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Mans, Douglas M.

Publications and source records attributed to Mans, Douglas M..

8 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

DOE BSSD Performance Management Metrics Report Q3

Microbiome data is complex, spanning information from microbial genomes within diverse communities, protein and metabolite readouts, and contextual information (metadata) captured from the environments from which these samples were collected. While the variety and scale of microbiome data generation has dramatically expanded over the past twenty years, infrastructure to support data management, sharing, and access has lagged. New ways to improve interoperability across existing resources and advancing community standards are necessary to support how researchers create, use, and reuse data. The National Microbiome Data Collaborative (NMDC) aims to advance a microbiome data sharing network through infrastructure, data standards, and community building.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

DOE BSSD Performance Management Metrics Report Q2

The vision of the National Microbiome Data Collaborative (NMDC) centers on the concept of connecting data, people, and ideas to advance microbiome innovation and discovery. Building data infrastructure, while key to NMDC’s ability to execute on our vision, can only go so far in creating scientific impact. By fostering strong community partnerships and developing a set of robust community outreach and training programs, we are able to turn our products – the Submission Portal, NMDC EDGE, and the Data Portal – into tools that empower the scientific community. Our multi-pronged community building approach spans individual researchers, research teams, consortia and scientific societies, and institutions and federal agencies. To foster a collaborative and inclusive community-centered environment, we have identified three strategic objectives to promote an inclusive and connected community: (1) recognize and support the diverse research needs and perspectives of the microbiome research community; (2) promote best practices across the microbiome community, from researchers to funders, through community-driven practices (FAIR, CARE, and TRUST); and (3) build a microbiome ecosystem that enables scientific discovery and innovation across stakeholders. These strategic objectives allow our team to focus on impact across a diverse range of activities, from launching the American Society for Microbiology (ASM) Microbiome Data Prize to supporting the Ambassador and Champions programs fostering learning and building a collaborative network. We broadly communicate our work through social media (X/Twitter, LinkedIn, and Instagram), The Microbiome Standard (our quarterly newsletter), and Annual Reports. All our work is underpinned by a strong commitment to diversity, equity, and inclusion as articulated in our Action Plan that tracks progress towards key metrics. A core component of our engagement strategy is user research. User research ensures the Submission Portal, NMDC EDGE, Data Portal, and the new Field Notes mobile app are designed with and for the scientific community. Our user research efforts consist of asking researchers exploratory questions to collect information on researcher priorities, methodologies, and perceptions to ensure that we are aware of the current state of microbiome research. Our usability testing provides researchers with prototypes or test environments of the NMDC products, and we capture valuable information on how users interact with the products to make improvements. Given the diverse nature of microbiome work, we acknowledge that we are not aware of all pressing data challenges and thus rely on the research community to help us identify the most important issues to prioritize. To date, we have conducted 24 interviews and one beta-testing call with 10 participants across all NMDC products, which have generated 321 insights and 120 action items. Herein, we describe the ways we engage with the microbiome research community to advance the NMDC mission.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2023

One thousand soils for molecular understanding of belowground carbon cycling

While significant progress has been made in understanding global carbon (C) cycling, the mechanisms regulating belowground C fluxes and storage are still uncertain. New molecular technologies have the power to elucidate these processes, yet we have no widespread standardized implementation of molecular techniques. To address this gap, we introduce the Molecular Observation Network (MONet), a decadal vision from the Environmental Molecular Sciences Laboratory (EMSL), to develop a national network for understanding the molecular composition, physical structure, and hydraulic and biological properties of soil and water. These data are essential for advancing the next generation of multiscale Earth systems models. In this paper, we discuss the 1000 Soils Pilot for MONet, including a description of standardized sampling materials and protocols and a use case to highlight the utility of molecular-level and microstructural measurements for assessing the impacts of wildfire on soil. While the 1000 Soils Pilot generated a plethora of data, we focus on assessments of soil organic matter (SOM) chemistry via Fourier-transform ion cyclotron resonance-mass spectrometry and microstructural properties via X-ray computed tomography to highlight the effects of recent fire history in forested ecosystems on belowground C cycling. We observed decreases in soil respiration, microbial biomass, and potential enzyme activity in soils with high frequency burns. Additionally, the nominal oxidation state of carbon in SOM increased with burn frequency in surface soils. This results in a quantifiable shift in the molecular signature of SOM and shows that wildfire may result in oxidation of SOM and structural changes to soil pore networks that persist into deeper soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale

The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.

NMDC, Microbiome↗
DOE OSTI2019

Development and Scale-up of Continuous Electrocatalytic Hydrogenation of Functionalized Nitro arenes, Nitriles and Unsaturated Aldehydes

Electrolysis reactors based on the filter-press architecture of redox flow batteries have proven to be effective and scalable towards the production of commercially relevant, pharmaceutical quantities of anilines (>500 kg/year) from halogen-, hydroxyl-, and carbonyl-substituted nitroarenes. Turbulent flow through the carbon felts on which the catalysts were supported facilitated scaling towards production levels because it conferred on the reactors scale-independent, plug flow-like residence time distributions and high mass transfer coefficients. Equipping the cells with micro-reference electrodes made it possible to transfer reaction conditions first developed in batch systems to the continuous flow reactors. The catalysts prepared by incipient wetness impregnation of metal salts into lightly oxidized carbon felt supports were readily generalizable.

Egbert, Jonathan D.↗