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At least 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Ozonized biochar filtrate effects on the growth of Pseudomonas putida and cyanobacteria Synechococcus elongatus PCC 7942

Background: Biochar ozonization was previously shown to dramatically increase its cation exchange capacity, thus improving its nutrient retention capacity. The potential soil application of ozonized biochar warrants the need for a toxicity study that investigates its effects on microorganisms. Results: In the study presented here, we found that the filtrates collected from ozonized pine 400 biochar and ozonized rogue biochar did not have any inhibitory effects on the soil environmental bacteria Pseudomonas putida, even at high dissolved organic carbon (DOC) concentrations of 300 ppm. However, the growth of Synechococcus elongatus PCC 7942 was inhibited by the ozonized biochar filtrates at DOC concentrations greater than 75 ppm. Further tests showed the presence of some potential inhibitory compounds (terephthalic acid and p-toluic acid) in the filtrate of non-ozonized pine 400 biochar; these compounds were greatly reduced upon wet-ozonization of the biochar material. Nutrient detection tests also showed that dry-ozonization of rogue biochar enhanced the availability of nitrate and phosphate in its filtrate, a property that may be desirable for soil application. Conclusion: Ozonized biochar substances can support soil environmental bacterium Pseudomonas putida growth, since ozonization detoxifies the potential inhibitory aromatic molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Identification, characterization, and structure of a tRNA splicing enzyme RNA 5′-OH kinase from the pathogenic fungi Mucorales

Fungal Trl1 is an essential tRNA splicing enzyme composed of C-terminal cyclic phosphodiesterase and central polynucleotide kinase end-healing domains that convert the 2′,3′-cyclic-PO 4 and 5′-OH ends of tRNA exons into the 3′-OH,2′-PO 4 and 5′-PO 4 termini required for sealing by an N-terminal ATP-dependent ligase domain. Trifunctional Trl1 enzymes are present in most human fungal pathogens and are untapped targets for antifungal drug discovery. Mucorales species, deemed high-priority human pathogens by WHO, elaborate a noncanonical tRNA splicing apparatus in which a stand-alone monofunctional RNA ligase enzyme joins 3′-OH,2′-PO 4 and 5′-PO 4 termini. Here we identify a stand-aloneMucor circinelloidespolynucleotide kinase (MciKIN) and affirm its biological activity in tRNA splicing by genetic complementation in yeast. Recombinant MciKIN catalyzes magnesium-dependent phosphorylation of 5′-OH RNA and DNA ends in vitro. MciKIN displays a strong preference for GTP as the phosphate donor in the kinase reaction, a trait shared with the stand-alone RNA kinase homologs from Mucorales speciesRhizopus azygosporus(RazKIN) andLichtheimia corymbifera(LcoKIN) and with the kinase domains of fungal Trl1 enzymes. We report a 1.65 Å crystal structure of RazKIN in complex with GDP•Mg 2+ that illuminates the basis for guanosine nucleotide specificity.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Metabolic Engineering of the Oleaginous Yeast Yarrowia lipolytica PO1f for Production of Erythritol from Glycerol

Yarrowia lipolytica was found natively to produce erythritol, mannitol, and arabitol during growth on glucose, fructose, mannose, and glycerol. Osmotic stress is known to increase sugar alcohol production, and was found to significantly increase erythritol production during growth on glycerol. To better understand erythritol production from glycerol, since it was the most promising sugar alcohol, we measured the expression of key genes and intracellular metabolites. Osmotic stress increased the expression of several key genes in the glycerol catabolic pathway and the pentose phosphate pathway. Analysis of intracellular metabolites revealed that amino acids, sugar alcohols, and polyamines are produced at higher levels in response to osmotic stress. Heterologous overexpression of the sugar alcohol phosphatase increased erythritol production and glycerol utilization in Y. lipolytica . We further increased erythritol production by increasing the expression of native glycerol kinase (GK), and transketolase (TKL). These data show the growth and titers produced.

