Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “isolation”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,243 records · Page 69

Layer-dependent topological phase in a two-dimensional quasicrystal and approximant

The electronic and topological properties of materials are derived from the interplay between crystalline symmetry and dimensionality. Simultaneously introducing “forbidden” symmetries via quasiperiodic ordering with low dimensionality into a material system promises the emergence of new physical phenomena. Here, we isolate a two-dimensional (2D) chalcogenide quasicrystal and approximant, and investigate their electronic and topological properties. The 2D layers of the materials with a composition close to Ta 1.6 Te, derived from a layered transition metal dichalcogenide, are isolated with standard exfoliation techniques, and investigated with electron diffraction and atomic resolution scanning transmission electron microscopy. Density functional theory calculations and symmetry analysis of the large unit cell crystalline approximant of the quasicrystal, Ta 21 Te 13 , reveal the presence of symmetry-protected nodal crossings in the quasicrystalline and approximant phases, whose presence is tunable by layer number. Our study provides a platform for the exploration of physics in quasicrystalline, low-dimensional materials and the interconnected nature of topology, dimensionality, and symmetry in electronic systems.

36 MATERIALS SCIENCE↗

Machine learning enables identification of an alternative yeast galactose utilization pathway

How genomic differences contribute to phenotypic differences is a major question in biology. The recently characterized genomes, isolation environments, and qualitative patterns of growth on 122 sources and conditions of 1,154 strains from 1,049 fungal species (nearly all known) in the yeast subphylum Saccharomycotina provide a powerful, yet complex, dataset for addressing this question. We used a random forest algorithm trained on these genomic, metabolic, and environmental data to predict growth on several carbon sources with high accuracy. Known structural genes involved in assimilation of these sources and presence/absence patterns of growth in other sources were important features contributing to prediction accuracy. By further examining growth on galactose, we found that it can be predicted with high accuracy from either genomic (92.2%) or growth data (82.6%) but not from isolation environment data (65.6%). Prediction accuracy was even higher (93.3%) when we combined genomic and growth data. After the GALactose utilization genes, the most important feature for predicting growth on galactose was growth on galactitol, raising the hypothesis that several species in two orders, Serinales and Pichiales (containing the emerging pathogen Candida auris and the genus Ogataea, respectively), have an alternative galactose utilization pathway because they lack the GAL genes. Growth and biochemical assays confirmed that several of these species utilize galactose through an alternative oxidoreductive D-galactose pathway, rather than the canonical GAL pathway. Machine learning approaches are powerful for investigating the evolution of the yeast genotype–phenotype map, and their application will uncover novel biology, even in well-studied traits.

59 BASIC BIOLOGICAL SCIENCES↗

Single-molecule tracking reveals dual front door/back door inhibition of Cel7A cellulase by its product cellobiose

Degrading cellulose is a key step in the processing of lignocellulosic biomass into bioethanol. Cellobiose, the disaccharide product of cellulose degradation, has been shown to inhibit cellulase activity, but the mechanisms underlying product inhibition are not clear. We combined single-molecule imaging and biochemical investigations with the goal of revealing the mechanism by which cellobiose inhibits the activity of Trichoderma reesei Cel7A, a well-characterized exo-cellulase. We find that cellobiose slows the processive velocity of Cel7A and shortens the distance moved per encounter; effects that can be explained by cellobiose binding to the product release site of the enzyme. Cellobiose also strongly inhibits the binding of Cel7A to immobilized cellulose, with a K i of 2.1 mM. The isolated catalytic domain (CD) of Cel7A was also inhibited to a similar degree by cellobiose, and binding of an isolated carbohydrate-binding module to cellulose was not inhibited by cellobiose, suggesting that cellobiose acts on the CD alone. Finally, cellopentaose inhibited Cel7A binding at micromolar concentrations without affecting the enzyme’s velocity of movement along cellulose. Together, these results suggest that cellobiose inhibits Cel7A activity both by binding to the “back door” product release site to slow activity and to the “front door” substrate-binding tunnel to inhibit interaction with cellulose. These findings point to strategies for engineering cellulases to reduce product inhibition and enhance cellulose degradation, supporting the growth of a sustainable bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗

