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At least 19 records

“Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system

Background In Nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine metaomics and enzymology to identify and describe a novel Bacteroidetes family (UMH11) composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa. Results The first metabolic reconstruction of UMH11-affiliated genome bins, with a particular focus on the provisionally named UParaporphyromonas polyenzymogenes, illustrated their capacity to degrade various lignocellulosic substrates via comprehensive inventories of singular and multi-modular carbohydrate active enzymes (CAZymes). Closer examination revealed an absence of archetypical polysaccharide utilization loci found in human-gut microbiota. Instead, we identified many multi-modular CAZymes putatively secreted via the Bacteroidetes-specific Type 9 secretion system (T9SS). This included cellulases with two or more catalytic domains, which are modular arrangements that are unique to Bacteroidetes species studied to date. Core metabolic proteins from UP. polyenzymogenes were detected in metaproteomic data and were enriched in rumen-incubated plant biomass, indicating that active saccharification and fermentation of complex carbohydrates could be assigned to members of this novel family. Biochemical analysis of selected UP. polyenzymogenes CAZymes further iterated the cellulolytic activity of this hitherto uncultured bacterium towards linear polymers, such as amorphous and crystalline cellulose as well as mixed linkage β-glucans. Conclusion We propose that UP. olyenzymogenes genotypes and other UMH11 members actively degrade plant biomass in the rumen of cows, sheep, and most likely other ruminants, utilizing singular and multi-domain catalytic CAZymes secreted through the T9SS. The discovery of a prominent role of multi-modular cellulases in the Gramnegative Bacteroidetes, together with similar findings for Gram-positive cellulosomal bacteria (Ruminococcus flavefaciens) and anaerobic fungi (Orpinomyces sp.), suggests that complex enzymes are essential and have evolved within all major cellulolytic dominions inherent to the rumen.

Environmental Molecular Sciences Laboratory↗

A modular reactor design for in situ synchrotron x-ray investigation of atomic layer deposition processes

Synchrotron characterization techniques provide some of the most powerful tools for the study of film structure and chemistry. The brilliance and tunability of the Advanced Photon Source allow access to scattering and spectroscopic techniques unavailable with in-house laboratory setups and provide the opportunity to probe various atomic layer deposition (ALD) processes in situ starting at the very first deposition cycle. Here, we present the design and implementation of a portable ALD instrument which possesses a modular reactor scheme that enables simple experimental switchover between various beamlines and characterization techniques. As first examples, we present in situ results for (1) X-ray surface scattering and reflectivity measurements of epitaxial ZnO ALD on sapphire, (2) grazing-incidence small angle scattering of MnO nucleation on silicon, and (3) grazing-incidence X-ray absorption spectroscopy of nucleation-regime Er{sub 2}O{sub 3} ALD on amorphous ALD alumina and single crystalline sapphire.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Quantum extremal modular curvature: modular transport with islands

Modular Berry transport is a useful way to understand how geometric bulk information is encoded in the boundary CFT: the modular curvature is directly related to the bulk Riemann curvature. We extend this approach by studying modular transport in the presence of a non-trivial quantum extremal surface. Focusing on JT gravity on an AdS background coupled to a non-gravitating bath, we compute the modular curvature of an interval in the bath in the presence of an island: the Quantum Extremal Modular Curvature (QEMC). We highlight some important properties of the QEMC, most importantly that it is non-local in general. In an OPE limit, the QEMC becomes local and probes the bulk Riemann curvature in regions with an island. Our work gives a new approach to probe physics behind horizons.

