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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus

ABSTRACT Giant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here, we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of the major capsid protein indicated the presence of other giant viruses in the sample matrix but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. However, our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics. IMPORTANCE The discovery of large and giant nucleocytoplasmic large DNA viruses (NCLDV) with genomes in the megabase range and equipped with a wide variety of features typically associated with cellular organisms was one of the most unexpected, intriguing, and spectacular breakthroughs in virology. Recent studies suggest that these viruses are highly abundant in the oceans, freshwater, and soil, impact the biology and ecology of their eukaryotic hosts, and ultimately affect global nutrient cycles. Genome-resolved metagenomics is becoming an increasingly popular tool to assess the diversity and coding potential of giant viruses, but this approach is currently lacking validation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Finite N indices and the giant graviton expansion

The superconformal index of N = 4 super-Yang Mills theory with U(N) gauge group can be written as a matrix integral over the gauge group. Recently, Murthy demonstrated that this integral can be reexpressed as a sum of terms corresponding to a giant graviton expansion of the index, and provided an explicit formula for the case of a single giant graviton. Here we give similar explicit formulae for an arbitrary number, m ≥ 1, of giant gravitons. We provide 1/2 and 1/16 BPS index examples up to the order where three giant gravitons contribute and demonstrate that the expansion of the matrix integral differs from the giant graviton expansion computed in the supergravity dual. This shows that the giant graviton expansion is not necessarily unique once two or more giant gravitons start appearing.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Adaptation strategies of giant viruses to low-temperature marine ecosystems

Abstract Microbes in marine ecosystems have evolved their gene content to thrive successfully in the cold. Although this process has been reasonably well studied in bacteria and selected eukaryotes, less is known about the impact of cold environments on the genomes of viruses that infect eukaryotes. Here, we analyzed cold adaptations in giant viruses (Nucleocytoviricota and Mirusviricota) from austral marine environments and compared them with their Arctic and temperate counterparts. We recovered giant virus metagenome-assembled genomes (98 Nucleocytoviricota and 12 Mirusviricota MAGs) from 61 newly sequenced metagenomes and metaviromes from sub-Antarctic Patagonian fjords and Antarctic seawater samples. When analyzing our data set alongside Antarctic and Arctic giant viruses MAGs already deposited in the Global Ocean Eukaryotic Viral database, we found that Antarctic and Arctic giant viruses predominantly inhabit sub-10°C environments, featuring a high proportion of unique phylotypes in each ecosystem. In contrast, giant viruses in Patagonian fjords were subject to broader temperature ranges and showed a lower degree of endemicity. However, despite differences in their distribution, giant viruses inhabiting low-temperature marine ecosystems evolved genomic cold-adaptation strategies that led to changes in genetic functions and amino acid frequencies that ultimately affect both gene content and protein structure. Such changes seem to be absent in their mesophilic counterparts. The uniqueness of these cold-adapted marine giant viruses may now be threatened by climate change, leading to a potential reduction in their biodiversity.

Environmental Sciences & Ecology↗
DOE OSTI2023

Giant Virus Infection Signatures Are Modulated by Euphotic Zone Depth Strata and Iron Regimes of the Subantarctic Southern Ocean

Viruses can alter the abundance, evolution, and metabolism of microorganisms in the ocean, playing a key role in water column biogeochemistry and global carbon cycles. Large efforts to measure the contribution of eukaryotic microorganisms (e.g., protists) to the marine food web have been made, yet the in situ activities of the ecologically relevant viruses that infect these organisms are not well characterized. Viruses within the phylum Nucleocytoviricota (“giant viruses”) are known to infect a diverse range of ecologically relevant marine protists, yet how these viruses are influenced by environmental conditions remains under-characterized. By employing metatranscriptomic analyses of in situ microbial communities along a temporal and depthresolved gradient, we describe the diversity of giant viruses at the Southern Ocean Time Series (SOTS), a site within the subpolar Southern Ocean. Using a phylogeny-guided taxonomic assessment of detected giant virus genomes and metagenome-assembled genomes, we observed depth-dependent structuring of divergent giant virus families mirroring dynamic physicochemical gradients in the stratified euphotic zone. Analyses of transcribed metabolic genes from giant viruses suggest viral metabolic reprogramming of hosts from the surface to a 200-m depth. Lastly, using on-deck incubations reflecting a gradient of iron availability, we show that modulating iron regimes influences the activity of giant viruses in the field. Specifically, we show enhanced infection signatures of giant viruses under both iron-replete and iron-limited conditions. Collectively, these results expand our understanding of how the water column’s vertical biogeography and chemical surroundings affect an important group of viruses within the Southern Ocean