Conversion↗
DOE OSTI2025

Data for Phylogenetic diversity of light-dependent phosphorylation of Thr78 in Rubisco activase

Rubisco activase is an ATP-dependent chaperone that facilitates dissociation of inhibitory sugar phosphates from the catalytic sites of Rubisco during photosynthesis. In Arabidopsis, Rubisco activase is negatively regulated by dark-dependent phosphorylation of Thr78. The prevalence of Thr78 in Rubisco activase was investigated across sequences from 91 plant species, finding that 29 (∼32%) species shared a threonine in the same position. Analysis of seven C3 species with an antibody raised against a Thr78 phospho-peptide demonstrated that this position is phosphorylated in multiple genera. However, light-dependent dephosphorylation of Thr78 was observed only in Arabidopsis. Further, phosphorylation of Thr78 could not be detected in any of the four C4 grass species examined. The results suggest that despite conservation of Thr78 in Rubisco activase from a wide range of species, a regulatory role for phosphorylation at this site is more limited. This provides a case study for how variation in post-translational regulation can amplify functional divergence across the phylogeny of plants beyond what is explained by sequence variation in a metabolically important protein.

photosynthesis↗
DOE OSTI2020

Data from Arabidopsis Plants Expressing Only the Redox-Regulated Rca-α Isoform Have Constrained Photosynthesis and Plant Growth

Rubisco activase (Rca) facilitates the release of sugar‐phosphate inhibitors from the active sites of Rubisco and thereby plays a central role in initiating and sustaining Rubisco activation. In Arabidopsis, alternative splicing of a single Rca gene results in two Rca isoforms, Rca‐α and Rca‐β. Redox modulation of Rca‐α regulates the function of Rca‐α and Rca‐β acting together to control Rubisco activation. Although Arabidopsis Rca‐α alone less effectively activates Rubisco in vitro , it is not known how CO2 assimilation and plant growth are impacted. Here, we show that two independent transgenic Arabidopsis lines expressing Rca‐α in the absence of Rca‐β (“Rca‐α only” lines) grew more slowly in various light conditions, especially under low light or fluctuating light intensity, and in a short day photoperiod compared to wildtype. Photosynthetic induction was slower in the Rca‐α only lines, and they maintained a lower rate of CO2 assimilation during both photoperiod types. Our findings suggest Rca oligomers composed of Rca‐α only are less effective in initiating and sustaining the activation of Rubisco than when Rca‐β is also present. Currently there are no examples of any plant species that naturally express Rca‐α only but numerous examples of species expressing Rca‐β only. That Rca‐α exists in most plant species, including many C3 and C4 food and bioenergy crops, implies its presence is adaptive under some circumstances.

Biomass Analytics↗
DOE OSTI2020

Sapphire advanced mitigation process: wet etch to expose sub-surface damage and increase laser damage resistance and mechanical strength

In this study, a novel, to the best of our knowledge, method of wet chemical etching of sapphire workpieces (such as optics, wafers, windows, and cones), called the sapphire advanced mitigation process (or sapphire AMP), has been developed that exposes sub-surface mechanical damage created during the optical fabrication process and significantly enhances the surface laser damage resistance (> 2×) and mechanical strength (up to ~ 2.6×). Sapphire AMP involves first treating the workpiece with a mixture of sulfuric and phosphoric acid ([H 2 SO 4 ]:[H 3 PO 4 ]= 1 : 3) at 220°C, followed with phosphoric acid at 160°C, then with sodium hydroxide base (NaOH) and surfactant at 40°C, and finally with a high-pressure deionized water spray rinse. Sapphire AMP has been demonstrated on both A- and C-plane sapphire workpieces. The mechanism of this etch process involves the reaction of the sapphire (Al 2 O 3 ) surface with sulfuric acid (H 2 SO 4 ) forming aluminum sulfate [Al2(SO4)3], which has low solubility. The high phosphoric acid content in the first and second steps of sapphire AMP results in the efficient conversion of Al 2 (SO 4 ) 3 to aluminum phosphate (AlPO 4 ), which is very soluble, greatly reducing reaction product redeposition on the workpiece surface. Sapphire AMP is shown to expose sub-surface mechanical damage on the sapphire surface created during the grinding and polishing processes, whose etched morphology has either isotropic or anisotropic evolution depending on the nature of the initial surface damage. Sapphire AMP was also designed to remove the key known surface, laser absorbing precursors (namely, foreign chemical impurities, the fracture surface layer of preexisting sub-surface damage, and reaction product or foreign species redeposition or precipitation). Static and sliding indention induced surface microfractures on sapphire are shown after sapphire AMP to have a significant decrease in the fast photoluminescence intensity (a known metric for measuring the degree of laser damaging absorbing precursors). In addition, the onset of laser damage (at 351 nm 3 ns) on sapphire AMP treated workpieces was shown to increase in fluence from ~ 4 to >9.5J/cm 2 . Finally, biaxial ball-on-ring mechanical tests on sapphire disks showed an increase in the failure stress from 340 MPa (with pre-existing 28 µm flaws) to ~ 900MPa after sapphire AMP, which is attributed to the blunting of the surface microfractures.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Impact of the optical parametric amplification phase on laser pulse compression

