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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 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Evaluation of new approaches to the access of official monitoring results for live bivalves molluscs

Abstract Background Live bivalve molluscs, echinoderms, tunicates and marine gastropod are referred in EU food laws, and require member states to implement official controls in classified production areas, with the monitoring and classification of those areas. If, due to contaminant tests results, a production area is closed, any product from there is prohibited to be commercialized. Mobile applications optical character recognition (OCR) functionalities could ease the access to contaminant levels and production area classifications. This study verifies what information is available in live bivalves’ labels, describes an OCR algorithm for those labels and evaluates it. Methods 86 labels were selected from four sale points in Lisbon, and photographed using smartphones. Each label was evaluated by a human to determine what data was available (either required or not). An OCR algorithm was developed and applied on the collected labels and validated against the data extracted by the human analysis. Results The analysis shows that all the labels included the required information, and 63% of the labels included the identifier for the production zone. The label-reading algorithm performs with an accuracy of 79.85% for the individual values. Conclusion High accuracy of the developed label-reading algorithm shows potential for providing instant automatic access to the date and production area, but is affected by the variability on the label structure. Although not required by food laws, the majority of the sampled labels included complementary information (classified production area) that will allow access to more precise information about the existing biotoxin tests and analysis results.

da Costa, Manuel Beja↗
DOE OSTI2021

Chromosome assembled and annotated genome sequence of Aspergillus flavus NRRL 3357

Abstract Aspergillus flavus is an opportunistic pathogen of crops, including peanuts and maize, and is the second leading cause of aspergillosis in immunocompromised patients. A. flavus is also a major producer of the mycotoxin, aflatoxin, a potent carcinogen, which results in significant crop losses annually. The A. flavus isolate NRRL 3357 was originally isolated from peanut and has been used as a model organism for understanding the regulation and production of secondary metabolites, such as aflatoxin. A draft genome of NRRL 3357 was previously constructed, enabling the development of molecular tools and for understanding population biology of this particular species. Here, we describe an updated, near complete, telomere-to-telomere assembly and re-annotation of the eight chromosomes of A. flavus NRRL 3357 genome, accomplished via long-read PacBio and Oxford Nanopore technologies combined with Illumina short-read sequencing. A total of 13,715 protein-coding genes were predicted. Using RNA-seq data, a significant improvement was achieved in predicted 5’ and 3’ untranslated regions, which were incorporated into the new gene models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Novel Toxin Biosynthetic Gene Cluster in Harmful Algal Bloom-Causing Heteroscytonema crispum : Insights into the Origins of Paralytic Shellfish Toxins

Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms are events of severe ecological, economic, and public health consequence, and their incidence has become more common of late. Despite coordinated research efforts to identify and characterize the genomes of harmful algal bloom-causing organisms, the genomic basis and evolutionary origins of paralytic shellfish toxins produced by harmful algal blooms remain at best incomplete. The paralytic shellfish toxin saxitoxin has an especially complex genomic architecture and enigmatic phylogenetic distribution, spanning dinoflagellates and multiple cyanobacterial genera. Using filtration and extraction techniques to target the desired cyanobacteria from nonaxenic culture, coupled with a combination of short- and long-read sequencing, we generated a reference-quality hybrid genome assembly for Heteroscytonema crispum UTEX LB 1556, a freshwater, paralytic shellfish toxin-producing cyanobacterium thought to have the largest known genome in its phylum. We report a complete, novel biosynthetic gene cluster for the paralytic shellfish toxin saxitoxin. Leveraging this biosynthetic gene cluster, we find support for the hypothesis that paralytic shellfish toxin production has appeared in divergent Cyanobacteria lineages through widespread and repeated horizontal gene transfer. This work demonstrates the utility of long-read sequencing and metagenomic assembly toward advancing our understanding of paralytic shellfish toxin biosynthetic gene cluster diversity and suggests a mechanism for the origin of paralytic shellfish toxin biosynthetic genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes

Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC–ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Base-resolution detection of N 4 -methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite-sequencing

