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At least 199 records · Page 11

Systems Analysis of NADH Dehydrogenase Mutants Reveals Flexibility and Limits of Pseudomonas taiwanensis VLB120’s Metabolism

Obligate aerobic organisms rely on a functional electron transport chain for energy conservation and NADH oxidation. Because of this essential requirement, the genes of this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance and energy shortage under fluctuating environmental conditions. In this work, we investigated the essentiality of the three NADH dehydrogenases of the respiratory chain of the obligate aerobe Pseudomonas taiwanensis VLB120 and the impact of the knockouts of corresponding genes on its physiology and metabolism. While a mutant lacking all three NADH dehydrogenases seemed to be nonviable, the single or double knockout mutant strains displayed no, or only a weak, phenotype. Only the mutant deficient in both type 2 dehydrogenases showed a clear phenotype with biphasic growth behavior and a strongly reduced growth rate in the second phase. In-depth analyses of the metabolism of the generated mutants, including quantitative physiological experiments, transcript analysis, proteomics, and enzyme activity assays revealed distinct responses to type 2 and type 1 dehydrogenase deletions. An overall high metabolic flexibility enables P. taiwanensis to cope with the introduced genetic perturbations and maintain stable phenotypes, likely by rerouting of metabolic fluxes. This metabolic adaptability has implications for biotechnological applications. While the phenotypic robustness is favorable in large-scale applications with inhomogeneous conditions, the possible versatile redirecting of carbon fluxes upon genetic interventions can thwart metabolic engineering efforts. While Pseudomonas has the capability for high metabolic activity and the provision of reduced redox cofactors important for biocatalytic applications, exploitation of this characteristic might be hindered by high, constitutive activity of and, consequently, competition with the NADH dehydrogenases of the respiratory chain. The in-depth analysis of NADH dehydrogenase mutants of Pseudomonas taiwanensis VLB120 presented here provides insight into the phenotypic and metabolic response of this strain to these redox metabolism perturbations. This high degree of metabolic flexibility needs to be taken into account for rational engineering of this promising biotechnological workhorse toward a host with a controlled and efficient supply of redox cofactors for product synthesis.

36 MATERIALS SCIENCE↗

Hydrogen Hub Systems Analysis and Mapping Tool (ParaCraft) v1

A plug and play techno-economic analysis (TEA) and lifecycle assessment (LCA) tool was built that could incorporate new projects into the California ARCHES LLC Hydrogen hub, and generate results for the project, as well as the overall hub on an annual basis. The model was first constructed in Microsoft Excel and ArcGIS, but required labor intensive updating and manual decision making regarding the matching of hydrogen supplier and offtaker and estimation of transportation distances and utility sources. The project team converted the Excel model used for the ARCHES LLC hub conceptualization into a highly flexible and nearly completely automated R code. The R code runs the TEA and LCA, as well as provides mapping capabilities that automatically link projects by latitude and longitude to nearby utilities.

Breunig, Hanna↗

Engineering Layer For System Analysis

ELSA offers various utility classes and methods to streamline the definition of regions, materials, and geometries in nuclear simulations. Key features include generating OpenMC regions, managing material properties, and providing convenient abstractions for complex geometrical and physical configurations. Additionally, ELSA supports the creation of submodels, enabling users to build modular and reusable components for their simulations. The codebase also includes robust extrusion and revolution capabilities, facilitating the efficient creation of 3D parametric geometries from 2D profiles through linear and rotational transformations.

Ferney, Paul [Idaho National Laboratory (INL), Ida↗

Data for System Analysis of Lipomyces starkeyi During Growth on Various Plant‑Based Sugars

Oleaginous yeasts have received significant attention due to their substantial lipid storage capability. The accumulated lipids can be utilized directly or processed into various bioproducts and biofuels. Lipomyces starkeyi is an oleaginous yeast capable of using multiple plant-based sugars, such as glucose, xylose, and cellobiose. It is, however, a relatively unexplored yeast due to limited knowledge about its physiology. In this study, we have evaluated the growth of L. starkeyi on different sugars and performed transcriptomic and metabolomic analyses to understand the underlying mechanisms of sugar metabolism. Principal component analysis showed clear differences resulting from growth on different sugars. We have further reported various metabolic pathways activated during growth on these sugars. We also observed non-specific regulation in L. starkeyi and have updated the gene annotations for the NRRL Y-11557 strain. This analysis provides a foundation for understanding the metabolism of these plant-based sugars and potentially valuable information to guide the metabolic engineering of L. starkeyi to produce bioproducts and biofuels.