Mechanisms of a novel regulatory light chain–dependent cardiac myosin inhibitor

Hypertrophic cardiomyopathy (HCM) is a genetic disease of the heart characterized by thickening of the left ventricle (LV), hypercontractility, and impaired relaxation. HCM is caused primarily by heritable mutations in sarcomeric proteins, such as β myosin heavy chain. Until recently, medications in clinical use for HCM did not directly target the underlying contractile changes in the sarcomere. Here, we investigate a novel small molecule, RLC-1, identified in a bovine cardiac myofibril high-throughput screen. RLC-1 is highly dependent on the presence of a regulatory light chain to bind to cardiac myosin and modulate its ATPase activity. In demembranated rat LV trabeculae, RLC-1 decreased maximal Ca2+-activated force and Ca2+ sensitivity of force, while it increased the submaximal rate constant for tension redevelopment. In myofibrils isolated from rat LV, both maximal and submaximal Ca2+-activated force are reduced by nearly 50%. Additionally, the fast and slow phases of relaxation were approximately twice as fast as DMSO controls, and the duration of the slow phase was shorter. Structurally, x-ray diffraction studies showed that RLC-1 moved myosin heads away from the thick filament backbone and decreased the order of myosin heads, which is different from other myosin inhibitors. In intact trabeculae and isolated cardiomyocytes, RLC-1 treatment resulted in decreased peak twitch magnitude and faster activation and relaxation kinetics. In conclusion, RLC-1 accelerated kinetics and decreased force production in the demembranated tissue, intact tissue, and intact whole cells, resulting in a smaller cardiac twitch, which could improve the underlying contractile changes associated with HCM.

Physiology↗

Ultrafast molecular frame electronic coherences from lab frame scattering anisotropies

Electronic coherences in molecules are ultrafast charge oscillations on the molecular frame (MF) and their direct observation and separation from electronic population dynamics is challenging. Here we present a valence shell lab frame (LF) scattering method suited to probing electronic coherences in isolated systems. MF electronic coherences lead to LF electronic anisotropies observable by ultrafast angle-resolved scattering. Moment analysis of the LF anisotropy completely separates electronic coherences from population dynamics, demonstrated in excited state NH 3 using ultrafast time-energy-angle-resolved photoelectron spectroscopy. Overall, this general approach applies equally to attosecond/femtosecond electronic coherences in isolated systems.

74 ATOMIC AND MOLECULAR PHYSICS↗

A parametric model for self-interacting dark matter halos

Abstract We propose a parametric model for studying self-interacting dark matter (SIDM) halos. The model uses an analytical density profile, calibrated using a controlled N-body SIDM simulation that covers the entire gravothermal evolution, including core-forming and -collapsing phases. By normalizing the calibrated density profile, we obtain a universal description for SIDM halos at any evolution phase. The model allows us to infer properties of SIDM halos based on their cold dark matter (CDM) counterparts. As a basic application, we only require two characteristic parameters of an isolated CDM halo atz = 0. We then extend the model to incorporate effects induced by halo mass changes, such as major mergers or tidal stripping, making it applicable to both isolated halos and subhalos. The parametric model is tested and validated using cosmological zoom-in SIDM simulations available in the literature.

Astronomy & Astrophysics↗

Neutrino identification with scintillation light in MicroBooNE

MicroBooNE is a neutrino experiment which employs a liquid argon (LAr) time projection chamber (TPC) to record neutrino interactions from Fermilab's neutrino beamlines. The experiment's primary objective is to study low-energy νe interactions from the Booster Neutrino Beamline (BNB). Located on the surface, the detector is affected by a continuous rate of cosmic-rays. This leads to one neutrino interaction for every 104 cosmic rays observed in the TPC, making it difficult to isolate neutrino interactions in the detector using charge alone. MicroBooNE's trigger makes use of prompt scintillation light and plays an essential role in both performing strong background rejection and significantly reducing data-rates. Furthermore, a series of novel techniques relying on scintillation light are used to isolate beam-induced activity. This document briefly presents MicroBooNE's scintillation-light based trigger and novel Flash-Matching pattern recognition techniques for cosmic-rejection. This work serves as the foundation of neutrino analyses in LArTPC detectors and is therefore of interest to the broader short- and long-baseline neutrino programs being launched at Fermilab.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Characterization and novel application of power over fiber for electronics in a harsh environment