Restriction-modification (R-M) systems pose a major barrier to DNA transformation and genetic engineering of bacterial species. Systematic identification of DNA methylation in R-M systems, including N 6 -methyladenine (6mA), 5-methylcytosine (5mC) and N 4 -methylcytosine (4mC), will enable strategies to make these species genetically tractable. Although single-molecule, real time (SMRT) sequencing technology is capable of detecting 4mC directly for any bacterial species regardless of whether an assembled genome exists or not, it is not as scalable to profiling hundreds to thousands of samples compared with the commonly used next-generation sequencing technologies. Here, we present 4mC-Tet-assisted bisulfite-sequencing (4mC-TAB-seq), a next-generation sequencing method that rapidly and cost efficiently reveals the genome-wide locations of 4mC for bacterial species with an available assembled reference genome. In 4mC-TAB-seq, both cytosines and 5mCs are read out as thymines, whereas only 4mCs are read out as cytosines, revealing their specific positions throughout the genome. We applied 4mC-TAB-seq to study the methylation of a member of the hyperthermophilc genus, Caldicellulosiruptor , in which 4mC-related restriction is a major barrier to DNA transformation from other species. Lastly, in combination with MethylC-seq, both 4mC- and 5mC-containing motifs are identified which can assist in rapid and efficient genetic engineering of these bacteria in the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

Here, the Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center. Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by `virtual integration' to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data

Abstract CRISPR arrays and CRISPR-associated (Cas) proteins comprise a widespread adaptive immune system in bacteria and archaea. These systems function as a defense against exogenous parasitic mobile genetic elements that include bacteriophages, plasmids and foreign nucleic acids. With the continuous spread of antibiotic resistance, knowledge of pathogen susceptibility to bacteriophage therapy is becoming more critical. Additionally, gene-editing applications would benefit from the discovery of new cas genes with favorable properties. While next-generation sequencing has produced staggering quantities of data, transitioning from raw sequencing reads to the identification of CRISPR/Cas systems has remained challenging. This is especially true for metagenomic data, which has the highest potential for identifying novel cas genes. We report a comprehensive computational pipeline, CasCollect, for the targeted assembly and annotation of cas genes and CRISPR arrays—even isolated arrays—from raw sequencing reads. Benchmarking our targeted assembly pipeline demonstrates significantly improved timing by almost two orders of magnitude compared with conventional assembly and annotation, while retaining the ability to detect CRISPR arrays and cas genes. CasCollect is a highly versatile pipeline and can be used for targeted assembly of any specialty gene set, reconfigurable for user provided Hidden Markov Models and/or reference nucleotide sequences.

Podlevsky, Joshua D.↗
DOE OSTI2025

Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass

Genomic prediction has accelerated breeding processes and provided mechanistic insights into the genetic bases of complex traits. To further optimize genomic prediction, we assess the impact of genome assemblies, genotyping approaches, variant types, allelic complexities, polyploidy levels, and population structures on the prediction of 20 complex traits in switchgrass (Panicum virgatum L.), a perennial biofuel feedstock. Surprisingly, short read-based genome assembly performs comparably to or even better than long read-based assembly. Due to higher gene coverage, exome capture and multi-allelic variants outperform genotyping-by-sequencing and bi-allelic variants, respectively. Tetraploid models show higher prediction accuracy than octoploid models for most traits, likely due to the greater genetic distances among tetraploids. Depending on the trait in question, different types of variants need to be integrated for optimal predictions. Furthermore, our study provides insights into the factors influencing genomic prediction outcomes, guiding best practices for future studies and for improving agronomic traits in switchgrass and other species through selective breeding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.

EndofungalMycetohabitans(formerlyBurkholderia) spp. rely on a type III secretion system to deliver mostly unidentified effector proteins when colonizing their host fungus,Rhizopus microsporus. The one known secreted effector family fromMycetohabitansconsists of homologues of transcription activator-like (TAL) effectors, which are used by plant pathogenicXanthomonasandRalstoniaspp. to activate host genes that promote disease. These ‘BurkholderiaTAL-like (Btl)’ proteins bind corresponding specific DNA sequences in a predictable manner, but their genomic target(s) and impact on transcription in the fungus are unknown. Recent phenotyping of Btl mutants of twoMycetohabitansstrains revealed that the single Btl in oneMycetohabitans endofungorumstrain enhances fungal membrane stress tolerance, while others in aMycetohabitans rhizoxinicastrain promote bacterial colonization of the fungus. The phenotypic diversity underscores the need to assess the sequence diversity and, given that sequence diversity translates to DNA targeting specificity, the functional diversity of Btl proteins. Using a dual approach to maximize capture of Btl protein sequences for our analysis, we sequenced and assembled nineMycetohabitansspp. genomes using long-read PacBio technology and also mined available short-read Illumina fungal–bacterial metagenomes. We show thatbtlgenes are present across diverseMycetohabitansstrains from Mucoromycota fungal hosts yet vary in sequences and predicted DNA binding specificity. Phylogenetic analysis revealed distinct clades of Btl proteins and suggested thatMycetohabitansmight contain more species than previously recognized. Within our data set, Btl proteins were more conserved acrossM. rhizoxinicastrains than acrossM. endofungorum, but there was also evidence of greater overall strain diversity within the latter clade. Overall, the results suggest that Btl proteins contribute to bacterial–fungal symbioses in myriad ways.

