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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation

Aureobasidium pullulans is a yeast-like fungus with remarkable phenotypic plasticity widely studied for its importance for the pharmaceutical and food industries. So far, genomic studies with strains from all over the world suggest they constitute a genetically unstructured population, with no association by habitat. However, the mechanisms by which this genome supports so many phenotypic permutations are still poorly understood. Recent works have shown the importance of sequencing yeast genomes from extreme environments to increase the repertoire of phenotypic diversity of unconventional yeasts. In this study, we present the genomic draft of A. pullulans strain from a Patagonian yeast diversity hotspot, re-evaluate its taxonomic classification based on taxogenomic approaches, and annotate its genome with high-depth transcriptomic data. Here, our analysis suggests this isolate could be considered a novel variant at an early stage of the speciation process. The discovery of divergent strains in a genomically homogeneous group, such as A. pullulans, can be valuable in understanding the evolution of the species. The identification and characterization of new variants will not only allow finding unique traits of biotechnological importance, but also optimize the choice of strains whose phenotypes will be characterized, providing new elements to explore questions about plasticity and adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. nov.

A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446T (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Taxogenomic Analysis of a Novel Yeast Species, Lachancea rosae Sp. Nov. F.A., Isolated From the Wild Rose Rosa californica

A novel Saccharomycotina yeast strain, yHQL494, was isolated from the rose hip of the wild rose Rosa californica from Castle Crags State Park, California, USA. Phylogenetic analyses of both whole genome data and the sequences from the D1/D2 region of the large ribosomal subunit (LSU) rRNA gene placed strain yHQL494 within the genus Lachancea and grouped it into a clade with Lachancea lanzarotensis and Lachancea meyersii. Taxogenomic analyses were conducted on publicly available genome sequences to gain a deeper insight into the carbon and nitrogen gene-trait associations across the Lachancea clade. The results of these analyses were found to be consistent across Lachancea species. Growth assays and microscopic analyses were conducted to determine the physiological characteristics of strain yHQL494, including the presence of hyphae or pseudohyphae, ascospore formation, fermentation abilities, and assimilation of carbon and nitrogen compounds. Based on the phenotypic and genomic characteristics of the strain yHQL494 T (=NRRL Y-64858 T , =CBS 18,574 T ), we propose a new species, Lachancea rosae sp. nov. f.a.

Bajgain, Yakendra [Villanova Univ., PA (United Sta↗
DOE OSTI2020

Chapter 5: Methods for Algal Protein Isolation and Proteome Analysis

Microalgae present promising feedstocks to produce renewable fuel and chemical intermediates, in part due to high storage carbon flux capacity to triacylglycerides or storage carbohydrates upon nutrient deprivation. However, the mechanism(s) governing deprivation-mediated carbon partitioning remain to be fully elucidated, limiting targeted strain engineering strategies in algal biocatalysts. Though genomic and transcriptomic analyses offer key insights into these mechanisms, active post-transcriptional regulatory mechanisms, ubiquitous in many microalgae, necessitate proteomic and post-translational (e.g., phospho- and nitroso-proteomic) analyses to more completely evaluate algal responsiveness to nutrient deprivation. Herein, we describe methods for isolating total algal protein and conducting proteomic, phosphoproteomic, and nitrosoproteomic analyses. We focus on methods deployed for the chlorophyte, Chlorella vulgaris, a model oleaginous alga with high flux to renewable fuel and chemical precursors.

BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS↗
DOE OSTI2023

Search for new phenomena in multi-body invariant masses in events with at least one isolated lepton and two jets using $\sqrt{s}$ = 13 TeV proton–proton collision data collected by the ATLAS detector

A search for resonances in events with at least one isolated lepton (e or μ ) and two jets is performed using 139 fb -1 of $\sqrt{s}$ = 13 TeV proton–proton collision data recorded by the ATLAS detector at the LHC. Deviations from a smoothly falling background hypothesis are tested in three- and four-body invariant mass distributions constructed from leptons and jets, including jets identified as originating from bottom quarks. Model-independent limits on generic resonances characterised by cascade decays of particles leading to multiple jets and leptons in the final state are presented. The limits are calculated using Gaussian shapes with different widths for the invariant masses. The multi-body invariant masses are also used to set 95% confidence level upper limits on the cross-section times branching ratios for the production and subsequent decay of resonances predicted by several new physics scenarios.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Measurement of the production cross section of pairs of isolated photons in pp collisions at 13 TeV with the ATLAS detector