Optical parametric chirped-pulse amplification (OPCPA) is an effective way to generate ultrashort pulses that has been used extensively for a variety of applications requiring high peak intensities. Precise control and measurement of a system’s spectral and spatial phases are required for Fourier transform–limited pulse compression and diffraction-limited focusing. Phase accumulated during optical parametric amplification (OPA) can degrade the compressibility and focusability of the pulse, reducing peak intensity. We used analytic and numerical analysis of OPA to study the influence of crystal parameters, wavefront of the pump and signal, and their relative optical alignment on the accumulated phase. Here, we show that the accumulated signal phase is largely independent of amplifier saturation and, with significant local wavefront gradients in the signal or pump beam, the quality of the compressed pulses can be degraded. We use first-order expressions for the pump- and signal-angle sensitivity to evaluate an OPCPA system consisting of a highly deuterated potassium dihydrogen phosphate (DKDP) amplifier designed to support bandwidth for 15 fs pulses centered at 920 nm.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Angular dependence of the transverse Raman scattering in KDP and DKDP in geometries suitable for beam polarization control

The angular dependance of the transverse Raman scattering in potassium dihydrogen phosphate (KDP) and its deuterated analogue (DKDP) for the entire range of crystal configurations suitable for laser beam polarization control has been investigated via experimental and modeling tools. This work was made possible by simultaneously rotating a spherical sample and the pump polarization to effectively measure the angular dependance of the transverse Raman signal in 360°. This novel method, which is applicable for the investigation of the Raman scattering in optically anisotropic materials, demonstrates that the spontaneous Raman scattering signal exhibits strong angular dependence that is modulated by depolarization and polarization rotation effects generated as the Raman signal traverses the material due to its birefringence. The results show that the total signal generated by the pump beam is the sum of the signals generated by the two components that have polarization parallel and orthogonal to the optic axis. The peak signal intensity, which is of importance for high-power laser applications, depends on the orientation of the optic axis and can vary by a factor of about 2. The excellent agreement between experimental data and modeling results validates the associated models and enables one to consider optimal crystal cut designs for specific applications.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Final amplifier of an ultra-intense all-OPCPA system with 13-J output signal energy and 41% pump-to-signal conversion efficiency

Optical parametric chirped-pulse amplification (OPCPA) using high-energy Nd:glass lasers has the potential to produce ultra-intense pulses (>10 23 W/cm 2 ). We report on the performance of the final high-efficiency amplifier in an OPCPA system based on large-aperture (63 × 63-mm 2 ) partially deuterated potassium dihydrogen phosphate (DKDP) crystals. The seed beam (180-nm bandwidth, 110 mJ) was provided by the preceding OPCPA stages. A maximum pump-to-signal conversion efficiency of 41% and signal energy up to 13 J were achieved with a 52-mm-long DKDP crystal due to the flattop super-Gaussian pump beam profile and flat-in-time pulse shape.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

High-efficiency narrow-bandwidth KTP optical parametric oscillator for kHz–MHz planar laser-induced fluorescence

The electronic excitation of key combustion species or flow tagging of chemical species requires a narrowband tunable UV source. In this work, a potassium titanyl phosphate (KTP) burst-mode optical parametric oscillator (OPO) pumped by a 532 nm laser is developed to generate a spectrally narrow signal and an idler output with 1.48 ± 0.19 cm −1 bandwidth without the need for injection seeding. The idler (1410–1550 nm range) is further mixed with 355 or 266 nm to generate 284 or 226 nm for OH or NO planar laser-induced fluorescence (PLIF), respectively, with up to 1.9% conversion efficiency from 1064 nm to the UV. MHz-rate burst profiles are reported, and OH and NO PLIF are demonstrated in a rotating detonation combustor at rates up to 200 kHz.

