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At least 1,513 records · Page 84
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

DNA viruses from different stages of a wastewater treatment plant in southwest Ohio

Wastewater treatment plants (WWTPs) house diverse populations of microbial communities that are dynamic across treatment stages. Although viruses, especially non-pathogenic ones are relatively less studied compared to their bacterial counterparts, they are equally important players in WWTP microbiomes. In this study, we sampled influent, activated sludge, and effluent stages of a WWTP in southwest Ohio to sequence their viral population using multiple displacement amplification (MDA) and metagenomic approaches. We recovered 1003 viral genomes, the majority of which were ssDNA (single-stranded DNA) viruses that formed distinct clusters representing novel species and phylogenetic groups not closely related to known human gut or terrestrial viruses. Additionally, tracking viruses across treatment stages showed several persisted across multiple treatment stages. These results suggest that further studies are needed to understand the persistence of viral populations, particularly non-pathogenic ones, across different stages of WWTPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Evidence of recombination and positive selection in cetacean papillomaviruses

Papillomaviruses (PVs) are small DNA viruses that have been associated with increased epithelial proliferation. Over one hundred PV types have been identified in humans; however, only three have been identified in bottlenose dolphins (Tursiops truncatus) to date. Using rolling circle amplification and degenerate PCR, we identified four novel PV genomes of bottlenose dolphins. TtPV4, TtPV5 and TtPV6 were identified in genital lesions while TtPV7 was identified in normal genital mucosa. Bayesian analysis of the full-length L1 genes found that TtPV4 and TtPV7 group within the Upsilonpapillomavirus genus while TtPV5 and TtPV6 group with Omikronpapillomavirus. However, analysis of the E1 gene did not distinguish these genera, implying that these genes may not share a common history, consistent with recombination. Recombination analyses identified several probable events. Signals of positive selection were found mostly in the E1 and E2 genes. Recombination and diversifying selection pressures constitute important driving forces of cetacean PV evolution.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Oral T4-like phage cocktail application to healthy adult volunteers from Bangladesh

The genomic diversity of 99 T4-like coliphages was investigated by sequencing an equimolar mixture with Illumina technology and screening them against different databases for horizontal gene transfer and undesired genes. A 9-phage cocktail was given to 15 healthy adults from Bangladesh at a dose of 3 Multiplication-Sign 10{sup 9} and 3 Multiplication-Sign 10{sup 7} plaque-forming units and placebo respectively. Phages were detected in 64% of the stool samples when subjects were treated with higher titer phage, compared to 30% and 28% with lower-titer phage and placebo, respectively. No Escherichia coli was present in initial stool samples, and no amplification of phage was observed. One percent of the administered oral phage was recovered from the feces. No adverse events were observed by self-report, clinical examination, or from laboratory tests for liver, kidney, and hematology function. No impact of oral phage was seen on the fecal microbiota composition with respect to bacterial 16S rRNA from stool.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

Proteotoxic stress induced by Autographa californica nucleopolyhedrovirus infection of Spodoptera frugiperda Sf9 cells

Baculovirus AcMNPV causes proteotoxicity in Sf9 cells as revealed by accumulation of ubiquitinated proteins and aggresomes in the course of infection. Inhibition of proteasomes by lactacystin increased markedly the stock of ubiquitinated proteins indicating a primary role of proteasomes in detoxication. The proteasomes were present in Sf9 cells as 26S and 20S complexes whose protease activity did not change during infection. Proteasome inhibition caused a delay in the initiation of viral DNA replication suggesting an important role of proteasomes at early stages in infection. However, lactacystin did not affect ongoing replication indicating that active proteasomes are not required for genome amplification. At late stages in infection (24-48 hpi), aggresomes containing the ubiquitinated proteins and HSP/HSC70s showed gradual fusion with the vacuole-like structures identified as lysosomes by antibody to cathepsin D. This result suggests that lysosomes may assist in protection against proteotoxicity caused by baculoviruses absorbing the ubiquitinated proteins.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