A measurement of prompt photon-pair production in proton-proton collisions at $\sqrt{s}$ = 13 TeV is presented. The data were recorded by the ATLAS detector at the LHC with an integrated luminosity of 139 fb -1 . Events with two photons in the well-instrumented region of the detector are selected. The photons are required to be isolated and have a transverse momentum of p T, γ1(2) > 40 (30) GeV for the leading (sub-leading) photon. The differential cross sections as functions of several observables for the diphoton system are measured and compared with theoretical predictions from state-of-the-art Monte Carlo and fixed-order calculations. The QCD predictions from next-to-next-to-leading-order calculations and multi-leg merged calculations are able to describe the measured integrated and differential cross sections within uncertainties, whereas lower-order calculations show significant deviations, demonstrating that higher-order perturbative QCD corrections are crucial for this process. The resummed predictions with parton showers additionally provide an excellent description of the low transverse-momentum regime of the diphoton system.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Deconstruction of plant biomass by a Cellulomonas strain isolated from an ultra-basic (lignin-stripping) spring

Plant material falling into the ultra-basic (pH 11.5-11.9) springs within The Cedars, an actively serpentinizing site in Sonoma County, California, is subject to conditions that mimic the industrial pretreatment of lignocellulosic biomass for biofuel production. In this research, we sought to obtain hemicellulolytic/cellulolytic bacteria from The Cedars springs that are capable of withstanding the extreme alkaline conditions wherein calcium hydroxide-rich water removes lignin, making cell wall polysaccharides more accessible to microorganisms and their enzymes. We enriched for such bacteria by adding plant debris from the springs into a synthetic alkaline medium with ground tissue of the biofuel crop switchgrass (Panicum virgatum L.) as the sole source of carbon. From the enrichment culture we isolated the facultative anaerobic bacterium Cellulomonas sp. strain FA1 (NBRC 114238), which tolerates high pH and catabolizes the major plant cell wall-associated polysaccharides cellulose, pectin, and hemicellulose. Strain FA1 in monoculture colonized the plant material and degraded switchgrass at a faster rate than the community from which it was derived. Cells of strain FA1 could be acclimated through subculturing to grow at a maximal concentration of 13.4% ethanol. A strain FA1-encoded β-1, 4-endoxylanase expressed in E. coli was active at a broad pH range, displaying near maximal activity at pH 6-9. Discovery of this bacterium illustrates the value of extreme alkaline springs in the search for microorganisms with potential for consolidated bioprocessing of plant biomass to biofuels and other valuable bio-inspired products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Isolation and characterization of lignocellulosic nanofibers from four kinds of organosolv-fractionated lignocellulosic materials

The objective of this research was to investigate the presence of residual lignin in cellulose fibers on the efficiency and energy consumption during nanofibers processing. Four kinds of lignin-containing cellulose nanofibers (LCNFs) from switchgrass, yellow poplar, hybrid poplar, and pine, respectively, were isolated via organosolv fractionation coupling mechanical grinding. Nanofibrils were observed after organosolv fractionation. The details of their morphological features, chemical structures, water retention value (WRV), and thermal degradation characteristics were revealed and compared. Mean diameters of nanofibers separated from switchgrass, yellow poplar, hybrid poplar, and pine were 27.9 nm, 25.4 nm, 24.6 nm, and 21.5 nm, respectively. The presence of lignin for the four types of LCNFs led to a decrease in energy consumption and an increase in WRV, among which pine nanofibers show the best with an average energy consumption of 0.511 kWh/kg and a WRV of 537%. It was also demonstrated that increasing lignin content for LCNFs could contribute to the sample’s thermal stability. In conclusion, exact benefits of residual lignin for nanofiber will facilitate its preparation process and extend its application.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Improved high-throughput screening technique to rapidly isolate Chlamydomonas transformants expressing recombinant proteins