Webb, Austin M. (ORCID:0000000155897474)↗
DOE OSTI2022

High-resolution mapping of phase-matching conditions in second-order nonlinear crystals

We demonstrate the spatial mapping of phase-matching conditions in nonlinear crystals using detuned second-harmonic generation. A beam-stabilization system cancels out the angular wobbling of the translation stages that scan the crystal under test in front of the static probe beam at the fundamental frequency. A submillimeter resolution over the full scanned aperture, 50 × 50 mm 2 , is demonstrated. The mapping of several partially deuterated potassium dihydrogen phosphate (DKDP) crystals reveals the spatially nonuniform phase-matching conditions due to internal variations in crystal properties and high-frequency surface variations.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Impact of longitudinal phase-matching variations on three-wave nonlinear interactions

A general study of three-wave nonlinear mixing in the presence of longitudinal variations in phase-matching conditions is presented. The efficiency of second-harmonic generation and optical parametric amplification is quantified using a normalized set of equations and a polynomial description of the wave-vector mismatch as a function of the longitudinal coordinate. These modeling results are used to estimate the impact of spatial variations in wave-vector mismatch experimentally obtained for five partially deuterated potassium dihydrogen phosphate crystals. The longitudinal inhomogeneities in the properties of crystals of similar quality are not expected to have a significant impact on their use for second-harmonic generation and optical parametric amplification, but the efficiency of nonlinear processes in crystals with larger variations could decrease.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Improved high-resolution mapping of phase-matching conditions in second-order nonlinear crystals via imaging

Large-aperture nonlinear crystals for frequency conversion and parametric amplification exhibit spatial variations in phase-matching conditions, which affect the performance of high-power laser systems. We demonstrate significant improvements in speed and resolution to a technique that spatially maps these phase-matching conditions using imaging of the beam resulting from detuned second-harmonic generation. The phase-matching conditions at the pyramidal sector boundary of partially deuterated potassium dihydrogen phosphate (DKDP) are mapped with sub-0.1-mm resolution. We examine the effect of further increases in scan rate on the precision of the technique and demonstrate a scan rate of 0.8 cm 2 per minute at the aforementioned resolution.

Wampler, R. [Univ. of Rochester, NY (United States↗
DOE OSTI2021

Identification and selection of optimal reference genes for qPCR-based gene expression analysis in Fucus distichus under various abiotic stresses

Quantitative gene expression analysis is an important tool in the scientist’s belt. The identification of evenly expressed reference genes is necessary for accurate quantitative gene expression analysis, whether by traditional RT-PCR (reverse-transcription polymerase chain reaction) or by qRT-PCR (quantitative real-time PCR; qPCR). In the Stramenopiles (the major line of eukaryotes that includes brown algae) there is a noted lack of known reference genes for such studies, largely due to the absence of available molecular tools. Here we present a set of nine reference genes (Elongation Factor 1 alpha (EF1A), Elongation Factor 2 alpha (EF2A), Elongation Factor 1 beta (EF1B), 14-3-3 Protein, Ubiquitin Conjugating Enzyme (UBCE2), Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH), Actin Related Protein Complex (ARP2/3), Ribosomal Protein (40s; S23), and Actin) for the brown alga Fucus distichus . These reference genes were tested on adult sporophytes across six abiotic stress conditions (desiccation, light and temperature modification, hormone addition, pollutant exposure, nutrient addition, and wounding). Suitability of these genes as reference genes was quantitatively evaluated across conditions using standard methods and the majority of the tested genes were evaluated favorably. However, we show that normalization genes should be chosen on a condition-by-condition basis. We provide a recommendation that at least two reference genes be used per experiment, a list of recommended pairs for the conditions tested here, and a procedure for identifying a suitable set for an experimenter’s unique design. With the recent expansion of interest in brown algal biology and accompanied molecular tools development, the variety of experimental conditions tested here makes this study a valuable resource for future work in basic biology and understanding stress responses in the brown algal lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Rapid estimation of photosynthetic leaf traits of tropical plants in diverse environmental conditions using reflectance spectroscopy