Power-over-Fiber (PoF) technology has been used extensively in settings where high voltages require isolation from ground. In a novel application of PoF, power is provided to photon detector modules located on a surface at ∼ 300 kV with respect to ground in the planned DUNE experiment. In cryogenic environments, PoF offers a reliable means of power transmission, leveraging optical fibers to transfer optical power. PoF technology excels in maintaining low noise levels when delivering power to sensitive electronic systems operating in extreme temperatures and high voltage environments. This paper presents the R&D effort of PoF in extreme conditions and underscores its capacity to revolutionize power delivery and management in critical applications, offering a dependable solution with low noise, optimal efficiency (∼ 51%), and superior isolation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Spin pumping from antiferromagnetic insulator spin-orbit-proximitized by adjacent heavy metal: a first-principles Floquet-nonequilibrium Green function study

Motivated by the recent experiment on spin pumping from sub-THz radiation-driven uniaxial antiferromagnetic insulator (AFI) MnF 2 into heavy metal (HM) Pt hosting strong spin-orbit (SO) coupling, we compute and compare pumped spin currents in Cu/MnF 2 /Cu and Pt/MnF 2 /Cu heterostructures. Recent theories of spin pumping by AFI have relied on simplistic Hamiltonians (such as tight-binding) and the scattering approach to quantum transport yielding the so-called interfacial spin mixing conductance (SMC), but the concept of SMC ceases to be applicable when SO coupling is present directly at the interface. In contrast, we use a more general first-principles quantum transport approach which combines noncollinear density functional theory with Floquet-nonequilibrium Green's functions in order to take into account: SO-proximitized AFI as a new type of quantum material, different from isolated AFI and brought about by AFI hybridization with adjacent HM layer; strong SO coupling at the interface; and evanescent wavefunctions penetrating from Pt or Cu into AFI layer to make its interfacial region conducting rather than insulating as in the isolated AFI. The DC component of pumped spin current $I_\mathrm{DC}^{S_z}$ vs. precession cone angle $\theta_{\boldsymbol{l}}$ of the Néel vector l of AFI does not follow putative $I^{S_z}_\mathrm{DC} \propto \sin^2 \theta_{\boldsymbol{l}}$, except for very small angles $\theta_{\boldsymbol{l}} \lesssim 10^\circ$ for which we define an effective SMC from the prefactor and find that it doubles from MnF2/Cu to MnF2/Pt interface. In addition, the angular dependence $I^{S_z}_\mathrm{DC}(\theta_{\boldsymbol{l}})$ differs for opposite directions of precession of the Néel vector, leading to twice as large SMC for the right-handed than for the left-handed chirality of the precession mode.

36 MATERIALS SCIENCE↗

ExoMars Mars Organic Molecule Analyzer (MOMA) Laser Desorption/Ionization Mass Spectrometry (LDI-MS) Analysis of Phototrophic Communities from a Silica-Depositing Hot Spring in Yellowstone National Park, USA

The Mars Organic Molecule Analyzer (MOMA) is a key scientific instrument on the ExoMars Rover mission. MOMA is designed to detect and characterize organic compounds, over a wide range of volatility and molecular weight, in samples obtained from up to two meters below the martian surface. Thorough analog sample studies are required to best prepare to interpret MOMA data collected on Mars. We present here the MOMA characterization of Mars analog samples collected from an alkaline silica depositing hot spring in Yellowstone National Park, WY, USA. These samples contain microbial streamer communities composed primarily of oxygenic and anoxygenic phototrophs. Additionally, in a study focused on detection of key classes of nonvolatile organics, samples of microbial streamers and their total lipid extract (TLE) have been measured on a MOMA Engineering Test Unit (ETU) instrument using its laser desorption/ionization mass spectrometry (LDI-MS) mode. MOMA LDI-MS detected a variety of lipids and pigments in the TLE sample. Species such as chlorophyll a were also detected from the streamer sample with the help of mass isolation. The results add to the LDI-MS sample characterization database, as well as demonstrate the benefit of using mass isolation on the MOMA instrument to reveal the presence of complex organics, and potential biomarkers, preserved in a natural sample, providing guidance to the in situ analysis of surface samples during Mars operations.