Abstract The single-celled eukaryotic green alga Chlamydomonas reinhardtii has long been a model system for developing genetic tools for algae, and is also considered a potential platform for the production of high-value recombinant proteins. Identifying transformants with high levels of recombinant protein expression has been a challenge in this organism, as random integration of transgenes into the nuclear genome leads to low frequency of cell lines with high gene expression. Here, we describe the design of an optimized vector for the expression of recombinant proteins in Chlamydomonas , that when transformed and screened using a dual antibiotic selection, followed by screening using fluorescence activated cell sorting (FACS), permits rapid identification and isolation of microalgal transformants with high expression of a recombinant protein. This process greatly reduces the time required for the screening process, and can produce large populations of recombinant algae transformants with between 60 and 100% of cells producing the recombinant protein of interest, in as little as 3 weeks, that can then be used for whole population sequencing or individual clone analysis. Utilizing this new vector and high-throughput screening (HTS) process resulted in an order of magnitude improvement over existing methods, which normally produced under 1% of algae transformants expressing the protein of interest. This process can be applied to other algal strains and recombinant proteins to enhance screening efficiency, thereby speeding up the discovery and development of algal-derived recombinant protein products. Key points • A protein expression vector using double-antibiotic resistance genes was designed • Double antibiotic selection causes fewer colonies with more positive for phenotype • Coupling the new vector with FACS improves microalgal screening efficiency > 60%

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Pseudomonas atagosis sp. nov., and Pseudomonas akappagea sp. nov., New Soil Bacteria Isolated from Samples on the Volcanic Island Izu Oshima, Tokyo

During the exploration of microbial natural resources, two strains of Pseudomonas, PS14 T and PS24 T , were isolated from samples taken from Izu Oshima, a volcanic island located 120 km southwest of central Tokyo. Phylogenetic analysis based on 16S rRNA gene sequences showed that PS14 T was most similar to Pseudomonas baetica a390T (99.6%) and Pseudomonas helmanticensis OHA11 T (99.5%), and that PS24T was most similar to Pseudomonas qingdaonensis JJ3 T (98.8%) and Pseudomonas lutea OK2 T (98.7%). The major fatty acids of these two strains were C 16:0 and C 17:0 cyclo, summed feature 3 (C 16:1 ω6c and/or C 16:1 ω7c), and summed feature 8 (C18:1 ω7c and/or 18:1 ω6c). The phylogenetic analyses, DNA-DNA hybridization results and phenotypic traits indicated that PS14 T and PS24 T constitute two novel species, Pseudomonas atagosis sp. nov. (type strain PS14 T = CECT 9940 T , = LMG 31496 T ) and Pseudomonas akappagea sp. nov. (type strain PS24T = CECT 9941T, = LMG 31497T), respectively. The sequence data of the draft genomes of PS14 T and PS24 T were deposited in the GenBank database under accession numbers VXCA00000000 and VXCP00000000, respectively, and the sequence data of their 16S rRNA genes were deposited in the GenBank database under accession numbers MN396717 and MN382268, respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Identification, isolation, and characterization of a novel type of Fukushima-derived microparticle

Abstract In the course of the Fukushima nuclear accident, radionuclides were released in various forms, including so-called radiocesium-bearing microparticles (CsMP). So far, four types of CsMP were described: Type A is smaller in size (< 10 μm), Types B, C, and D are larger (> 100 μm). In this work, we present a novel type of CsMP (proclaimed Type E). Three particles of Type E were extracted from a contaminated blade of grass that was sampled 1.5 km from the Fukushima Daiichi nuclear power plant in late 2011. They were located using autoradiography, isolated using an optical microscope and micromanipulator, and characterized using scanning electron microscopy, energy dispersive x-ray spectroscopy, and low-level gamma-ray spectrometry. Type E CsMPs are 10–20 μm in size and exhibit an unusually low and barely detectable 137 Cs activity of only ≤ 10 mBq per particle. Their brittle and fragile character may indicate a high surface tension.