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Energy density functional and sensitivity of energies of giant resonances to bulk nuclear matter properties

The development of a modern and more realistic nuclear energy density functional (EDF) for accurate predictions of properties of nuclei is the subject of enhanced activity, since it is very important for the study of properties of nuclear matter (NM), giant resonances and, in particular, of properties of rare nuclei with unusual neutron-to-proton ratios. Here, we provide a short review of the current status of the nuclear EDF and the theoretical results obtained for properties of nuclei and nuclear matter. We will first describe a method for determining the parameters of the EDF, associated with the Skyrme type effective interaction, by carrying out a Hartree-Fock based fit to extensive set of data of ground state properties and constraints. Next we will describe the fully self-consistent Hartree-Fock (HF) based random-phase-approximation (RPA) theory for calculating the strength functions S(E) and centroid energies E CEN of giant resonances and the folding model (FM) distorted wave Вorn approximation (DWBA) to calculate the excitation cross section of giant resonances by α scattering. Then we will provide results for: (i) the Skyrme parameters of the KDE0v1 EDF; (ii) consequences of violation of self-consistently in HF-based RPA; (iii) FM-DWBA calculation of excitation cross section; (iv) values of the E CEN of isoscalar and isovector giant resonances of multipolarities L=0–3 for a wide range of spherical nuclei, using 33 EDFs associated with standard form of the Skyrme type interactions, commonly employed in the literature; and (v) the sensitivities E CEN of the giant resonances to bulk properties of NM. We also determine constraints on NM properties, such as the incompressibility coefficient and effective mass, by comparing with experimental data on E CEN of giant resonances.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Rotationally Driven Ultraviolet Emission of Red Giant Stars

Main-sequence stars exhibit a clear rotation-activity relationship, in which rapidly rotating stars drive strong chromospheric/coronal ultraviolet and X-ray emission. While the vast majority of red giant stars are inactive, a few percent exhibit strong ultraviolet emission. Here we use a sample of 133 red giant stars observed by Sloan Digital Sky Survey APOGEE and Galaxy Evolution Explorer to demonstrate an empirical relationship between near-UV (NUV) excess and rotational velocity (v sin i). Beyond this simple relationship, we find that NUV excess also correlates with rotation period and with Rossby number in a manner that shares broadly similar trends to those found in M dwarfs, including activity saturation among rapid rotators. Our data also suggest that the most extremely rapidly rotating giants may exhibit so-called supersaturation, which could be caused by centrifugal stripping of these stars rotating at a high fraction of breakup speed. As an example application of our empirical rotation-activity relation, we demonstrate that the NUV emission observed from a recently reported system comprising a red giant with a black hole companion is fully consistent with arising from the rapidly rotating red giant in that system. Most fundamentally, our findings suggest a common origin of chromospheric activity in rotation and convection for cool stars from main sequence to red giant stages of evolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

WIYN Open Cluster Study. LXXXI. Caught in the Act? The Peculiar Red Giant NGC 2243-W2135