2D Gravity↗

Modularization of Small Modular Reactor Facilities: Physical Protection Recommendations

U.S. nuclear power facilities face increasing challenges in meeting dynamic security requirements caused by evolving and expanding threats while keeping costs reasonable to make nuclear energy competitive. In consideration of the economic viability of small modular reactor (SMR) facilities, many designers and utilities are considering a modular approach to the construction and operation of these facilities. This modular approach considers building and operating a first unit; once the first reactor is in operation, construction will begin on a second reactor. This process would allow the vendor or utility to ensure production of energy and financial income while the second reactor is under construction. This project evaluates the feasibility of modular construction in terms of physical protection and identifies several recommendations for vendors and utilities considering this approach. To conduct this evaluation, a hypothetical three-unit SMR facility was developed, a physical protection system (PPS) was considered for the design, and a hypothetical design basis threat (DBT) was used to evaluate this PPS. Multiple outsider sabotage scenarios were examined, with adversary team sizes ranging from 4-to-8 to determine security system effectiveness. The results of this work will influence PPS designs and facility designs for U.S. domestic SMRs. This work will also demonstrate how a series of experimental and modeling capabilities across the Department of Energy (DOE) complex can impact the design and completion of security-by-design (SeBD) for SMRs considering modular construction. The conclusions and recommendations in this document may be applicable to all SMR designs.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

The Energy in Modular (EMOD) Buildings Method: A Guide to Energy-Efficient Design for Industrialized Construction of Modular Buildings

Industrialized construction has immense potential to address the growing need globally to build and upgrade the building stock to be affordable, energy-efficient, and resilient. It can also help achieve the United States' goal of a 50% reduction in U.S. greenhouse gas (GHG) emissions by 2030. Despite this potential, and the ever-increasing push for electrification and decarbonization of households in the United States, industrialized construction has not yet been leveraged specifically to help address these challenges and accelerate the pathway to meet these goals. The National Renewable Energy Laboratory (NREL) aims to claim this missed opportunity by focusing on delivering affordable, grid-efficient net-zero energy (NZE) modular buildings for underserved communities to ensure an equitable transition to the future of clean energy, accelerate decarbonization of the built environment, and support the development of a high-productivity construction and energy efficiency workforce. The Energy in Modular (EMOD) method is our approach to designing, producing, and delivering affordable, net-zero energy, low-carbon, and healthier buildings at scale. The following energy efficiency strategies are part of the scope of this guide: envelope thermal control, envelope infiltration control, mechanical, electrical, and plumbing systems, smart controls, and solar plus storage. We draw synergies between design for manufacturing and assembly, process optimization, retrofit technologies, and digitization. Our goal is to influence the improvement and production of buildings to increase performance, enhance energy efficiency, and reduce GHG emissions. This guide documents the research and development efforts initiated by a set of design objectives to "modularize" a set of energy efficiency and low-carbon strategies into a housing unit while preserving and enhancing energy efficiency benefits and decarbonization pathways. This guide is intended to serve as a framework for housing developers, housing agencies, architects, energy experts, and process engineers or factory operator personnel who are critical to today's modular builder teams. This guide focuses on specific energy efficiency strategies, decarbonization pathways, and associated processes as part of NREL's research efforts. Stakeholders may substitute other means, methods, and technologies for the ones evaluated in this study.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Split green fluorescent protein as a modular binding partner for protein crystallization

A strategy using a new split green fluorescent protein (GFP) as a modular binding partner to form stable protein complexes with a target protein is presented. The modular split GFP may open the way to rapidly creating crystallization variants. A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP β-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was tested by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10–11) hairpin in complex with GFP(1–9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10–11) hairpin with a variety of GFP(1–9) mutants engineered for favorable crystallization.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Modular CO 2 Capture Processes for Integration with Modular Scale Gasification Technologies: Literature Review and Gap Analysis for Future R&D

The motivation for this report is the recent focus of the U.S. Department of Energy’s (DOE) gasification program to develop modular scale gasification processes for electricity generation and other applications. Mass-produced, modular gasification systems have been proposed to decrease the upfront capital costs and to encourage flexible deployment of advanced gasification technology using a diverse set of feedstocks. To fully realize the benefits of advanced gasification technology for power generation as well as other chemical applications, precombustion carbon dioxide (CO 2 ) capture must be considered. Therefore, the aim of this report is to assess the potential of integrating modular scale carbon capture processes with modular scale coal gasification technologies, and to help guide future research and development efforts in this area.