Genetics & Heredity↗
DOE OSTI2015

Using populations of human and microbial genomes for organism detection in metagenomes

Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can address this problem, dramatically increasing the scaffold contiguity of assemblies. Here, we describe a simpler approach (“Chicago”) based on in vitro reconstituted chromatin. We generated two Chicago data sets with human DNA and developed a statistical model and a new software pipeline (“HiRise”) that can identify poor quality joins and produce accurate, long-range sequence scaffolds. We used these to construct a highly accurate de novo assembly and scaffolding of a human genome with scaffold N50 of 20 Mbp. We also demonstrated the utility of Chicago for improving existing assemblies by reassembling and scaffolding the genome of the American alligator. With a single library and one lane of Illumina HiSeq sequencing, we increased the scaffold N50 of the American alligator from 508 kbp to 10 Mbp.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Chiral superconductivity from a parent Chern band and its non-Abelian generalization

Here, we propose a minimal model starting from a parent Chern band with quartic dispersion that can describe the spin-valley polarized electrons in rhombohedral tetralayer graphene. The interplay between repulsive and attractive interactions on top of that parent Chern band is studied. We conduct standard self-consistent mean-field calculations, and find a rich phase diagram that consists of metal, quantum anomalous Hall crystal, chiral topological superconductor, as well as trivial gapped Bose-Einstein condensate. In particular, there exists a topological phase transition from the chiral superconductor to the Bose-Einstein condensate at zero temperature. Motivated by the recent experimental and theoretical studies of composite Fermi liquid in rhombohedral stacked multilayer graphene, we further generalize the physical electron model to its composite fermion counterpart based on a field theory analysis. The chiral superconductor phase of the composite fermion becomes the non-abelian Moore-Read quantum Hall phase. We argue that a chiral (pseudo-)spin liquid phase can emerge in the vicinity of this Moore-Read quantum Hall phase. Our work suggests rhombohedral multilayer graphene as a potential platform for rich correlated topological phases.

Wang, Yan-Qi [University of Maryland, College Park↗
DOE OSTI2020

Robust Skyrmion Shift Device Through Engineering the Local Exchange-Bias Field

Magnetic skyrmions are topologically protected spin structures, offering great promise as information carriers for future spintronic devices. However, a series of challenges, such as unreliable skyrmion motion, pinning effects, and a weak read-out signal, prevent the development of skyrmionic applications. The recently demonstrated capability to engineer the local exchange-bias field (LEBF) in an exchange biased composite, provides solutions to these challenges. By exploiting LEBF, we design and analyze a robust skyrmion shift device. LEBF-induced magnetic domain walls form the boundary of the device channel, and LEBF potential wells are implemented in the channel for positioning skyrmions. Based on simulations with comprehensive models, we demonstrate the proposed device has the advantages of (i) localizing the skyrmions in the absence of current, (ii) suppressing skyrmion annihilation during transport, (iii) promoting steady skyrmion motion, (iv) enhancing the skyrmion velocity, and (v) magnifying the read-out signal. Our results form the basis for the design of robust skyrmion devices through LEBF engineering.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Tunable Noncollinear Antiferromagnetic Resistive Memory through Oxide Superlattice Design