Conversion↗

Systems Analysis of hiRX for Improved Reprocessing Safeguards

The goal of this work was to examine the potential safeguards improvement of the High Resolution X-ray (hiRX) technology for aqueous reprocessing plants. Existing plants utilize KEdge and Hybrid K-Edge Densitometry for routine accountancy measurements for the key input and output accountability tanks. The IAEA also use these technologies for verification measurements. The hiRX technology has the potential to significantly reduce the measurement uncertainty with an equally simple but less costly instrument that uses a much smaller sample size. Such a technology could be highly desirable for both the operator and inspector. This work utilizes a Separations and Safeguards Performance Model of a PUREX reprocessing plant to determine the safeguards improvement offered by the reduced measurement uncertainty of hiRX. Results show that a significant improvement in the ability to detect a protracted diversion may be possible.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Bottom-Up Energy Analysis System - Methodology and Results

The main objective of the development of BUENAS is to provide a global model with sufficient detail and accuracy for technical assessment of policy measures such as energy efficiency standards and labeling (EES&L) programs. In most countries where energy efficiency policies exist, the initial emphasis is on household appliances and lighting. Often, equipment used in commercial buildings, particularly heating, air conditioning and ventilation (HVAC) is also covered by EES&L programs. In the industrial sector, standards and labeling generally covers electric motors and distribution transformers, although a few more types of industrial equipment are covered by some programs, and there is a trend toward including more of them. In order to make a comprehensive estimate of the total potential impacts, development of the model prioritized coverage of as many end uses commonly targeted by EES&L programs as possible, for as many countries as possible.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Next Generation Workload Management and Analysis System for Big Data

We report on the activities and accomplishments of a four-year project (a three-year grant followed by a one-year no cost extension) to develop a next generation workload management system for Big Data. The new system is based on the highly successful PanDA software developed for High Energy Physics (HEP) in 2005. PanDA is used by the ATLAS experiment at the Large Hadron Collider (LHC), and the AMS experiment at the space station. The program of work described here was carried out by two teams of developers working collaboratively at Brookhaven National Laboratory (BNL) and the University of Texas at Arlington (UTA). These teams worked closely with the original PanDA team – for the sake of clarity the work of the next generation team will be referred to as the BigPanDA project. Their work has led to the adoption of BigPanDA by the COMPASS experiment at CERN, and many other experiments and science projects worldwide.

97 MATHEMATICS AND COMPUTING↗

Cost and Systems Analysis of Innovative Fuel Resources Concepts

Economically recovered uranium from seawater can have a transformative effect on the way policy makers view the long-term viability of uranium based fuel cycles. Seawater uranium, even when estimated to cost more than terrestrially mined uranium, is integral in establishing an economic backstop, thus reducing uncertainty in future nuclear power costs. While a passive recovery scheme relying on a field of polymer adsorbents prepared via radiation induced grafting has long been considered the leading technology for full scale deployment, non-trivial cost and logistical barriers persist. Consequently, university partners of the nation-wide consortium for seawater uranium recovery have developed variants of this technology, each aiming to address a substantial weakness. The focus of this NEUP project is the economic impacts of the proposed variant technologies. The team at University of Alabama has pursued an adsorbent synthesis method that replaces the synthetic fiber backbone with a natural waste product. Chitin fibers suitable for ligand grafting have been prepared from shrimp shell waste. These environmental benefits could be realized at a comparable cost to the reference fiber so long as the uptake can be increased or the chemical consumption cost decreased.

54 ENVIRONMENTAL SCIENCES↗

Advanced SAPHIRE 8 Modeling Methods for Probabilistic Risk Assessment via the Systems Analysis Program for Hands-On Integrated Reliability Evaluations (SAPHIRE) Software P-202

1.1. Overview of the Advanced SAPHIRE Material The Advanced SAPHIRE course material is intended to both (1) provide guidance for learning advanced SAPHIRE features during the class and (2) become a stand-alone reference document after finishing the class. Thus, the format for the class material is a combination of the traditional “overhead-type” of presentation information with a structured, reference-type document. Major topics that are covered in the Advanced SAPHIRE class include: Advanced data base concepts such as Model Type (e.g., random, seismic, fire, flood). Definition of house events and how they are used on a sequence-by-sequence basis to manipulate individual fault tree logic using sequence flag sets or fault tree flag sets. ? Basic event templates, compound basic event equation editors, and human error worksheets. A rule-based event tree top event substitution feature (called the Link Event Tree Rule Editor) which allows for top event substitutions. A rule-based cut set post-processing feature (called the Recovery Rules) which allows cut set manipulation. Cut set analysis based upon rule-based end state categories (called End State Analysis). Cut set generation options for both fault trees and event tree sequences. The large event tree methodology and how SAPHIRE can be used to generate sequence cut sets for this method. The transfer of data between SAPHIRE data bases and between other PRA codes (MAR-D).

97 MATHEMATICS AND COMPUTING↗