59 BASIC BIOLOGICAL SCIENCES↗

Island of misfit tortoises: waif gopher tortoise health assessment following translocation

Translocation, the intentional movement of animals from one location to another, is a common management practice for the gopher tortoise (Gopherus polyphemus). Although the inadvertent spread of pathogens is a concern with any translocation effort, waif tortoises—individuals that have been collected illegally, injured and rehabilitated or have unknown origins—are generally excluded from translocation efforts due to heightened concerns of introducing pathogens and subsequent disease to naïve populations. However, repurposing these long-lived animals for species recovery is desirable when feasible, and introducing waif tortoises may bolster small populations facing extirpation. The objective of this study was to assess the health of waif tortoises experimentally released at an isolated preserve in Aiken County, SC, USA. Our assessments included visual examination, screening for 14 pathogens using conventional or quantitative polymerase chain reaction (qPCR) and haematological evaluation. Of the 143 individuals assessed in 2017 and 2018, most individuals (76%; n = 109 of 143) had no overt clinical evidence of disease and, when observed, clinical findings were mild. In both years, we detected two known tortoise pathogens, Mycoplasma agassizii and Mycoplasma testudineum, at a prevalence of 10.2–13.9% and 0.0–0.8%, respectively. Additionally, we found emydid Mycoplasma, a bacterium commonly found in box turtles (Terrapene spp.), in a single tortoise that showed no clinical evidence of infection. The presence of nasal discharge was an important, but imperfect, predictor of Mycoplasma spp. infection in translocated tortoises. Hemogram data were comparable with wild populations. Our study is the first comprehensive effort to assess pathogen prevalence and hemogram data of waif gopher tortoises following translocation. Although caution is warranted and pathogen screening necessary, waif tortoises may be an important resource for establishing or augmenting isolated populations when potential health risks can be managed.

60 APPLIED LIFE SCIENCES↗

Insights into community of photosynthetic microorganisms from permafrost

ABSTRACT This work integrates cultivation studies of Siberian permafrost and analyses of metagenomes from different locations in the Arctic with the aim of obtaining insights into the community of photosynthetic microorganisms in perennially frozen deposits. Cyanobacteria and microalgae have been described in Arctic aquatic and surface soil environments, but their diversity and ability to withstand harsh conditions within the permafrost are still largely unknown. Community structure of photosynthetic organisms in permafrost sediments was explored using Arctic metagenomes available through the MG-RAST. Sequences affiliated with cyanobacteria represented from 0.25 to 3.03% of total sequences, followed by sequences affiliated with Streptophyta (algae and vascular plants) 0.01–0.45% and Chlorophyta (green algae) 0.01–0.1%. Enrichment and cultivation approaches revealed that cyanobacteria and green algae survive in permafrost and they could be revived during prolonged incubation at low light intensity. Among photosynthetic microorganisms isolated from permafrost, the filamentous Oscillatoria-like cyanobacteria and unicellular green algae of the genus Chlorella were dominant. Our findings suggest that permafrost cyanobacteria and green algae are expected to be effective members of the re-assembled community after permafrost thawing and soil collapse.

Vishnivetskaya, Tatiana A.↗

Tracking fungal species-level responses in soil environments exposed to long-term warming and associated drying

Climate change is affecting fungal communities and their function in terrestrial ecosystems. Despite making progress in the understanding of how the fungal community responds to global change drivers in natural ecosystems, little is known on how fungi respond at the species level. Understanding how fungal species respond to global change drivers, such as warming, is critical, as it could reveal adaptation pathways to help us to better understand ecosystem functioning in response to global change. Here, we present a model study to track species-level responses of fungi to warming—and associated drying—in a decade-long global change field experiment; we focused on two free-living saprotrophic fungi which were found in high abundance in our site, Mortierella and Penicillium. Using microbiological isolation techniques, combined with whole genome sequencing of fungal isolates, and community level metatranscriptomics, we investigated transcription-level differences of functional categories and specific genes involved in catabolic processes, cell homeostasis, cell morphogenesis, DNA regulation and organization, and protein biosynthesis. We found that transcription-level responses were mostly species-specific but that under warming, both fungi consistently invested in the transcription of critical genes involved in catabolic processes, cell morphogenesis, and protein biosynthesis, likely allowing them to withstand a decade of chronic stress. Overall, our work supports the idea that fungi that invest in maintaining their catabolic rates and processes while growing and protecting their cells may survive under global climate change.

