational burden and assesses the importance of modeling fidelity on the eigenvalue and pin power distribution. Two two-dimensional (2-D) problems were analyzed to assess the impact on eigenvalue and pin power distributions with low-fidelity, coarse square cell reflector representations: (1) a Watts Bar Nuclear Plant Unit 1 (WBN1) quarter-core slice with depletion and (2) an AP1000 quarter-core slice. In this work, the analyses showed that the effect on eigenvalue is fairly small, but the effect on pin power is more pronounced, especially locally in the assemblies closest to the periphery, where the maximum pin power difference is nearly 3.5% in the AP1000 case. Two additional 2-D problems were used to assess the comparison between the low-fidelity coarse square cell treatment and a high-fidelity geometric representation that uses subpin material specification: (1) the same WBN1 quarter-core slice and (2) a representative model of the NuScale small modular reactor (SMR), which features a solid reflector design with moderator holes. These results demonstrate that even a coarse, low-fidelity representation adequately captures the necessary simulation characteristics. Last, these capabilities were applied to the 2-D WBN1 quarter-core depletion to assess the impact on vessel fluence using VeraShift. From adjoint calculations, pins along the periphery were observed to be of highest importance for fluence calculation, so the impact of the reflector representation in MPACT could theoretically substantially affect the predicted result. However, it was observed that the change in pin powers along the periphery minimally impacts the maximum vessel fluence with a difference within the statistical uncertainty but provides terrific insight on the sensitivity of the peripheral pins.
The Consortium for Advanced Simulation of Light Water Reactors (CASL) Virtual Environment for Reactor Applications (VERA) is a reactor simulation software. It offers unique capabilities by combining high-fidelity in-core radiation transport with temperature feedback by using MPACT (a deterministic neutron transport code) and COBRA-TF (a thermal-hydraulic code) with follow-on, fixed-source transport calculations using the Shift Monte Carlo code to calculate ex-core quantities of interest. In these coupled calculations, MPACT provides Shift with the fission source for follow-on ex-core calculations. These ex-core simulations can be set up to calculate detector responses, as well as the flux and fluence in ex-core regions of interest, such as the reactor pressure vessel, nozzle, and irradiated capsules. A Watts Bar Nuclear Plant Unit 1 (WBN1) ex-core model was developed, as described in this paper, and this model was used to perform coupon calculations. The results for the coupon flux calculations show close agreement with the reference values for cycle 1 produced by the two-dimensional Discrete Ordinates Transport (DORT) code and presented in a BWXT Services Inc. report. However, differences in the results (10%) seen in cycles 2 and 3 and the reasons for these differences are discussed in this paper. The VERA WBN1 model was also used to perform a vessel fluence calculation for cycle 1. Additionally, a collaboration between CASL and Duke Energy led to the first code-to-code validation of VERA for reactor ex-core applications that used a model for the Shearon Harris reactor. Results from this collaboration show excellent agreement between VERA and the Monte Carlo N-Particle Transport Code for the detector response calculations. The work performed under this collaboration is also detailed in this paper.