Growth and characterization of different human rhinovirus C types in three-dimensional human airway epithelia reconstituted in vitro

New molecular diagnostic tools have recently allowed the discovery of human rhinovirus species C (HRV-C) that may be overrepresented in children with lower respiratory tract complications. Unlike HRV-A and HRV-B, HRV-C cannot be propagated in conventional immortalized cell lines and their biological properties have been difficult to study. Recent studies have described the successful amplification of HRV-C15, HRV-C11, and HRV-C41 in sinus mucosal organ cultures and in fully differentiated human airway epithelial cells. Consistent with these studies, we report that a panel of clinical HRV-C specimens including HRV-C2, HRV-C7, HRV-C12, HRV-C15, and HRV-C29 types were all capable of mediating productive infection in reconstituted 3D human primary upper airway epithelial tissues and that the virions enter and exit preferentially through the apical surface. Similar to HRV-A and HRV-B, our data support the acid sensitivity of HRV-C. We observed also that the optimum temperature requirement during HRV-C growth may be type-dependent. - Highlights: • A 3D human upper airway epithelia reconstituted in vitro supports HRV-C growth. • HRV-Cs enter and exit preferentially at the apical side of this ALI culture system. • HRV-Cs are acid sensitive. • Temperature sensitivity may be type-dependent for HRV-Cs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Human papillomavirus E5 oncoproteins bind the A4 endoplasmic reticulum protein to regulate proliferative ability upon differentiation

Human papillomaviruses (HPV) infect stratified epithelia and link their life cycles to epithelial differentiation. The HPV E5 protein plays a role in the productive phase of the HPV life cycle but its mechanism of action is still unclear. We identify a new binding partner of E5, A4, using a membrane-associated yeast-two hybrid system. The A4 protein co-localizes with HPV 31 E5 in perinuclear regions and forms complexes with E5 and Bap31. In normal keratinocytes, A4 is found primarily in basal cells while in HPV positive cells high levels of A4 are seen in both undifferentiated and differentiated cells. Reduction of A4 expression by shRNAs, enhanced HPV genome amplification and increased cell proliferation ability following differentiation but this was not seen in cells lacking E5. Our studies suggest that the A4 protein is an important E5 binding partner that plays a role in regulating cell proliferation ability upon differentiation. - Highlights: • A4 associates with HPV 31 E5 proteins. • A4 is localized to endoplasmic reticulum. • HPV proteins induce A4 expression in suprabasal layers of stratified epithelium. • E5 is important for proliferation ability of differentiating HPV positive cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL

Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput Fluidigm TM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N 2 fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. As a result, this research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

The Growth arrest specific 1 (Gas1) gene is transcriptionally regulated by NeuroD1 via two distal E-boxes

Growth arrest specific 1 (GAS1) is a signaling mediator for the development of the central nervous system that works as a co-receptor for sonic hedgehog (SHH) to induce the amplification of neural progenitors during the patterning of the mammalian neural tube and establishing granular cells in the cerebellum. Recently, we confirmed that Gas1 is also expressed by neural progenitors of the developing cortex and the dentate gyrus of the hippocampus. The presence of GAS1 in progenitor stages indicates that one of its principal roles is the maintenance of these cells during neurogenic events. However, the signals responsible for the expression of Gas1 in progenitor cells are unknown, an aspect that is relevant to understand its functions during neurogenesis. Here, we focused on elucidating the mechanisms of the transcriptional regulation of Gas1 and using comparative genomics methods found two highly conserved E-boxes in the Gas1 promoter which mediate its up-regulation by NeuroD1. Additionally, we found that GAS1 and NeuroD1 co-localize in the neocortex, the dentate gyrus of the hippocampus and the external granular layer of the cerebellum, suggesting a previously unsuspected regulatory relationship. Our data indicate that Gas1 is a direct target of NeuroD1 during the induction of the neurogenic program.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Human adipose-derived mesenchymal stromal cells from face and abdomen undergo replicative senescence and loss of genetic integrity after long-term culture