59 BASIC BIOLOGICAL SCIENCES↗

The genome of the polyextremophilic yeast, Naganishia friedmannii, reveals adaptations involved in stress response pathways, carbohydrate metabolism expansion, and a limited DNA repair repertoire

Here we report the draft genome sequence of Naganishia friedmannii (formerly Cryptococcus friedmannii) isolate, a Basidiomycota yeast commonly found in some of the most extreme environments of the Earth's cryosphere. We isolated N. friedmannii strain Llullensis from soils at 6000 m above sea level on Volcán Llullaillaco, Argentina. The genome was 22.2 Mb with 6251 identified protein coding genes. Proteins known to be associated with thermal, osmotic, and radiation stress were identified in the genome. Comparative analysis with seven other Naganishia genomes revealed unique features underlying its polyextremophilic lifestyle. Naganishia friedmannii showed an expansion of genes involved in breaking down plant-derived carbohydrates, supporting the hypothesis that it survives at high elevations by metabolizing wind-deposited organic matter. Surprisingly, many genes involved in cell-cycle checkpoints and DNA repair were missing, as in several other Naganishia species. This extensive loss may be adaptive in extreme environments prone to abiotic stress, where a high mutation rate could generate advantageous traits, and reduced cell-cycle control may allow for faster reproduction that would be advantageous for rapid growth during brief periods of soil wetting following rare snow events.

Vimercati, Lara↗

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↗

Barcoded reciprocal hemizygosity analysis via sequencing illuminates the complex genetic basis of yeast thermotolerance

Decades of successes in statistical genetics have revealed the molecular underpinnings of traits as they vary across individuals of a given species. But standard methods in the field cannot be applied to divergences between reproductively isolated taxa. Genome-wide reciprocal hemizygosity mapping (RH-seq), a mutagenesis screen in an interspecies hybrid background, holds promise as a method to accelerate the progress of interspecies genetics research. Here, we describe an improvement to RH-seq in which mutants harbor barcodes for cheap and straightforward sequencing after selection in a condition of interest. As a proof of concept for the new tool, we carried out genetic dissection of the difference in thermotolerance between two reproductively isolated budding yeast species. Experimental screening identified dozens of candidate loci at which variation between the species contributed to the thermotolerance trait. Hits were enriched for mitosis genes and other housekeeping factors, and among them were multiple loci with robust sequence signatures of positive selection. Together, these results shed new light on the mechanisms by which evolution solved the problems of cell survival and division at high temperature in the yeast clade, and they illustrate the power of the barcoded RH-seq approach.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of a novel polyextremotolerant fungus, Exophiala viscosa , with insights into its melanin regulation and ecological niche

Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primary yeast form. These fungi grow in xeric, nutrient depletes environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community are not well understood. We have isolated 2 novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e. E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin which can potentially provide ultraviolet resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.

60 APPLIED LIFE SCIENCES↗

Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast

Abstract Variation in gene copy number can alter gene expression and influence downstream phenotypes; thus copy-number variation provides a route for rapid evolution if the benefits outweigh the cost. We recently showed that genetic background significantly influences how yeast cells respond to gene overexpression, revealing that the fitness costs of copy-number variation can vary substantially with genetic background in a common-garden environment. But the interplay between copy-number variation tolerance and environment remains unexplored on a genomic scale. Here, we measured the tolerance to gene overexpression in four genetically distinct Saccharomyces cerevisiae strains grown under sodium chloride stress. Overexpressed genes that are commonly deleterious during sodium chloride stress recapitulated those commonly deleterious under standard conditions. However, sodium chloride stress uncovered novel differences in strain responses to gene overexpression. West African strain NCYC3290 and North American oak isolate YPS128 are more sensitive to sodium chloride stress than vineyard BC187 and laboratory strain BY4743. Consistently, NCYC3290 and YPS128 showed the greatest sensitivities to overexpression of specific genes. Although most genes were deleterious, hundreds were beneficial when overexpressed—remarkably, most of these effects were strain specific. Few beneficial genes were shared between the sodium chloride-sensitive isolates, implicating mechanistic differences behind their sodium chloride sensitivity. Transcriptomic analysis suggested underlying vulnerabilities and tolerances across strains, and pointed to natural copy-number variation of a sodium export pump that likely contributes to strain-specific responses to overexpression of other genes. Our results reveal extensive strain-by-environment interactions in the response to gene copy-number variation, raising important implications for the accessibility of copy-number variation-dependent evolutionary routes under times of stress.

60 APPLIED LIFE SCIENCES↗