High-dispersion spectra for giants through turnoff stars in the Li 6708 Å region have been obtained and analyzed in the old, metal-deficient open cluster, NGC 2243. When combined with high-dispersion data from other surveys, the cluster is found to contain a uniquely peculiar star at the luminosity level of the red clump. The giant is the reddest star at its luminosity, exhibits variability at a minimum 0.1 mag level on a timescale of days, is a single-lined, radial-velocity variable, and has vsin i between 35 and 40 km s{sup −1}. In sharp contrast with the majority of the red giant cluster members, the star has a detectable Li abundance, potentially as high or higher than other giants observed to date while at or just below the boundary normally adopted for Li-rich giants. The observed anomalies may be indicators of the underlying process by which the giant has achieved its unusual Li abundance, with a recent mass transfer episode being the most probable within the currently limited constraints.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Complex transcriptional regulations of a hyperparasitic quadripartite system in giant viruses infecting protists

Abstract Hyperparasitism is a common pattern in nature that is not limited to cellular organisms. Giant viruses infecting protists can be hyperparasitized by smaller ones named virophages. In addition, both may carry episomal DNA molecules known as transpovirons in their particles. They all share transcriptional regulatory elements that dictate the expression of their genes within viral factories built by giant viruses in the host cytoplasm. This suggests the existence of interactions between their respective transcriptional networks. Here we investigatedAcanthamoeba castellaniicells infected by a giant virus (megavirus chilensis), and coinfected with a virophage (zamilon vitis) and/or a transpoviron (megavirus vitis transpoviron). Infectious cycles were monitored through time-course RNA sequencing to decipher the transcriptional program of each partner and its impact on the gene expression of the others. We found highly diverse transcriptional responses. While the giant virus drastically reshaped the host cell transcriptome, the transpoviron had no effect on the gene expression of any of the players. In contrast, the virophage strongly modified the giant virus gene expression, albeit transiently, without altering the protein composition of mature viral particles. The virophage also induced the overexpression of transpoviron genes, likely through the indirect upregulation of giant virus-encoded transcription factors. Together, these analyses document the intricated transcriptionally regulated networks taking place in the infected cell.

Science & Technology - Other Topics↗
DOE OSTI2020

A giant planet candidate transiting a white dwarf

Astronomers have discovered thousands of planets outside the Solar System1, most of which orbit stars that will eventually evolve into red giants and then into white dwarfs. During the red giant phase, any close-orbiting planets will be engulfed by the star2, but more distant planets can survive this phase and remain in orbit around the white dwarf3,4. Some white dwarfs show evidence for rocky material floating in their atmospheres5, in warm debris disks6,7,8,9 or orbiting very closely10,11,12, which has been interpreted as the debris of rocky planets that were scattered inwards and tidally disrupted13. Recently, the discovery of a gaseous debris disk with a composition similar to that of ice giant planets14 demonstrated that massive planets might also find their way into tight orbits around white dwarfs, but it is unclear whether these planets can survive the journey. So far, no intact planets have been detected in close orbits around white dwarfs. Here we report the observation of a giant planet candidate transiting the white dwarf WD 1856+534 (TIC 267574918) every 1.4 days. We observed and modelled the periodic dimming of the white dwarf caused by the planet candidate passing in front of the star in its orbit. The planet candidate is roughly the same size as Jupiter and is no more than 14 times as massive (with 95 per cent confidence). Other cases of white dwarfs with close brown dwarf or stellar companions are explained as the consequence of common-envelope evolution, wherein the original orbit is enveloped during the red giant phase and shrinks owing to friction. In this case, however, the long orbital period (compared with other white dwarfs with close brown dwarf or stellar companions) and low mass of the planet candidate make common-envelope evolution less likely. Instead, our findings for the WD 1856+534 system indicate that giant planets can be scattered into tight orbits without being tidally disrupted, motivating the search for smaller transiting planets around white dwarfs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Genomic Mysteries of Giant Bacteria: Insights and Implications