Body fat depots are heterogeneous concerning their embryonic origin, structure, exposure to environmental stressors, and availability. Thus, investigating adipose-derived mesenchymal stromal cells (ASCs) from different sources is essential to standardization for future therapies. In vitro amplification is also critical because it may predispose cell senescence and mutations, reducing regenerative properties and safety. Here, we evaluated long-term culture of human facial ASCs (fASCs) and abdominal ASCs (aASCs) and showed that both met the criteria for MSCs characterization but presented differences in their immunophenotypic profile, and differentiation and clonogenic potentials. The abdominal tissue yielded more ASCs, and these had higher proliferative potential, but facial cells displayed fewer mitotic errors at higher passages. However, both cell types reduced clonal efficiency over time and entered replicative senescence around P12, as evaluated by progressive morphological alterations, reduced proliferative capacity, and SA-β-galactosidase expression. Loss of genetic integrity was detected by a higher proportion of cells showing nuclear alterations and γ-H2AX expression. Our findings indicate that the source of ASCs can substantially influence their phenotype and therefore should be carefully considered in future cell therapies, avoiding, however, long-term culture to ensure genetic stability.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)

Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Modeling of transverse stimulated Raman scattering in KDP/DKDP in large-aperture plates suitable for polarization control

Transverse stimulated Raman scattering (TSRS) in potassium dihydrogen phosphate (KDP) and deuterated potassium dihydrogen phosphate (DKDP) plates for large-aperture, inertial confinement fusion (ICF)-class laser systems is a well-recognized limitation giving rise to parasitic energy conversion and laser-induced damage. The onset of TSRS is manifested in plates exposed to the ultraviolet section of the beam. TSRS amplification is a coherent process that grows exponentially and is distributed nonuniformly in the crystal and at the crystal surfaces. To understand the growth and spatial distribution of TSRS energy in various configurations, a modeling approach has been developed to simulate the operational conditions relevant to ICF-class laser systems. Specific aspects explored in this work include (i) the behavior of TSRS in large-aperture crystal plates suitable for third-harmonic generation and use as wave plates for polarization control in current-generation ICF-class laser system configurations; (ii) methods, and their limitations, of TSRS suppression and (iii) optimal geometries to guide future designs.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Plasma-based prism compressor design for high-intensity laser pulses

A concept for a femtosecond pulse compressor based on underdense plasma prisms is presented. An analytical model is developed to calculate the spectral phase incurred and the expected pulse compression. A 2D particle-in-cell simulation verifies the analytical model. Simulated intensities ( ∼10 16 W/cm 2 ) were orders of magnitude higher than the damage threshold for conventional gratings used in chirped pulse amplification. Theoretical geometries for compact (tens of cm scale) compressors for 1, 10 and 100 PW power levels are proposed.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Pointing stabilization of a 1 Hz high-power laser via machine learning

Abstract High-power lasers are vital for particle acceleration, imaging, fusion and materials processing, requiring precise control and high-energy delivery. Laser plasma accelerators (LPAs) demand laser positional stability at focus to ensure consistent electron beams in applications such as X-ray free-electron lasers and high-energy colliders. Achieving this stability is especially challenging for the low-repetition-rate lasers in current LPAs. We present a machine learning method that predicts and corrects laser pointing instabilities in real-time using a high-frequency pilot beam. By preemptively adjusting a correction mirror, this approach overcomes traditional feedback limits. Demonstrated on the BELLA petawatt laser operating at the terawatt level (30 mJ amplification), our method achieved root mean square pointing stabilization of 0.34 and 0.59 $\unicode{x3bc} \mathrm{rad}$ in the x and y directions, reducing jitter by 65% and 47%, respectively. This is the first successful application of predictive control for shot-to-shot stabilization in low-repetition-rate laser systems, paving the way for full-energy petawatt lasers and transformative advances across science, industry and security.

