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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 1,549 records · Page 86
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

SU-F-T-146: Comparing Monte Carlo Simulations with Commissioning Beam Data for Mevion S250 Proton Therapy System

Purpose: To evaluate the Monte Carlo simulated beam data with the measured commissioning data for the Mevion S250 proton therapy system. Method: The Mevion S250 proton therapy system utilizes a passive double scattering technique with a unique gantry mounted superconducting accelerator and offers effective proton therapy in a compact design concept. The field shaping system (FSS) includes first scattering foil, range modulator wheel (RMW), second scattering foil and post absorber and offers two field sizes and a total of 24 treatment options from proton range of 5 cm to 32 cm. The treatment nozzle was modeled in detail using TOPAS (TOolkit for PArticle Simulation) Monte Carlo code. The timing feathers of the moving modulator wheels were also implemented to generate the Spread Out Bragg Peak (SOBP). The simulation results including pristine Bragg Peak, SOBP and dose profiles were compared with the data measured during beam commissioning. Results: The comparison between the measured data and the simulation data show excellent agreement. For pristine proton Bragg Peaks, the simulated proton range (depth of distal 90%) values agreed well with the measured range values within 1 mm accuracy. The differences of the distal falloffs (depth from distal 80% to 20%) were also found to be less than 1 mm between the simulations and measurements. For the SOBP, the widths of modulation (depth of proximal 95% to distal 90%) were also found to agree with the measurement within 1 mm. The flatness of the simulated and measured lateral profiles was found to be 0.6 % and 1.1 %, respectively. Conclusion: The agreement between simulations and measurements demonstrate that TOPAS could be used as a viable platform to proton therapy applications. The matched simulation results offer a great tool and open opportunity for variety of applications.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-315: Comparative Studies of Planar Dose with Different Spatial Resolution for Head and Neck IMRT QA

Purpose: To quantitatively investigate the planar dose difference and the γ value between the reference fluence map with the 1 mm detector-to-detector distance and the other fluence maps with less spatial resolution for head and neck intensity modulated radiation (IMRT) therapy. Methods: For ten head and neck cancer patients, the IMRT quality assurance (QA) beams were generated using by the commercial radiation treatment planning system, Pinnacle3 (ver. 8.0.d Philips Medical System, Madison, WI). For each beam, ten fluence maps (detector-to-detector distance: 1 mm to 10 mm by 1 mm) were generated. The fluence maps with larger than 1 mm detector-todetector distance were interpolated using MATLAB (R2014a, the Math Works,Natick, MA) by four different interpolation Methods: for the bilinear, the cubic spline, the bicubic, and the nearest neighbor interpolation, respectively. These interpolated fluence maps were compared with the reference one using the γ value (criteria: 3%, 3 mm) and the relative dose difference. Results: As the detector-to-detector distance increases, the dose difference between the two maps increases. For the fluence map with the same resolution, the cubic spline interpolation and the bicubic interpolation are almost equally best interpolation methods while the nearest neighbor interpolation is the worst.For example, for 5 mm distance fluence maps, γ≤1 are 98.12±2.28%, 99.48±0.66%, 99.45±0.65% and 82.23±0.48% for the bilinear, the cubic spline, the bicubic, and the nearest neighbor interpolation, respectively. For 7 mm distance fluence maps, γ≤1 are 90.87±5.91%, 90.22±6.95%, 91.79±5.97% and 71.93±4.92 for the bilinear, the cubic spline, the bicubic, and the nearest neighbor interpolation, respectively. Conclusion: We recommend that the 2-dimensional detector array with high spatial resolution should be used as an IMRT QA tool and that the measured fluence maps should be interpolated using by the cubic spline interpolation or the bicubic interpolation for head and neck IMRT delivery. This work was supported by Radiation Technology R&D program through the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning (No. 2013M2A2A7038291)

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-498: A Comparative Evaluation of 6MV Flatten Beam and Flattening Filter Free Photon Beam in Carcinoma Breast