Bacteria and Archaea are traditionally regarded as organisms with a simple morphology constrained to a size of 2–3 µm. Nevertheless, the history of microbial research is rich in the description of giant bacteria exceeding tens and even hundreds of micrometers in length or diameter already from its early days, for example, Beggiatoa spp., to the present, for example, Candidatus Thiomargarita magnifica. While some of these giants are still being studied, some were lost to science, with merely drawings and photomicrographs as evidence for their existence. The physiology and biogeochemical role of giant bacteria have been studied, with a large focus on those involved in the sulfur cycle. With the onset of the genomic era, no special emphasis has been given to this group, in an attempt to gain a novel, evolutionary, and molecular understanding of the phenomenon of bacterial gigantism. The few existing genomic studies reveal a mysterious world of hyperpolyploid bacteria with hundreds to hundreds of thousands of chromosomes that are, in some cases, identical and in others, extremely different. These studies on giant bacteria reveal novel organelles, cellular compartmentalization, and novel mechanisms to combat the accumulation of deleterious mutations in polyploid bacteria. In this perspective paper, we provide a brief overview of what is known about the genomics of giant bacteria and build on that to highlight a few burning questions that await to be addressed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

High-resolution Spectra of Earth-like Planets Orbiting Red Giant Host Stars

In the near future we will have ground- and space-based telescopes that are designed to observe and characterize Earth-like planets. While attention is focused on exoplanets orbiting main-sequence stars, more than 150 exoplanets have already been detected orbiting red giants, opening the intriguing question of what rocky worlds orbiting in the habitable zone (HZ) of red giants would be like and how to characterize them. We present a high-resolution spectral database of reflection and emission spectra for nominal Earth-like planets orbiting in the red giant HZ from the visible to infrared (0.4–20 μm) for planets orbiting at the Earth-equivalent distance. We also show the change of such planetary spectra through the evolution of their red giant hosts. While the luminosity of the host increases the contrast ratio between star and planet, the increased orbital distance of the HZ for red giant hosts relaxes the light suppression requirements close to the star, which could make such planets interesting targets to characterize and search for signs of life, if new coronagraph designs with higher suppression at larger orbital separations could be developed. We assess the feasibility of characterizing atmospheric features including biosignatures for such planets with the proposed mission concept Large UV/Optical/IR Surveyor (LUVOIR).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

High-energy emission from a magnetar giant flare in the Sculptor galaxy

Magnetars are the most highly magnetized neutron stars in the cosmos (with magnetic field 10 13 –10 15 G). Giant flares from magnetars are rare, short-duration (about 0.1 s) bursts of hard X-rays and soft γ rays. Owing to the limited sensitivity and energy coverage of previous telescopes, no magnetar giant flare has been detected at gigaelectronvolt (GeV) energies. Here, we report the discovery of GeV emission from a magnetar giant flare on 15 April 2020 (refs. 3,4 and A. J. Castro-Tirado et al., manuscript in preparation). The Large Area Telescope (LAT) on board the Fermi Gamma-ray Space Telescope detected GeV γ rays from 19 s until 284 s after the initial detection of a signal in the megaelectronvolt (MeV) band. Our analysis shows that these γ rays are spatially associated with the nearby (3.5 megaparsecs) Sculptor galaxy and are unlikely to originate from a cosmological γ-ray burst. Thus, we infer that the γ rays originated with the magnetar giant flare in Sculptor. Furthermore, we suggest that the GeV signal is generated by an ultra-relativistic outflow that first radiates the prompt MeV-band photons, and then deposits its energy far from the stellar magnetosphere. After a propagation delay, the outflow interacts with environmental gas and produces shock waves that accelerate electrons to very high energies; these electrons then emit GeV γ rays as optically thin synchrotron radiation. This observation implies that a relativistic outflow is associated with the magnetar giant flare, and suggests the possibility that magnetars can power some short γ-ray bursts.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Giant magnetostriction and nonsaturating electric polarization up to 60 T in the polar magnet $\mathrm{CaBaCo_4O_7}$

