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Wilson, James

Publications and source records attributed to Wilson, James.

10 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Origin of biogeographically distinct ecotypes during laboratory evolution

Resource partitioning is central to the incredible productivity of microbial communities, including gigatons in annual methane emissions through syntrophic interactions. Previous work revealed how a sulfate reducer (Desulfovibrio vulgaris, Dv) and a methanogen (Methanococcus maripaludis, Mm) underwent evolutionary diversification in a planktonic context, improving stability, cooperativity, and productivity within 300-1000 generations. Here, we show that mutations in just 15 Dv and 7 Mm genes within a minimal assemblage of this evolved community gave rise to co-existing ecotypes that were spatially enriched within a few days of culturing in a fluidized bed reactor. The spatially segregated communities partitioned resources in the simulated subsurface environment, with greater lactate utilization by attached Dv but partial utilization of resulting H 2 by low affinity hydrogenases of Mm in the same phase. The unutilized H 2 was scavenged by high affinity hydrogenases of planktonic Mm, producing copious amounts of methane. Our findings show how a few mutations can drive resource partitioning amongst niche-differentiated ecotypes, whose interplay synergistically improves productivity of the entire mutualistic community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes

Longitudinal sampling of the stool has yielded important insights into the ecological dynamics of the human gut microbiome. However, human stool samples are available approximately once per day, while commensal population doubling times are likely on the order of minutes-to-hours. Despite this mismatch in timescales, much of the prior work on human gut microbiome time series modeling has assumed that day-to-day fluctuations in taxon abundances are related to population growth or death rates, which is likely not the case. Here, we propose an alternative model of the human gut as a stationary system, where population dynamics occur internally and the bacterial population sizes measured in a bolus of stool represent a steady-state endpoint of these dynamics. We formalize this idea as stochastic logistic growth. We show how this model provides a path toward estimating the growth phases of gut bacterial populations in situ. We validate our model predictions using an in vitro Escherichia coli growth experiment. Finally, we show how this method can be applied to densely-sampled human stool metagenomic time series data. We discuss how these growth phase estimates may be used to better inform metabolic modeling in flow-through ecosystems, like animal guts or industrial bioreactors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A Storm Safari in Subtropical South America: Proyecto RELAMPAGO

In this article, we provide an overview of the experimental design, execution, education and public outreach, data collection, and initial scientific results from the Remote Sensing of Electrification, Lightning, and Mesoscale/Microscale Processes with Adaptive Ground Observations (RELAMPAGO) field campaign. RELAMPAGO was a major field campaign conducted in the Córdoba and Mendoza provinces in Argentina and western Rio Grande do Sul State in Brazil in 2018–19 that involved more than 200 scientists and students from the United States, Argentina, and Brazil. This campaign was motivated by the physical processes and societal impacts of deep convection that frequently initiates in this region, often along the complex terrain of the Sierras de Córdoba and Andes, and often grows rapidly upscale into dangerous storms that impact society. Observed storms during the experiment produced copious hail, intense flash flooding, extreme lightning flash rates, and other unusual lightning phenomena, but few tornadoes. The five distinct scientific foci of RELAMPAGO—convection initiation, severe weather, upscale growth, hydrometeorology, and lightning and electrification—are described, as are the deployment strategies to observe physical processes relevant to these foci. The campaign’s international cooperation, forecasting efforts, and mission planning strategies enabled a successful data collection effort. In addition, the legacy of RELAMPAGO in South America, including extensive multinational education, public outreach, and social media data gathering associated with the campaign, is summarized.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions

Abstract Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR− and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Issues Affecting the Assessment of Impacts of Disposal of Radioactive and Hazardous Waste - 18177

BIOPROTA is an international collaborative forum that seeks to address the key uncertainties in long term assessments of radionuclide and other contaminant releases into the environment arising from solid radioactive waste disposal. (see www.bioprota.org). Two workshops have been organized through the BIOPROTA forum to consider the non-radiological post-disposal impacts of radioactive waste disposal. In these workshops, it was noted that, ideally, the assessment of radionuclides and hazardous materials should be such that consistent assumptions and criteria are used in risk evaluation and that in cases where this is not possible, a clear understanding of the reasons why needs to be provided. Accordingly, a detailed review was organized through BIOPROTA to provide information to support development of a consensus on how to address this issue. The study suggests that there is a continuing need for some common measure of hazard that supports identification of risk management priorities for mixed hazardous waste. Without it, effective optimization of management of these mixed hazardous wastes will be restricted. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2018

Modeling the Long-Term Behavior of Cementitious Barriers - 18188

Cementitious materials are commonly included as backfill/barrier materials in geological repositories for radioactive waste. An understanding of the long-term behavior of cement-based barriers is therefore required to provide confidence in their safety functions within an environmental safety case. Geochemical modelling has been undertaken on several different radioactive waste repository concepts (and their natural/industrial analogues), to explore the nature of cement degradation over timescales relevant to postclosure safety (many tens of thousands of years to c. 1 Ma). In radionuclide transport calculations undertaken as part of performance assessments, it is typically considered that the properties of cementitious engineered barrier materials change as they degrade, potentially resulting in an increase in porosity hydraulic conductivity, and effective diffusion coefficients. However, reactive transport modelling (supported by some analogue data) suggests that, in some repository systems, a degree of clogging of the cement pore space could occur and that some advective flow paths (cracks in the barriers, fractures in the host rock) could become (to some extent) infilled by cement and rock alteration products. This could result in a reduction in water flow and contaminant transport in the vicinity of the cement-rock interface, but some uncertainties remain (especially process couplings and the nature of water flow in complex fracture networks that are becoming clogged). In addition, the armoring of fracture surfaces could result in decreased potential for diffusion of solutes into the rock matrix. It is envisaged that ongoing work will continue to improve reactive-transport model capabilities, such that the implications cement degradation has for contaminant transport can be predicted with greater confidence. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

Gas Gun-Configured Magnetic Flux Compression Generator, NLV-013-17, Year 1 of 3

Presentation on project to explore the concept of achieving current amplification by principles of high-explosive magnetic compression generation but without high explosives and demonstrate that a gas gun or launcher could be configured to provide the input energy and action necessary for magnetic compression generation performance in a more controlled, cost-effective manner with improved safety.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS1992

TUNS/TCIS information model/process model

An Information Model is comprised of graphical and textual notation suitable for describing and defining the problem domain - in our case, TUNS or TCIS. The model focuses on the real world under study. It identifies what is in the problem and organizes the data into a formal structure for documentation and communication purposes. The Information Model is composed of an Entity Relationship Diagram (ERD) and a Data Dictionary component. The combination of these components provide an easy to understand methodology for expressing the entities in the problem space, the relationships between entities and the characteristics (attributes) of the entities. This approach is the first step in information system development. The Information Model identifies the complete set of data elements processed by TUNS. This representation provides a conceptual view of TUNS from the perspective of entities, data, and relationships. The Information Model reflects the business practices and real-world entities that users must deal with.

Wilson, James↗
NASA NTRS1992

Repository-based software engineering program

The activities performed during September 1992 in support of Tasks 01 and 02 of the Repository-Based Software Engineering Program are outlined. The recommendations and implementation strategy defined at the September 9-10 meeting of the Reuse Acquisition Action Team (RAAT) are attached along with the viewgraphs and reference information presented at the Institute for Defense Analyses brief on legal and patent issues related to software reuse.

Wilson, James↗