Purpose: Aim of the current study is to look plan quality, treatment beam ON time for IMRT using 6MV FB (Flatten Beam) and FFFB (Flattening Filter Free Beam) in left breast cancer cases. Methods: Ten left breast cancer patients treated with breast conserving surgical (BCS) procedure approach and adjuvant radiotherapy were selected from the department database. Simultaneous Integrated boost (SIB) technique was used to irradiate the total left breast (PTV) to a dose of 50.40Gy with concomitant enhance to the lumpectomy cavity known as gross tumour volume (GTV) to a dose of 59.40Gy in 28 fractions. Plans 6MV FB IMRT and 6MV FFFB IMRT had been generated to achieve dose to 95% target volume (TV) and spare Organ at risks (OAR’s). Homogeneity index (HI), conformity index (CI), treatment monitor unit (MU),normal tissues integral dose (NTID) and low dose volume of normal tissue were compared. Results: There was no statistically huge difference among the plans with respect to target volume coverage, CI HI, Ipsilateral Lung and Breast. But statistically significant difference (p< 0.05) as observed in Heart, V5Gy of Contralateral Lung, MU’s NTID and low dose volume of normal tissue. Conclusion: 6MV FB and FFF beam produce almost equivalent plans in IMRT modality with admire to target volume coverage, HI, CI. Beam on time and NTID was determined to be much less in 6MV FFFB IMRT. FFF beam leads to a time saving treatment delivery and fewer NTID in cancer of left breast cases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-526: A Comparative Study On Gating Efficiency of Varian RPM Device and Calypso System

Purpose: In general, the linear accelerator is gated using respiratory signal obtained by way of external sensors to account for the breathing motion during radiotherapy. One of the commonly used gating devices is the Varian RPM device. Calypso system that uses electromagnetic tracking of implanted or surface transponders could also be used for gating. The aim of this study is to compare the gating efficiency of RPM device and the calypso system by phantom studies. Methods: An ArcCheck insert was used as the phantom with a Gafchromic film placed in its holder. The ArcCheck insert was placed on a Motion Sim platform and moved in the longitudinal direction simulating a respiratory motion with a period of 5 seconds and amplitude of ±6mm. The Gafchromic film was exposed to a 2 × 2cm{sup 2} field, i) with the phantom static, ii) phantom moving but ungated iii) gated with gating window of 2mm and 3mm. This was repeated with Calypso system using surface transponders with the same gating window. The Gafchromic films were read with an EPSON 11000 flatbed scanner and analysed with ‘Medphysto’ software. Results: The full width at half maximum (FWHM) as measured with film at the level of the film holder was 1.65cm when the phantom was static. FWHM measured with phantom moving and without gating was 1.16 cm and penumbra was 7 mm (80–20%) on both sides. When the beam was gated with 2 mm gating window the FWHM was 1.8 cm with RPM device and 1.9 cm with Calypso. Similarly, when the beam was gated with 3 mm window, the FWHM was 1.9cm with RPM device and 2cm with Calypso. Conclusion: This work suggests that the gating efficiency of RPM device is better than that of the Calypso with surface transponder, with reference to the latency in gating.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TU-H-CAMPUS-TeP1-02: Seated Treatment: Setup Uncertainty Comparable to Supine

Purpose: For some head and neck patients, positioning in the supine position is not well tolerated. For these patients, treatment in a seated position would be preferred. We have evaluated inter- and intra- fraction uncertainty of patient set-up in a novel treatment chair which is compatible with modern linac designs. Methods: Five head-and-neck cancer patients were positioned in the chair, fitted with immobilization devices, and imaged with orthogonal X-rays. The couch (with chair attached) was rotated to simulate delivery (without actual treatment), another set of images were acquired, providing a measure of intra-fraction displacement. The patient then got off of and back onto the chair and the process was repeated, thus providing a measure of inter-fraction set-up uncertainty. Six sub-regions in the head-and-neck were rigidly registered to evaluate local intra- and interfraction displacement. Image guidance was simulated by first registering one sub-region; the residual displacement of other sub-regions was then measured. Additionally, a patient questionnaire was administered to evaluate tolerance of the seated position. Results: The chair design is such that all advantages of couch motions may be utilized. Average inter- and intrafraction displacements of all sub-regions in the seated position were less than 2 and 3 mm, respectively. When image guidance was simulated, interfraction displacements were reduced by an average of 4 mm, providing comparable setup to the supine position. The enrolled patients, who had no indication for a seated treatment position, reported no preference for the seated or the supine position. Conclusion: The novel chair design provides acceptable inter- and intra-fraction displacement, with reproducibility similar to that observed for patients in the supine position. Such a chair will be utilized for patients who cannot tolerate the supine position and use with CBCT images for planning, in a fixed-beam linac system, and for other treatment sites is under investigation. Funding: Varian Medical Systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Sensitive detection of structural dynamics using a statistical framework for comparative crystallography