Amodio, Alessio↗
DOE OSTI2016

Numerical investigation of the role of free-stream turbulence in boundary-layer separation

The aerodynamic performance of lifting surfaces operating at low Reynolds number conditions is impaired by laminar separation. In most cases, transition to turbulence occurs in the separated shear layer as a result of a series of strong hydrodynamic instability mechanisms. Although the understanding of these mechanisms has been significantly advanced over the past decades, key questions remain unanswered about the influence of external factors such as free-stream turbulence (FST) and others on transition and separation. The present study is driven by the need for more accurate predictions of separation and transition phenomena in ‘real world’ applications, where elevated levels of FST can play a significant role (e.g. turbomachinery). Numerical investigations have become an integral part in the effort to enhance our understanding of the intricate interactions between separation and transition. Due to the development of advanced numerical methods and the increase in the performance of supercomputers with parallel architecture, it has become feasible for low Reynolds number application ( $O(10^{5})$ ) to carry out direct numerical simulations (DNS) such that all relevant spatial and temporal scales are resolved without the use of turbulence modelling. Because the employed high-order accurate DNS are characterized by very low levels of background noise, they lend themselves to transition research where the amplification of small disturbances, sometimes even growing from numerical round-off, can be examined in great detail. When comparing results from DNS and experiment, however, it is beneficial, if not necessary, to increase the background disturbance levels in the DNS to levels that are typical for the experiment. For the current work, a numerical model that emulates a realistic free-stream turbulent environment was adapted and implemented into an existing Navier–Stokes code based on a vorticity–velocity formulation. The role FST plays in the transition process was then investigated for a laminar separation bubble forming on a flat plate. FST was shown to cause the formation of the well-known Klebanoff mode that is represented by streamwise-elongated streaks inside the boundary layer. Increasing the FST levels led to accelerated transition, a reduction in bubble size and better agreement with the experiments. Moreover, the stage of linear disturbance growth due to the inviscid shear-layer instability was found to not be ‘bypassed’.

Mechanics↗
DOE OSTI2017

Numerical study of variable density turbulence interaction with a normal shock wave

Accurate numerical simulations of shock–turbulence interaction (STI) are conducted with a hybrid monotonicity-preserving–compact-finite-difference scheme for a detailed study of STI in variable density flows. Theoretical and numerical assessments of data confirm that all turbulence scales as well as the STI are well captured by the computational method. Linear interaction approximation (LIA) convergence tests conducted with the shock-capturing simulations exhibit a similar trend of converging to LIA predictions to shock-resolving direct numerical simulations (DNS). The effects of density variations on STI are studied by comparing the results corresponding to an upstream multi-fluid mixture with the single-fluid case. Here the results show that for the current parameter ranges, the turbulence amplification by the normal shock wave is much higher and the reduction in turbulence length scales is more significant when strong density variations exist. Turbulent mixing enhancement by the shock is also increased and stronger mixing asymmetry in the postshock region is observed when there is significant density variation. The turbulence structure is strongly modified by the shock wave, with a differential distribution of turbulent statistics in regions having different densities. The dominant mechanisms behind the variable density STI are identified by analysing the transport equations for the Reynolds stresses, vorticity, normalized mass flux and density specific volume covariance.