Giant magnetostriction in insulating magnetic materials is highly required for applications but is rarely observed. Here we show that giant magnetostriction (> 1500 ppm) can be achieved in an insulating transition metal oxide CaBaCo 4 O 7 where the ferrimagnetic ordering at T c ~ 62K is associated with a huge change in the lattice. Moreover, because this material is pyroelectric with a nonswitchable electric polarization (P), the giant magnetostriction results in a pronounced magnetoelectric effect—a huge change of electric polarization (ΔP ~ 1.6μC/cm 2 ) in response to the applied magnetic field up to 60 T. Geometric frustration as well as the orbital instability of Co 2+ /Co 3+ ions is believed to play a crucial role in the giant magnetostriction. Here our study provides insights on how to achieve both giant magnetostriction and pronounced magnetoelectric effect in insulating transition metal oxides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Checking It Twice: Using [C/N] Masses and Asteroseismic Masses as a Diagnostic of Mass Loss and Transfer on the Red Giant Branch

Red giants experience significant mass loss, but the mechanism is poorly understood. The surface [C/N] of red giants is correlated with birth mass but not directly impacted by mass loss. Exploiting this, we compare asteroseismic masses of red giants with the same [C/N] but different evolutionary states. We find bulk differences between stars at the beginning of the red giant branch (RGB) and in the subsequent evolutionary phase, the red clump, providing a direct constraint on the strength of net RGB mass loss in field stars. We find that net mass loss decreases with metallicity and mass, matching recent studies for field giants but contradicting expectations from the widely used Reimers’s mass-loss formula. We propose a mass- and metallicity-dependent Reimers’s η calibration that reproduces the empirical trends that we see. In addition, we identify 200 stars (3.12% of our sample) that are clear outliers from their population in these birth mass bins, which we believe are likely candidates for mass transfer events. These stars do not show any obvious discrepancies in abundances or binary properties from their counterparts. This population should be accounted for in Galactic archeological studies. Further follow-up is required to quantify their occurrence rate and origin.

Roberts, John D. [The Ohio State Univ., Columbus, ↗
DOE OSTI2021

Chemical Compositions of Red Giant Stars from Habitable Zone Planet Finder Spectroscopy

We have used the Habitable Zone Planet Finder (HPF) to gather high-resolution, high signal-to-noise near-infrared spectra of 13 field red horizontal branch (RHB) stars, one open cluster giant, and one very metal-poor halo red giant. The HPF spectra cover the 0.81–1.28 μm wavelength range of the zyJ bands, partially filling the gap between the optical (0.4–1.0 μm) and infrared (1.5–2.4 μm) spectra already available for the program stars. We derive abundances of 17 species from LTE-based computations involving equivalent widths and spectrum syntheses, and estimate abundance corrections for the species that are most affected by departures from LTE in RHB stars. Generally good agreement is found between HPF-based metallicities and abundance ratios and those from the optical and infrared spectral regions. Light element transitions dominate the HPF spectra of these red giants, and HPF data can be used to derive abundances from species with poor or no representation in optical spectra (e.g., C i, P i, S i, K i). Attention is drawn to the HPF abundances in two field solar-metallicity RHB stars of special interest: one with an extreme carbon isotope ratio, and one with a rare, very large lithium content. The latter star is unique in our sample in exhibiting very strong He i 10830 Å absorption. The abundances of the open cluster giant concur with those derived from other wavelength regions. Detections of C i and S i in HD 122563 are reported, yielding the lowest metallicity determination of [S/Fe] from more than one multiplet.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Chemometric optimisation of pressurised liquid extraction for the determination of alliin and S‐allyl‐cysteine in giant garlic ( Allium ampeloprasum L.) by liquid chromatography tandem mass spectrometry

