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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

The Intracellular Scots Pine Shoot Symbiont Methylobacterium extorquens DSM13060 Aggregates around the Host Nucleus and Encodes Eukaryote-Like Proteins

Endophytes are microbes that inhabit plant tissues without any apparent signs of infection, often fundamentally altering plant phenotypes. While endophytes are typically studied in plant roots, where they colonize the apoplast or dead cells, Methylobacterium extorquens strain DSM13060 is a facultatively intracellular symbiont of the meristematic cells of Scots pine ( Pinus sylvestris L. ) shoot tips. The bacterium promotes host growth and development without the production of known plant growth-stimulating factors. Our objective was to examine intracellular colonization by M. extorquens DSM13060 of Scots pine and sequence its genome to identify novel molecular mechanisms potentially involved in intracellular colonization and plant growth promotion. Reporter construct analysis of known growth promotion genes demonstrated that these were only weakly active inside the plant or not expressed at all. We found that bacterial cells accumulate near the nucleus in intact, living pine cells, pointing to host nuclear processes as the target of the symbiont’s activity. Genome analysis identified a set of eukaryote-like functions that are common as effectors in intracellular bacterial pathogens, supporting the notion of intracellular bacterial activity. These include ankyrin repeats, transcription factors, and host-defense silencing functions and may be secreted by a recently imported type IV secretion system. Potential factors involved in host growth include three copies of phospholipase A2, an enzyme that is rare in bacteria but implicated in a range of plant cellular processes, and proteins putatively involved in gibberellin biosynthesis. Our results describe a novel endophytic niche and create a foundation for postgenomic studies of a symbiosis with potential applications in forestry and agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Plasmid-Encoded Traits Vary across Environments

Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities

Here, we investigated overlooked microbes in soil, candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

data-encoder-circuits v1.0

Lightweight python package built on top of Qiskit to generate quantum circuits that can be used to load classical data (sequence of numbers) on a quantum computer.

Camps, Daan↗
DOE OSTI2024

Data for the Expression of Genes Encoding Novel Sesame Oleosin Variants Facilitates Enhanced Triacylglycerol Accumulation in Arabidopsis Leaves and Seeds

Triacylglycerols (TAG), accumulate within lipid droplets (LD), predominantly surrounded by OLEOSINs (OLE), that protect TAG from hydrolysis. We tested the hypothesis that identifying and removing degradation signals from OLE would promote its abundance, preventing TAG degradation and enhancing TAG accumulation. We tested whether mutating potential ubiquitin-conjugation sites in a previously reported improved Sesamum indicum OLE ( SiO ) variant, o3-3 Cys-OLE ( SiCO herein), would stabilize it and increase its lipogenic potential. SiCOv1 was created by replacing all five lysines in SiCO with arginines. Separately, six cysteine residues within SiCO were deleted to create SiCOv2. SiCOv1 and SiCOv2 mutations were combined to create SiCOv3. Transient expression of SiCOv3 in Nicotiana benthamiana increased TAG by two-fold relative to SiCO. Constitutive expression of SiCOv3 or SiCOv5 , containing the five predominant TAG-increasing mutations from SiCOv3 , in Arabidopsis along with mouse DGAT2 ( mD ) increased TAG accumulation by 54% in leaves and 13% in seeds compared with control lines coexpressing SiCO and mD . Lipid synthesis rates increased, consistent with an increase in lipid sink strength that sequesters newly synthesized TAG, thereby relieving the constitutive BADC-dependent inhibition of ACCase reported for WT Arabidopsis. These OLE variants represent novel factors for potentially increasing TAG accumulation in a variety of oil crops.