Chemical and conformational changes are crucial to protein function and its pharmacological control. X-ray crystallography can reveal these changes in atomic detail, but standard analysis methods, which refine separate datasets, often overlook differences that are subtle or arise in only a subset of molecules. Direct comparison of crystallographic datasets is, in principle, more powerful, but systematic errors (“scales”) often mask changes in the crystallographic observables (“structure factors”). Machine learning algorithms that jointly estimate scales and structure factors can address this limitation. Here, we augment this approach with multivariate, structured priors derived from crystallographic theory, implemented in the variational deep learning framework Careless. Doing so strongly improves the detection of protein dynamics, element-specific anomalous signals, and the binding of drug candidates, offering a robust approach to comparative crystallography and, potentially, to detection of protein dynamics by other structure determination methods.

Hekstra, Doeke R. [Harvard Univ., Cambridge, MA (U↗
DOE OSTI2024

Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties

KRAS, the most frequently mutated oncogene in human cancer, produces two isoforms, KRAS4a and KRAS4b, through alternative splicing. These isoforms differ in exon 4, which encodes the final 15 residues of the G-domain and hypervariable regions (HVRs), vital for trafficking and membrane localization. While KRAS4b has been extensively studied, KRAS4a has been largely overlooked. Our multidisciplinary study compared the structural and functional characteristics of KRAS4a and KRAS4b, revealing distinct structural properties and thermal stability. Position 151 influences KRAS4a’s thermal stability, while position 153 affects binding to RAF1 CRD protein. Nuclear magnetic resonance analysis identified localized structural differences near sequence variations and provided a solution-state conformational ensemble. Notably,KRAS4aexhibits substantial transcript abundance in bile ducts, liver, and stomach, with transcript levels approachingKRAS4bin the colon and rectum. Functional disparities were observed in full-length KRAS variants, highlighting the impact of HVR variations on interaction with trafficking proteins and downstream effectors like RAF and PI3K within cells.

Science & Technology - Other Topics↗
DOE OSTI2025

Comparing photosynthetic light harvesting of single photons and pseudothermal light under ultraweak illumination

Photosynthesis in vivo is driven by sunlight, an ultraweak incoherent thermal source. However, most experiments and theories have studied photosynthetic light harvesting driven by strong coherent laser sources. The quantum states of light are characterized by their photon statistics, in addition to classical properties such as intensity and frequency spectrum. Here, we report experiments that investigate how photon statistics affect a natural photosynthetic system and vice versa. We directly compare how single photons and pseudothermal light from spontaneous parametric down-conversion drive light harvesting in the light-harvesting 2 complex from a purple bacterium. We find that the fluorescence lifetime and quantum efficiency are unchanged while the fluorescence photon statistics are markedly different, resembling that of the incident light, implying that the dynamics do not fundamentally modify the photon statistics. This represents a step toward clarification of the similarities and differences between photosynthetic light harvesting in laboratory and in natural sunlight conditions.

Li, Quanwei [University of California, Berkeley, C↗
DOE OSTI2015

Comparative Analysis of Extremely Thermophilic Caldicellulosiruptor Species Reveals Common and Unique Cellular Strategies for Plant Biomass Utilization

Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70 degrees C to simple sugars, acetate, lactate, CO2, and H-2. Caldicellulosiruptor bescii, C. kronotskyensis, and C. saccharolyticus solubilized 38%, 36%, and 29% (by weight) of unpretreated switchgrass (Panicum virgatum) (5 g/liter), respectively, which was about half of the amount of crystalline cellulose (Avicel; 5 g/liter) that was solubilized under the same conditions. The lower yields with C. saccharolyticus, not appreciably greater than the thermal control for switchgrass, were unexpected, given that its genome encodes the same glycoside hydrolase 9 (GH9)-GH48 multidomain cellulase (CelA) found in the other two species. However, the genome of C. saccharolyticus lacks two other cellulases with GH48 domains, which could be responsible for its lower levels of solubilization. Transcriptomes for growth of each species comparing cellulose to switchgrass showed that many carbohydrate ABC transporters and multidomain extracellular glycoside hydrolases were differentially regulated, reflecting the heterogeneity of lignocellulose. However, significant differences in transcription levels for conserved genes among the three species were noted, indicating unexpectedly diverse regulatory strategies for deconstruction for these closely related bacteria. Genes encoding the Che-type chemotaxis system and flagellum biosynthesis were upregulated in C. kronotskyensis and C. bescii during growth on cellulose, implicating motility in substrate utilization. The results here show that capacity for plant biomass deconstruction varies across Caldicellulosiruptor species and depends in a complex way on GH genome inventory, substrate composition, and gene regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins ($ T\overline{a}pirins\ $) from Extremely Thermophilic Caldicellulosiruptor Species