42 ENGINEERING↗
DOE OSTI2026

Simulations of a hypersonic turbulent boundary layer over wavy surfaces

Here, we conduct large-eddy simulations of a Mach 5.84 cold wall turbulent boundary layer over one-dimensional wavy walls with varying amplitudes and wavelengths. Across all wall topologies, a series of alternating shock and expansion waves is shown to influence the entire boundary layer, and generate repeating wave patterns in the turbulent stresses, dispersive stresses, and turbulent kinetic energy budget. The series of alternating shocks and expansions imposes repeating adverse and favourable pressure gradients across the wavy wall, and at sufficient wall amplitude, triggers flow separation in the trough of the wave. Flow separation is demonstrated to influence the behaviour of wall pressure fluctuations over the wavy wall. In attached flows, the prominent frequencies are consistent with integral-scale boundary layer turbulence, whereas in separated flows, a two-decade frequency range is present, akin to two-dimensional shock–boundary layer interactions. Counter-rotating streamwise-oriented structures are observed on the windward side of the wave, which diminish over the wave crest. A conditional analysis demonstrates that these structures are present in the upstream boundary layer, and are amplified with increasing wall amplitude. An examination of the Görtler number and probability density function (PDF) of the fluctuating lateral wall shear stress demonstrates the strong correlation between a large Görtler number and growth of the PDF tail density, suggesting that the amplification of the counter-rotating streamwise-oriented structures are linked to centrifugal instabilities in regions of streamline concavity.

boundary layers↗
DOE OSTI2020

Fluctuation dynamo in a weakly collisional plasma

The turbulent amplification of cosmic magnetic fields depends upon the material properties of the host plasma. In many hot, dilute astrophysical systems, such as the intracluster medium (ICM) of galaxy clusters, the rarity of particle–particle collisions allows departures from local thermodynamic equilibrium. These departures – pressure anisotropies – exert anisotropic viscous stresses on the plasma motions that inhibit their ability to stretch magnetic-field lines. We present an extensive numerical study of the fluctuation dynamo in a weakly collisional plasma using magnetohydrodynamic (MHD) equations endowed with a field-parallel viscous (Braginskii) stress. When the stress is limited to values consistent with a pressure anisotropy regulated by firehose and mirror instabilities, the Braginskii-MHD dynamo largely resembles its MHD counterpart, particularly when the magnetic field is dynamically weak. If instead the parallel viscous stress is left unabated – a situation relevant to recent kinetic simulations of the fluctuation dynamo and, we argue, to the early stages of the dynamo in a magnetized ICM – the dynamo changes its character, amplifying the magnetic field while exhibiting many characteristics reminiscent of the saturated state of the large-Prandtl-number ( ${Pm}\gtrsim {1}$ ) MHD dynamo. We construct an analytic model for the Braginskii-MHD dynamo in this regime, which successfully matches simulated dynamo growth rates and magnetic-energy spectra. A prediction of this model, confirmed by our numerical simulations, is that a Braginskii-MHD plasma without pressure-anisotropy limiters will not support a dynamo if the ratio of perpendicular and parallel viscosities is too small. This ratio reflects the relative allowed rates of field-line stretching and mixing, the latter of which promotes resistive dissipation of the magnetic field. Finally, in all cases that do exhibit a viable dynamo, the generated magnetic field is organized into folds that persist into the saturated state and bias the chaotic flow to acquire a scale-dependent spectral anisotropy.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Preparation, Applications, and Digital Simulation of Carbon Interdigitated Array Electrodes

Carbon interdigitated array (IDA) electrodes with features sizes down to 1.2 μm were fabricated by controlled pyrolysis of patterned photoresist. Cyclic voltam-metry of reversible redox species produced the expected steady-state currents. The collection efficiency depends on the IDA electrode spacing, which ranged from around 2.7 to 16.5 μm, with the smaller dimensions achieving higher collection efficiencies of up to 98%. The signal amplification because of redox cycling makes it possible to detect species at relatively low concentrations (10–5 molar) and the small spacing allows detection of transient electrogenerated species with much shorter lifetimes (submillisecond). Digital simulation software that accounts for both the width and height of electrode elements as well as the electrode spacing was developed to model the IDA electrode response. The simulations are in quantitative agreement with experimental data for both a simple fast one electron redox reaction and an electron transfer with a following chemical reaction at the IDAs with larger gaps whereas currents measured for the smallest IDA electrodes, that were larger than the simulated currents, are attributed to convection from induced charge electrokinetic flow. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the Department of Energy, Office of Science Office of Basic Energy Sciences.

Liu, Fei↗