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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

“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↗
DOE OSTI2023

Source-encoded waveform inversion in the Northern Hemisphere

SUMMARY We use source-encoded waveform inversion to image Earth’s Northern Hemisphere. The encoding method is based on measurements of Laplace coefficients of stationary wavefields. By assigning to each event a unique frequency, we compute Fréchet derivatives for all events simultaneously based on one ‘super’ forward and one ‘super’ adjoint simulation for a small fraction of the computational cost of classical waveform inversion with the same data set. No cross-talk noise is introduced in the process, and the method does not require all events to be recorded by all stations. Starting from global model GLAD_M25, we performed 100 conjugate gradient iterations using a data set consisting of 786 earthquakes recorded by 9846 stations. Synthetic inversion tests show that we achieve good convergence based on this data set, and we see a consistent misfit reduction during the inversion. The new model, named SE100, has much higher spatial resolution than GLAD_M25, revealing details of the Yellowstone and Iceland hotspots, subduction beneath the Western United States and the upper mantle structure beneath the Arctic Ocean.

Cui, Congyue↗
DOE OSTI2024

Spherical time-encoded radiation imaging simulations

Radiation source localization is important for nuclear nonproliferation and can be obtained using time-encoded imaging systems with unsegmented detectors. A scintillation crystal can be used with a moving coded-aperture mask to vary the detected count rate produced from radiation sources in the far field. The modulation of observed counts over time can be used to reconstruct an image with the known coded-aperture mask pattern. Current time-encoded imaging systems incorporate cylindrical coded-aperture masks and have limits to their fully coded imaging field-of-view. This work focuses on expanding the field-of-view to 4π by using a novel spherical coded-aperture mask. A regular icosahedron is used to approximate a spherical mask. This icosahedron consists of 20 equilateral triangles; the faces of which are each subdivided into four equilateral triangle-shaped voxels which are then projected onto a spherical surface, creating an 80-voxel coded-aperture mask. Furthermore, these polygonal voxels can be made from high-Z materials for gamma-ray modulation and/or low-Z materials for neutron modulation. In this work, we present Monte Carlo N-Particle (MCNP) simulations and simple models programmed in Mathematica to explore image reconstruction capabilities of this 80-voxel coded-aperture mask.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides

Abstract Disulfide‐rich peptides represent an important protein family with broad pharmacological potential. Recent advances in computational methods have made it possible to design new peptides which adopt a stable conformation de novo. Here, we describe a system to produce disulfide‐rich de novo peptides using Escherichia coli as the expression host. The advantage of this system is that it enables production of uniformly 13 C‐ and 15 N‐labeled peptides for solution nuclear magnetic resonance (NMR) studies. This expression system was used to isotopically label two previously reported de novo designed peptides, and to determine their solution structures using NMR. The ensemble of NMR structures calculated for both peptides agreed well with the design models, further confirming the accuracy of the design protocol. Collection of NMR data on the peptides under reducing conditions revealed a dependency on disulfide bonds to maintain stability. Furthermore, we performed long‐time molecular dynamics (MD) simulations with tempering to assess the stability of two families of de novo designed peptides. Initial designs which exhibited a stable structure during simulations were more likely to adopt a stable structure in vitro , but attempts to utilize this method to redesign unstable peptides to fold into a stable state were unsuccessful. Further work is therefore needed to assess the utility of MD simulation techniques for de novo protein design.

Buchko, Garry W.↗
DOE OSTI2012

Phylogenomic analysis of polyketide synthase-encoding genes in Trichoderma

Members of the economically important ascomycete genus Trichoderma are ubiquitously distributed around the world. The mycoparasitic lifestyle and plant defense inducing interactions of Trichoderma spp. make them ideal biocontrol agents. Of the Trichoderma enzymes that produce secondary metabolites, some of which likely play important roles in biocontrol processes, polyketide synthases have garnered less attention that non-ribosomal peptide synthetases such as those that produce peptaibols. We have taken a phylogenomic approach to study the polyketide synthase repertoire encoded in the genomes of Trichoderma reesei, Trichoderma atroviride and Trichoderma virens. Our analysis lays a foundation for future research related to polyketide synthases within the Trichoderma genus and other filamentous fungi.

Trichoderma, polyketide, genomic, phylogenomic, fu↗
DOE OSTI2016

WE-DE-206-03: MRI Image Formation - Slice Selection, Phase Encoding, Frequency Encoding, K-Space, SNR

Magnetic resonance imaging (MRI) has become an essential part of clinical imaging due to its ability to render high soft tissue contrast. Instead of ionizing radiation, MRI use strong magnetic field, radio frequency waves and field gradients to create diagnostic useful images. It can be used to image the anatomy and also functional and physiological activities within the human body. Knowledge of the basic physical principles underlying MRI acquisition is vitally important to successful image production and proper image interpretation. This lecture will give an overview of the spin physics, imaging principle of MRI, the hardware of the MRI scanner, and various pulse sequences and their applications. It aims to provide a conceptual foundation to understand the image formation process of a clinical MRI scanner. Learning Objectives: Understand the origin of the MR signal and contrast from the spin physics level. Understand the main hardware components of a MRI scanner and their purposes Understand steps for MR image formation including spatial encoding and image reconstruction Understand the main kinds of MR pulse sequences and their characteristics.

60 APPLIED LIFE SCIENCES↗