Genomes of extremely thermophilic Caldicellulosiruptor species encode novel cellulose binding proteins, called $ t\overline{a}pirins\ $, located proximate to the type IV pilus locus. The C-terminal domain of Caldicellulosiruptor kronotskyensis $ t\overline{a}pirin\ $ 0844 (Calkro_0844) is structurally unique and has a cellulose binding affinity akin to that seen with family 3 carbohydrate binding modules (CBM3s). Here, full-length and C-terminal versions of $ t\overline{a}pirins\ $ from Caldicellulosiruptor bescii (Athe_1870), Caldicellulosiruptor hydrothermalis (Calhy_0908), Caldicellulosiruptor kristjanssonii (Calkr_0826), and Caldicellulosiruptor naganoensis (NA10_0869) were produced recombinantly in Escherichia coli and compared to Calkro_0844. All five $ t\overline{a}pirins\ $ bound to microcrystalline cellulose, switchgrass, poplar, and filter paper but not to xylan. Densitometry analysis of bound protein fractions visualized by SDS-PAGE revealed that Calhy_0908 and Calkr_0826 (from weakly cellulolytic species) associated with the cellulose substrates to a greater extent than Athe_1870, Calkro_0844, and NA10_0869 (from strongly cellulolytic species). Perhaps this relates to their specific needs to capture glucans released from lignocellulose by cellulases produced in Caldicellulosiruptor communities. Calkro_0844 and NA10_0869 share a higher degree of amino acid sequence identity (>80% identity) with each other than either does with Athe_1870 (~50%). The levels of amino acid sequence identity of Calhy_0908 and Calkr_0826 to Calkro_0844 were only 16% and 36%, respectively, although the three-dimensional structures of their C-terminal binding regions were closely related. Unlike the parent strain, C. bescii mutants lacking the $ t\overline{a}pirin\ $ genes did not bind to cellulose following short-term incubation, suggesting a role in cell association with plant biomass. Given the scarcity of carbohydrates in neutral terrestrial hot springs, $ t\overline{a}pirins\ $ likely help scavenge carbohydrates from lignocellulose to support growth and survival of Caldicellulosiruptor species.The mechanisms by which microorganisms attach to and degrade lignocellulose are important to understand if effective approaches for conversion of plant biomass into fuels and chemicals are to be developed. Caldicellulosiruptor species grow on carbohydrates from lignocellulose at elevated temperatures and have biotechnological significance for that reason. Novel cellulose binding proteins, called $ t\overline{a}pirins\ $, are involved in the way that Caldicellulosiruptor species interact with microcrystalline cellulose, and additional information about the diversity of these proteins across the genus, including binding affinity and three-dimensional structural comparisons, is provided here.