Antiferromagnets (AFMs) have recently gathered a large amount of attention as a potential replacement for ferromagnets (FMs) in spintronic devices due to their lack of stray magnetic fields, invisibility to external magnetic probes, and faster magneti- zation dynamics. Their development into a practical technology, however, has been hampered by the small number of materials where the antiferromagnetic state can be both controlled and read out. We show here, that by relaxing the strict criterion on pure antiferromagnetism, we can engineer a new class of magnetic materials that 1 overcome these limitations. This is accomplished by stabilizing a non-collinear mag- netic phase in LaNiO 3 /La 2/3 Sr 1/3 MnO 3 superlattices. This state can be continuously tuned between AFM and FM coupling through varying either superlattice spacing, strain, applied magnetic field, or temperature. By using this new “knob” to tune magnetic ordering, we take a nanoscale materials-by-design approach to engineering ferromagnetic-like controllability into antiferromagnetic synthetic magnetic structures. This approach can be used to trade-off between the favorable and unfavorable proper- ties of FMs and AFMs when designing realistic resistive antiferromagnetic memories. We demonstrate a memory device in one such superlattice, where the magnetic state of the non-collinear antiferromagnet is reversibly switched between different orientations using a small magnetic field and read out in real time with anisotropic magnetoresistance measurements.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Composite fermions in Fock space: Operator algebra, recursion relations, and order parameters

We develop recursion relations, in particle number, for all (unprojected) Jain composite fermion (CF) wave functions. These recursions generalize a similar recursion originally written down by Read for Laughlin states, in mixed first-second quantized notation. In contrast, our approach is purely second-quantized, giving rise to an algebraic, “pure guiding center” definition of CF states that de-emphasizes first quantized many-body wave functions. Key to the construction is a second-quantized representation of the flux attachment operator that maps any given fermion state to its CF counterpart. An algebra of generators of edge excitations is identified. In particular, in those cases where a well-studied parent Hamiltonian exists, its properties can be entirely understood in the present framework, and the identification of edge state generators can be understood as an instance of “microscopic bosonization.” Here, the intimate connection of Read's original recursion with “nonlocal order parameters” generalizes to the present situation, and we are able to give explicit second-quantized formulas for nonlocal order parameters associated with CF states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Disentangling ( 2 + 1 ) D topological states of matter with entanglement negativity

We use the entanglement negativity, a bipartite measure of entanglement in mixed quantum states, to study how multipartite entanglement constrains the real-space structure of the ground state wavefunctions of (2 + 1)-dimensional topological phases. We focus on the (Abelian) Laughlin and (non-Abelian) Moore-Read states at filling fraction ν = 1/m. We show that a combination of entanglement negativities, calculated with respect to specific cylinder and torus geometries, determines a necessary condition for when a topological state can be disentangled, i.e., factorized into a tensor product of states defined on cylinder subregions. This condition, which requires the ground state to lie in a definite topological sector, is sufficient for the Laughlin state. On the other hand, we find that a general Moore-Read ground state cannot be disentangled even when the disentangling condition holds.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Stability of the particle-hole Pfaffian state and the 5 2 -fractional quantum Hall effect

Here we present a method for the exact construction of the fully particle-hole symmetric Pfaffian (PH-Pfaffian) ground state and its charged excitations on a sphere. We adopt the Moore-Read state, but with a nonholomorphic pairing component as in previous studies, and project it to the lowest Landau level. We study the energetics as well as other properties of these states and find that in a pure system interacting with the Coulomb forces the PH-Pfaffian cannot compete with either the Moore-Read state or its particle-hole conjugate, the anti-Pfaffian state, as an explanation for the 5/2 effect.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Fractional quantum Hall bilayers at half filling: Tunneling-driven non-Abelian phase

Multicomponent quantum Hall systems with internal degrees of freedom provide a fertile ground for the emergence of exotic quantum liquids. Here, we investigate the possibility of non-Abelian topological order in the half-filled fractional quantum Hall (FQH) bilayer system driven by the tunneling effect between two layers. By means of the state-of-the-art density-matrix renormalization group, we unveil “fingerprint” evidence of the non-Abelian Moore-Read Pfaffian state emerging in the intermediate-tunneling regime, including the ground-state degeneracy on the torus geometry and the topological entanglement spectroscopy (entanglement spectrum and topological entanglement entropy) on the spherical geometry, respectively. Remarkably, the phase transition from the previously identified Abelian (331) Halperin state to the non-Abelian Moore-Read Pfaffian state is determined to be continuous, which is signaled by the continuous evolution of the universal part of the entanglement spectrum, and discontinuities in the excitation gap and the derivative of the ground-state energy. Our results not only provide a “proof-of-principle” demonstration of realizing a non-Abelian state through coupling different degrees of freedom, but also open up a possibility in FQH bilayer systems for detecting different chiral p-wave pairing states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