Abstract Introduction Giant garlic is a functional food that contains different kinds of bioactive molecules with beneficial effects on chronic noncommunicable diseases like diabetes and cardiovascular conditions. Considering biosynthesis pathways, abundance, and biological activity, alliin and S‐allyl‐cysteine were used as chemical markers of organosulphur compounds present in giant garlic. Objective To establish a chemometric optimisation of pressurised liquid extraction for the determination of alliin and S‐allyl‐cysteine in giant garlic by liquid chromatography tandem mass spectrometry (LC–MS/MS). Methodology Samples were blanched (ca. 90°C for 10 min) to inactivate alliinase and γ‐glutamyl transpeptidase enzymes and then freeze‐dried. Chemometric optimisation was performed via response surface methodology based on central composite design (CCD). Organosulphur compound yields were determined applying a validated LC–MS/MS method in multiple reaction monitoring (MRM) mode using the following transitions: for alliin m/z 178 → 74 and for S‐allyl‐cysteine m/z 162 → 41. Results According to CCD results, under constant conditions of pressure (1500 psi) and time (20 min), the optimal conditions for pressurised liquid extraction of alliin and S‐allyl‐cysteine were 70.75 and 68.97% v/v of ethanol in extraction solvent and 76.45 and 98.88°C as extraction temperature, respectively. Multiple response optimisation for the simultaneous extraction of both organosulphur compounds was established via desirability function. Under these conditions, 2.70 ± 0.27 mg g −1 dry weight (DW) of alliin and 2.79 ± 0.22 mg g −1 DW of S‐allyl‐cysteine were extracted. Conclusions These results clearly demonstrated that pressurised liquid extraction is an efficient green technique to extract bioactive organosulphur compounds from giant garlic. Extraction yields were significantly ( p < 0.05) higher than those obtained with conventional ultra‐turrax extraction.

Peterssen‐Fonseca, Darlene↗
DOE OSTI2022

Origin of giant electric-field-induced strain in faulted alkali niobate films

A large electromechanical response in ferroelectrics is highly desirable for developing high-performance sensors and actuators. Enhanced electromechanical coupling in ferroelectrics is usually obtained at morphotropic phase boundaries requiring stoichiometric control of complex compositions. Recently it was shown that giant piezoelectricity can be obtained in films with nanopillar structures. Here, we elucidate its origin in terms of atomic structure and demonstrate a different system with a greatly enhanced response. This is in non-stoichiometric potassium sodium niobate epitaxial thin films with a high density of self-assembled planar faults. A giant piezoelectric coefficient of ~1900 picometer per volt is demonstrated at 1 kHz, which is almost double the highest ever reported effective piezoelectric response in any existing thin films. The large oxygen octahedral distortions and the coupling between the structural distortion and polarization orientation mediated by charge redistribution at the planar faults enable the giant electric-field-induced strain. Our findings demonstrate an important mechanism for realizing the unprecedentedly giant electromechanical coupling and can be extended to many other material functions by engineering lattice faults in non-stoichiometric compositions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Giant uniaxial negative thermal expansion in FeZr 2 alloy over a wide temperature range

Negative thermal expansion (NTE) alloys possess great practical merit as thermal offsets for positive thermal expansion due to its metallic properties. However, achieving a large NTE with a wide temperature range remains a great challenge. Herein, a metallic framework-like material FeZr 2 is found to exhibit a giant uniaxial (1D) NTE with a wide temperature range (93-1078 K, $\overline{α}_{l}$=–34.01×10 –6 K –1 ). Such uniaxial NTE is the strongest in all metal-based NTE materials. The direct experimental evidence and DFT calculations reveal that the origin of giant NTE is the couple with phonons, flexible framework-like structure, and soft bonds. Interestingly, the present metallic FeZr 2 excites giant 1D NTE mainly driven by high-frequency optical branches. It is unlike the NTE in traditional framework materials, which are generally dominated by low energy acoustic branches. In the present study, a giant uniaxial NTE alloy is reported, and the complex mechanism has been revealed. It is of great significance for understanding the nature of thermal expansion and guiding the regulation of thermal expansion.

36 MATERIALS SCIENCE↗