20 FOSSIL-FUELED POWER PLANTS↗

Modularized Production of Fuels and other Value-Added Products from Distributed, Wasted, or Stranded Feedstocks

Distributed, wasted, or stranded feedstocks, when converted and upgraded into fuels, could replace about 6% of the US demand for liquid fuels, which is about 25% of the net import of petroleum by the US. We review the current state of modular approaches for conversion of these feedstocks, including the technology and economics associated with processing carbon-containing waste and stranded, carbon-containing gas. The wide geographic distribution of the feedstocks will require technology that can be scaled down effectively and that can be manufactured, installed, operated and monitored in ways that gain economies of mass production rather than economies of throughput scaling.

Weber, Robert S.↗

Modeling the use of mobile modular gas samplers in near-field detection

The Wireless Independent Noble Gas Sampler (WINGS) is a mobile, modular gas sampling system designed for use in low infrastructure environments. In the case of a suspected underground nuclear explosion (UNE), WINGS units could be deployed to detect noble gases emanating from the suspected explosion site or identify gases originating from another source entering the local area from offsite. In conclusion, this work uses the atmospheric transport modeling tool inline WRF-HYSPLIT to test the effectiveness of WINGS units around a suspected UNE site as a function of sampler density and distance from the emission point of gases from a UNE.

Air sampling↗

Modular Total Absorption Spectrometer at the HRIBF (ORNL, Oak Ridge)

The Modular Total Absorption Spectrometer (MTAS) array has been designed, constructed, characterized, and applied to the decay studies of {sup 238}U fission products at the Holifield Radioactive Ion Beam Facility (HRIBF) at Oak Ridge National Laboratory. A MTAS commissioning run was performed in January 2012 at the mass separator on-line to the HRIBF Tandem accelerator. Preliminary results of MTAS data confirm known decay patterns of {sup 142}Ba and {sup 142}La deduced from an earlier study using a total absorption spectrometer technique.

43 PARTICLE ACCELERATORS↗

Modular focusing ring imaging Cherenkov detector for electron–ion collider experiments

A powerful new electron-ion collider (EIC) has been recommended in the 2015 Long Range Plan for Nuclear Science for probing the partonic structure inside nucleons and nuclei with unprecedented precision and versatility [1]. EIC detectors are currently under development [2], all of which require hadron identification over a broad kinematic range. A prototype ring imaging Cherenkov detector has been developed for hadron identification in the momentum range from 3 GeV/c to 10 GeV/c. The key feature of this new detector is a compact and modular design, achieved by using aerogel as radiator and a Fresnel lens for ring focusing. In this paper, the results from a beam test of a prototype device at Fermilab are reported.

aerogel↗

Multiobjective Modular Biorefinery Configuration under Uncertainty

With increasing interest in using biomass as a raw material for fuel, the development of biorefineries is an active area of research. However, increasing market competition, uncertainty, and environmental concerns are a few of the challenges that need to be addressed. In this work, mathematical optimization formulations are proposed to address these challenges simultaneously. A multiobjective deterministic optimization framework is proposed to address economic and environmental objectives. A two-stage stochastic optimization framework is proposed to account for uncertainties in material flow and product yields. To model the environmental objective, an environmental risk metric is proposed. Finally, as modularization is gaining popularity in the process industry due to its ability to save capital cost because of standardization and reduce time to market, a formulation for simultaneously achieving modular process design and biorefinery configuration is proposed. Furthermore, the results demonstrate the efficacy of the proposed approach.

09 BIOMASS FUELS↗

Diblock Copolymer Micelles and Supported Films with Noncovalently Incorporated Chromophores: A Modular Platform for Efficient Energy Transfer

Here we report generation of modular, artificial light-harvesting assemblies where an amphiphilic diblock copolymer, poly(ethylene oxide)-block-poly(butadiene), serves as the framework for noncovalent organization of BODIPY-based energy donor and bacteriochlorin-based energy acceptor chromophores. The assemblies are adaptive and form well-defined micelles in aqueous solution and high-quality monolayer and bilayer films on solid supports, with the latter showing greater than 90% energy transfer efficiency. Ultimately, this study lays the groundwork for further development of modular, polymer-based materials for light harvesting and other photonic applications.

36 MATERIALS SCIENCE↗

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

97 MATHEMATICS AND COMPUTING↗