137Cs↗
DOE OSTI2024

Isolation and characterization of microalgae strains able to grow on complex biomass hydrolysate for industrial application

Producing algae biomass economically remains one of the chief bottlenecks for commercializing algae products. The aim of this work is to identify new strains of algae that can grow on cost effective media derived from cellulosic waste streams, characterize the potential of these strains to produce compounds of high industrial value, and identify those strains capable of facile genetic transformation. Here we report, out of 45 strains initially isolated, three were selected based on their ability to efficiently grow on organic waste material (corn stover hydrolysate) as a carbon source; Chlorococcum sp., Desmodesmus sp., and Chlamydomonas debaryana. Untargeted metabolomics was performed on each strain, identifying several metabolites of high relative abundances that are of commercial interest, such as lactic acid, butane-2,3-diol, amino acids, tartaric acid, triacylglycerols, and lipid species containing different, mono- and polyunsaturated fatty acids, depending on the strain and growth condition. The strains also produced carbohydrates of industrial relevance. Chlorococcum sp. was found to be genetically transformable using standard simple transformation protocols. These results suggest that with further development, these strains could open the door to economic production of high value commercial compounds utilizing waste streams from cellulosic biomass.

09 BIOMASS FUELS↗
DOE OSTI2021

Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects

SARS-CoV-2 is one of three coronaviruses that have crossed the animal-to-human barrier and caused widespread disease in the past two decades. The development of a universal human coronavirus vaccine could prevent future pandemics. We characterize 198 antibodies isolated from four COVID-19+ subjects and identify 14 SARS-CoV-2 neutralizing antibodies. One targets the N-terminal domain (NTD), one recognizes an epitope in S2, and 11 bind the receptor-binding domain (RBD). Three anti-RBD neutralizing antibodies cross-neutralize SARS-CoV-1 by effectively blocking binding of both the SARS-CoV-1 and SARS-CoV-2 RBDs to the ACE2 receptor. Using the K18-hACE transgenic mouse model, we demonstrate that the neutralization potency and antibody epitope specificity regulates the in vivo protective potential of anti-SARS-CoV-2 antibodies. All four cross-neutralizing antibodies neutralize the B.1.351 mutant strain. Thus, our study reveals that epitopes in S2 can serve as blueprints for the design of immunogens capable of eliciting cross-neutralizing coronavirus antibodies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Isotope harvesting from a NSCL beam blocker: Isolation of 173,174 lu

A decommissioned beam blocker from the National Superconducting Cyclotron Laboratory was processed for recovery of long-lived Lu radioisotopes at Lawrence Livermore National Laboratory. The beam blocker was a W alloy that had built up considerable levels of activation from high energy particle irradiation over the course of 20 years. The isolation of 173,174 Lu from the bulk material required a complex chemical separation scheme due to the large mass and the wide variety of elements present. The final yield of 173,174 Lu was 76.7 ± 4.8% with an extremely high radiopurity and chemical purity. The reduction in W mass from the initial material to the final sample was 8 × 10 10 . In conclusion, the results show great promise for extracting large quantities of Lu radioisotopes from these types of W beam blockers at the Facility for Rare Isotope Beams, which will be irradiated at levels significantly higher than the beam blocker investigated here.

and nuclear chemistry↗
DOE OSTI2020

Single crystal yield criterion for chromium based on atomistic studies of isolated 1/2[111] screw dislocations

Using the recently developed Bond Order Potential for Cr, we investigate the mobility of isolated 1/2[111] screw dislocations under stress at 0 K. These studies provide the dependence of the critical resolved shear stress (i.e., the Peierls stress) on the orientation of the maximum resolved shear stress plane and on the shear stress perpendicular to the slip direction. Similar studies are made for loading in tension and compression to show that the onset of yielding in Cr single crystals can be described using a combination of the shear stresses parallel and perpendicular to the slip direction. Based on these results, we develop a single crystal yield criterion for Cr that includes all non-Schmid contributions to the Peierls stress. This criterion is used to predict the shape of the yield surface and compare it with the regular Tresca's hexagon arising from the Schmid law. For all directions of uniaxial load, the criterion is used to quantify the character and magnitude of the tension-compression asymmetry.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Investigation of the alkaline hydrogen peroxide pretreatment: From cellulose saccharification to lignin isolation