09 BIOMASS FUELS↗
DOE OSTI2019

Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities

Plant polysaccharide breakdown by microbes in the rumen is fundamental to digestion in ruminant livestock. Bacterial species belonging to the rumen genera Butyrivibrio and Pseudobutyrivibrio are important degraders and utilizers of lignocellulosic plant material. These bacteria degrade polysaccharides and ferment the released monosaccharides to yield short-chain fatty acids that are used by the ruminant for growth and the production of meat, milk, and fiber products. Although rumen Butyrivibrio and Pseudobutyrivibrio species are regarded as common rumen inhabitants, their polysaccharide-degrading and carbohydrate-utilizing enzymes are not well understood. In this study, we analyzed the genomes of 40 Butyrivibrio and 6 Pseudobutyrivibrio strains isolated from the plant-adherent fraction of New Zealand dairy cows to explore the polysaccharide-degrading potential of these important rumen bacteria. Comparative genome analyses combined with phylogenetic analysis of their 16S rRNA genes and short-chain fatty acid production patterns provide insight into the genomic diversity and physiology of these bacteria and divide Butyrivibrio into 3 species clusters. Rumen Butyrivibrio bacteria were found to encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) and binding proteins. In total, 4,421 glycoside hydrolases (GHs), 1,283 carbohydrate esterases (CEs), 110 polysaccharide lyases (PLs), 3,605 glycosyltransferases (GTs), and 1,706 carbohydrate-binding protein modules (CBM) with predicted activities involved in the depolymerization and transport of the insoluble plant polysaccharides were identified. Butyrivibrio genomes had similar patterns of CAZyme families but varied greatly in the number of genes within each category in the Carbohydrate-Active Enzymes database (CAZy), suggesting some level of functional redundancy. These results suggest that rumen Butyrivibrio species occupy similar niches but apply different degradation strategies to be able to coexist in the rumen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Comparative Genomics Guides Elucidation of Vitamin B 12 Biosynthesis in Novel Human-Associated Akkermansia Strains

Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most humans and is considered a “next-generation probiotic.” However, knowledge of the genomic and physiological diversity of human-associated Akkermansia sp. strains is limited. Here, we reconstructed 35 metagenome-assembled genomes and combined them with 40 publicly available genomes for comparative genomic analysis. We identified at least four species-level phylogroups (AmI to AmIV), with distinct functional potentials. Most notably, we identified genes for cobalamin (vitamin B 12 ) biosynthesis within the AmII and AmIII phylogroups. To verify these predictions, 10 Akkermansia strains were isolated from adults and screened for vitamin B 12 biosynthesis genes via PCR. Two AmII strains were positive for the presence of cobalamin biosynthesis genes, while all 9 AmI strains tested were negative. To demonstrate vitamin B 12 biosynthesis, we measured the production of acetate, succinate, and propionate in the presence and absence of vitamin supplementation in representative strains of the AmI and AmII phylogroups, since cobalamin is an essential cofactor in propionate metabolism. Results showed that the AmII strain produced acetate and propionate in the absence of supplementation, which is indicative of vitamin B 12 biosynthesis. In contrast, acetate and succinate were the main fermentation products for the AmI strains when vitamin B 12 was not supplied in the culture medium. Lastly, two bioassays were used to confirm vitamin B 12 production by the AmII phylogroup. This novel physiological trait of human-associated Akkermansia strains may affect how these bacteria interact with the human host and other members of the human gut microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis

ABSTRACT The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus -associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida . Genes specific to Populus -associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens , which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Comparative Genomics of Early-Diverging Brucella Strains Reveals a Novel Lipopolysaccharide Biosynthesis Pathway

Volume 3, no. 5, doi:10.1128/mBio.00246-12, 2012. After careful review of Fig. 3, the accuracy of the electrophoretic profiles of the control lipopolysaccharides (LPSs) was called into question compared to profiles of similar LPSs analyzed by M. S. Zygmunt et al. (Clin. Vaccine Immunol. 19:1370 –1373, 2012). After further gel experimentation, it was confirmed that the profiles of the control LPSs in Fig. 3 only were not correct. The revised Fig. 3 (below) shows the correct profiles of the LPSs of strains 2308 and BO1. We thank Axel Cloeckaert for notifying us of this issue.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Comparative genomics and stable isotope analysis reveal the saprotrophic-pathogenic lifestyle of a neotropical fungus

In terrestrial forested ecosystems, fungi may interact with trees in at least three distinct ways: (i) associated with roots as symbionts; (ii) as pathogens in roots, trunks, leaves, flowers, and fruits; or (iii) decomposing dead tree tissues on soil or even on dead tissues in living trees. Distinguishing the latter two nutrition modes is rather difficult in Hymenochaetaceae (Basidiomycota) species. Herein, we have used an integrative approach of comparative genomics, stable isotopes, host tree association, and bioclimatic data to investigate the lifestyle ecology of the scarcely known neotropical genus Phellinotus, focusing on the unique species Phellinotus piptadeniae. This species is strongly associated with living Piptadenia gonoacantha (Fabaceae) trees in the Atlantic Forest domain on a relatively high precipitation gradient. Phylogenomics resolved P. piptadeniae in a clade that also includes both plant pathogens and typical wood saprotrophs. Furthermore, both genome-predicted Carbohydrate-Active Enzymes (CAZy) and stable isotopes (δ 13 C and δ 15 N) revealed a rather flexible lifestyle for the species. Altogether, our findings suggest that P. piptadeniae has been undergoing a pathotrophic specialization in a particular tree species while maintaining all the metabolic repertoire of a wood saprothroph.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Comparative Assessment of Severe Acute Respiratory Syndrome Coronavirus 2 Variants in the Ferret Model

The continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans necessitates evaluation of variants for enhanced virulence and transmission. We used the ferret model to perform a comparative analysis of four SARS-CoV-2 strains, including an early pandemic isolate from the United States (WA1), and representatives of the Alpha, Beta, and Delta lineages. While Beta virus was not capable of pronounced replication in ferrets, WA1, Alpha, and Delta viruses productively replicated in the ferret upper respiratory tract, despite causing only mild disease with no overt histopathological changes. Strain-specific transmissibility was observed; WA1 and Delta viruses transmitted in a direct contact setting, whereas Delta virus was also capable of limited airborne transmission. Viral RNA was shed in exhaled air particles from all inoculated animals but was highest for Delta virus. Prior infection with SARS-CoV-2 offered varied protection against reinfection with either homologous or heterologous variants. Notable genomic variants in the spike protein were most frequently detected following WA1 and Delta virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Comparative Molecular and Immunoregulatory Analysis of Extracellular Vesicles from Candida albicans and Candida auris

Candida auris is a recently described multidrug-resistant pathogenic fungus that is increasingly responsible for health care-associated outbreaks across the world. Bloodstream infections of this fungus cause death in up to 70% of cases. Aggravating this scenario, the disease-promoting mechanisms of C. auris are poorly understood. Fungi release extracellular vesicles (EVs) that carry a broad range of molecules, including proteins, lipids, carbohydrates, pigments, and RNA, many of which are virulence factors. Here, we carried out a comparative molecular characterization of C. auris and Candida albicans EVs and evaluated their capacity to modulate effector mechanisms of host immune defense. Using proteomics, lipidomics, and transcriptomics, we found that C. auris released EVs with payloads that were significantly different from those of EVs released by C. albicans. EVs released by C. auris potentiated the adhesion of this yeast to an epithelial cell monolayer, while EVs from C. albicans had no effect. C. albicans EVs primed macrophages for enhanced intracellular yeast killing, whereas C. auris EVs promoted survival of the fungal cells. Moreover, EVs from both C. auris and C. albicans induced the activation of bone marrow-derived dendritic cells. Together, our findings show distinct profiles and properties of EVs released by C. auris and by C. albicans and highlight the potential contribution of C. auris EVs to the pathogenesis of this emerging pathogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Influenza A Virus Multicycle Replication Yields Comparable Viral Population Emergence in Human Respiratory and Ocular Cell Types

While primarily considered a respiratory pathogen, influenza A virus (IAV) is nonetheless capable of spreading to, and replicating in, numerous extrapulmonary tissues in humans. However, within-host assessments of genetic diversity during multicycle replication have been largely limited to respiratory tract tissues and specimens. As selective pressures can vary greatly between anatomical sites, there is a need to examine how measures of viral diversity may vary between influenza viruses exhibiting different tropisms in humans, as well as following influenza virus infection of cells derived from different organ systems. Here, we employed human primary tissue constructs emulative of the human airway or corneal surface, and we infected both with a panel of human- and avian-origin IAV, inclusive of H1 and H3 subtype human viruses and highly pathogenic H5 and H7 subtype viruses, which are associated with both respiratory disease and conjunctivitis following human infection. While both cell types supported productive replication of all viruses, airway-derived tissue constructs elicited greater induction of genes associated with antiviral responses than did corneal-derived constructs. We used next-generation sequencing to examine viral mutations and population diversity, utilizing several metrics. With few exceptions, generally comparable measures of viral diversity and mutational frequency were detected following homologous virus infection of both respiratory-origin and ocular-origin tissue constructs. Expansion of within-host assessments of genetic diversity to include IAV with atypical clinical presentations in humans or in extrapulmonary cell types can provide greater insight into understanding those features most prone to modulation in the context of viral tropism.

59 BASIC BIOLOGICAL SCIENCES↗