Feedstock Production↗
DOE OSTI2016

Frequency-encoded photonic qubits for scalable quantum information processing

Among the objectives for large-scale quantum computation is the quantum interconnect: a device that uses photons to interface qubits that otherwise could not interact. However, the current approaches require photons indistinguishable in frequency—a major challenge for systems experiencing different local environments or of different physical compositions altogether. Here, we develop an entirely new platform that actually exploits such frequency mismatch for processing quantum information. Labeled “spectral linear optical quantum computation” (spectral LOQC), our protocol offers favorable linear scaling of optical resources and enjoys an unprecedented degree of parallelism, as an arbitrary Ν-qubit quantum gate may be performed in parallel on multiple Ν-qubit sets in the same linear optical device. Here, not only does spectral LOQC offer new potential for optical interconnects, but it also brings the ubiquitous technology of high-speed fiber optics to bear on photonic quantum information, making wavelength-configurable and robust optical quantum systems within reach.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Audio misinformation encoding via an on-phone sub-terahertz metasurface

We demonstrate a wireless security application to protect the weakest link in phone-to-phone communication, using a terahertz metasurface. To our knowledge, this is the first example of an eavesdropping countermeasure in which the attacker is actively misled.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2

In May of 2011, an enteroaggregative Escherichia coli O104:H4 strain that had acquired a Shiga toxin 2-converting phage caused a large outbreak of bloody diarrhea in Europe which was notable for its high prevalence of hemolytic uremic syndrome cases. Several studies have described the genomic inventory and phylogenies of strains associated with the outbreak and a collection of historical E. coli O104:H4 isolates using draft genome assemblies. We present the complete, closed genome sequences of an isolate from the 2011 outbreak (2011C–3493) and two isolates from cases of bloody diarrhea that occurred in the Republic of Georgia in 2009 (2009EL–2050 and 2009EL–2071). Comparative genome analysis indicates that, while the Georgian strains are the nearest neighbors to the 2011 outbreak isolates sequenced to date, structural and nucleotide-level differences are evident in the Stx2 phage genomes, the mer/tet antibiotic resistance island, and in the prophage and plasmid profiles of the strains, including a previously undescribed plasmid with homology to the pMT virulence plasmid of Yersinia pestis. In addition, multiphenotype analysis showed that 2009EL–2071 possessed higher resistance to polymyxin and membrane-disrupting agents. Finally, we show evidence by electron microscopy of the presence of a common phage morphotype among the European and Georgian strains and a second phage morphotype among the Georgian strains. The presence of at least two stx2 phage genotypes in host genetic backgrounds that may derive from a recent common ancestor of the 2011 outbreak isolates indicates that the emergence of stx2 phage-containing E. coli O104:H4 strains probably occurred more than once, or that the current outbreak isolates may be the result of a recent transfer of a new stx2 phage element into a pre-existing stx2-positive genetic background.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Transfer Learning using Denoising Auto-Encoders for Cellular-Level Annotation of Tumor in Pathology Slides

Adversarial examples can produce altered classifications using only seemingly innocuous, imperceptible perturbations to the original image. The imperceptibility of adversarial perturbations suggests that the corresponding classifiers use decision criteria different than those of a human. In a medical setting, inexplicable decision criteria confound a pathologist’s willingness to trust machine-generated annotations. Here, we analyze denoising tumor detection models to see if they are robust to imperceptible adversarial perturbations. Moreover, to be more fully trusted by pathologists, we require tumor detectors that generate interpretable annotations which segment pathology slides into tumorous and normal regions at the cellular level. We therefore compare transfer learning based on two different autoencoder architectures, one derived from a deep denoising bottleneck autoencoder and one from an over-complete sparse autoencoder. Both autoencoders were first trained in an unsupervised manner on a set of pathology slides drawn from the Camelyon16 dataset. The latent representations produced by each autoencoder were then passed to separate neural networks that were trained in a supervised manner on binary tumor-normal masks generated by pathologists at cellular resolution. Both tumor detectors supported better than 90% AUC PR as measured by the area under the precision/recall curve on a held-out pathology slide. To assess the underlying decision criteria used by both tumor detectors, we constructed imperceptible adversarial examples which reduced the AUC PR of both models to less than 70%. Random noise of the same amplitude had almost no effect on the AUC PR of either model. Additionally, each tumor detector was resistant to adversarial “transfer” attacks targeting the other. The adversarial perturbations showed strong characteristic differences: the deep denoising models perturbations were a very diffuse, seemingly unrecognizable pattern while the sparse coding models perturbations showed traces of tissue cells.

47 OTHER INSTRUMENTATION↗