Alkaline hydrogen peroxide (AHP) pretreatment, a green and effective technology for biomass fractionation, was studied to overcome the recalcitrance of bamboo for lignin isolation and facilitating enzymatic saccharification. In order to explore the impact of AHP pretreatment on the cellulose saccharification of bamboo, the glucan/xylan recovery, lignin removal, and structural properties of solid substrate were investigated in this research. AHP pretreatment at 90 °C for 60 min with 3.0 % H 2 O 2 resulted in the maximum glucan/xylan hydrolysis yield reaching 90.62 % and 88.30 %, respectively. Specially, for the first time, the recovered lignin from the AHP liquid possesses up to 59.84/100Ar of β-O-4 linkages, abundant ferulic acid (FA), and p-coumarate (pCE) structures, as well as a homogeneous molecular structure with high purity (84.04%-96.20%) and preferable antioxidant activities (IC50: 0.015–0.018 mg/mL). Finally, these results provided theoretical support for the comprehensive valorization of lignocellulose, which is favorable for achieving viable biorefineries.

09 BIOMASS FUELS↗
DOE OSTI2023

Efficacy of antivirals and mRNA vaccination against an XBF clinical isolate

Recombination events occur frequently in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in genetic diversity. Because these events contribute to altered host immune evasion and antiviral susceptibility, it is crucial to evaluate the efficacy of COVID-19 vaccines and antivirals against recombinant variants. As of March 2023, XBB.1.5, a recombinant sublineage of XBB, is currently the dominant form globally (Fig. S1A, Supplementary Appendix). XBB emerged as a result of recombination between two BA.2 descendants, BJ.1 and BM.1.1.1 (a progeny of BA.2.75). We and other groups have shown that XBB.1.5 is resistant to several therapeutic monoclonal antibodies and effectively evades humoral immunity elicited by natural infection or COVID-19 vaccination.1, 2, 3 By March 30, 2023, an additional recombinant variant, XBF, had been sampled 8966 times in 47 countries and territories in GISAID, reaching it highest prevalence in Australia and New Zealand (Fig. S2, Supplementary Appendix). XBF is still increasing in frequency, although the prevalence of XBB.1.5 appears to be increasing at a faster pace in most regions (Fig. S1B, Supplementary Appendix). XBF is a recombinant of BA.5.2.3 (a descendant of BA.5) and CJ.1 (a descendant of BA.2.75) and, like CJ.1, has an additional three substitutions (R346T, F486P, and F490S) in the receptor-binding domain (RBD) of the consensus form of its spike protein compared to baseline BA.2.75 (Fig. S3A, Supplementary Appendix). CJ.1 and its related sublineage CJ.1.1 did not expand as extensively as XBF, being sampled in GISAID only 1589 and 142 times respectively. CJ.1 was found circulating in many countries, but most commonly sampled in South Korea, where it is still increasing and has currently reached about 5% of the sampled population. CJ.1.1 was most frequently sampled in Malaysia and Singapore, but remained rare in both nations, peaking at about 1% of the sample in December of 2022. Despite the importance of these related variants, we have no information about the antiviral efficacy and immunity induced by COVID-19 vaccines against a clinical isolate of XBF.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Single and Dual-Solute Transport in Quaternary Ammonium-Functionalized Anion Exchange Membranes: Isolating the Impact of Water Volume Fraction

Membranes are essential components of photoelectrochemical CO 2 reduction cells (PEC-CRC), as they regulate solute transport and impact device efficiency. These cells are a promising approach for converting carbon dioxide into valuable chemicals. However, electrochemical reactions involve not just a single electrolyte; membrane transport typically includes multiple electrolytes. When a mixture of solutes is present, the presence of one solute in the membrane can impact the diffusion and sorption of other solutes. In complex systems where multiple solutes are diffusing simultaneously through a hydrated, dense polymer membrane, the resulting transport behavior is poorly understood. This study highlights the individual and two solute transport behavior of potassium formate, acetate, and bicarbonate ions in neutral membranes and quaternary ammonium-functionalized anion exchange membranes (AEMs) based on phenyl acrylate polymer backbones. By isolating the effect of water content, we emphasize how fixed charge density and solute-membrane interactions influence transport behavior. In neutral membranes, the diffusivity follows the order of potassium formate > potassium acetate > potassium bicarbonate. However, in AEMs, the order shifts due to changes in ion-membrane interactions, with potassium bicarbonate diffusivity surpassing that of potassium acetate. These results underscore the importance of ion exchange membranes and ion-membrane interaction in modulating transport properties, providing valuable insights for optimizing membranes in electrochemical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