Tropical forests are one of the main carbon sinks on Earth, but the magnitude of CO 2 absorbed by tropical vegetation remains uncertain. Terrestrial biosphere models (TBMs) are commonly used to estimate the CO 2 absorbed by forests, but their performance is highly sensitive to the parameterization of processes that control leaf-level CO 2 exchange. Direct measurements of leaf respiratory and photosynthetic traits that determine vegetation CO 2 fluxes are critical, but traditional approaches are time-consuming. Reflectance spectroscopy can be a viable alternative for the estimation of these traits and, because data collection is markedly quicker than traditional gas exchange, the approach can enable the rapid assembly of large datasets. However, the application of spectroscopy to estimate photosynthetic traits across a wide range of tropical species, leaf ages and light environments has not been extensively studied. Here, we used leaf reflectance spectroscopy together with partial least-squares regression (PLSR) modeling to estimate leaf respiration ( R dark25 ), the maximum rate of carboxylation by the enzyme Rubisco ( V cmax25 ), the maximum rate of electron transport ( J max25 ), and the triose phosphate utilization rate ( T p25 ), all normalized to 25°C. We collected data from three tropical forest sites and included leaves from fifty-three species sampled at different leaf phenological stages and different leaf light environments. Our resulting spectra-trait models validated on randomly sampled data showed good predictive performance for V cmax25 , J max25 , T p25 and R dark25 (RMSE of 13, 20, 1.5 and 0.3 μmol m -2 s -1 , and R 2 of 0.74, 0.73, 0.64 and 0.58, respectively). The models showed similar performance when applied to leaves of species not included in the training dataset, illustrating that the approach is robust for capturing the main axes of trait variation in tropical species. We discuss the utility of the spectra-trait and traditional gas exchange approaches for enhancing tropical plant trait studies and improving the parameterization of TBMs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes

Unraveling the metabolism of Treponema pallidum is a key component to understanding the pathogenesis of the human disease that it causes, syphilis. For decades, it was assumed that glucose was the sole carbon/energy source for this parasitic spirochete. But the lack of citric-acid-cycle enzymes suggested that alternative sources could be utilized, especially in microaerophilic host environments where glycolysis should not be robust. Recent bioinformatic, biophysical, and biochemical evidence supports the existence of an acetogenic energy-conservation pathway in T . pallidum and related treponemal species. In this hypothetical pathway, exogenous D-lactate can be utilized by the bacterium as an alternative energy source. Herein, we examined the final enzyme in this pathway, acetate kinase (named TP0476), which ostensibly catalyzes the generation of ATP from ADP and acetyl-phosphate. We found that TP0476 was able to carry out this reaction, but the protein was not suitable for biophysical and structural characterization. We thus performed additional studies on the homologous enzyme (75% amino-acid sequence identity) from the oral pathogen Treponema vincentii , TV0924. This protein also exhibited acetate kinase activity, and it was amenable to structural and biophysical studies. We established that the enzyme exists as a dimer in solution, and then determined its crystal structure at a resolution of 1.36 Å, showing that the protein has a similar fold to other known acetate kinases. Mutation of residues in the putative active site drastically altered its enzymatic activity. A second crystal structure of TV0924 in the presence of AMP (at 1.3 Å resolution) provided insight into the binding of one of the enzyme’s substrates. On balance, this evidence strongly supported the roles of TP0476 and TV0924 as acetate kinases, reinforcing the hypothesis of an acetogenic pathway in pathogenic treponemes.

Deka, Ranjit K.↗
DOE OSTI2026

Leveraging a synthetic biology approach to enhance BCG-mediated expansion of Vγ9Vδ2 T cells

There is an urgent need to develop a more efficacious anti-tuberculosis vaccine as the current live-attenuated vaccine strain BCG fails to prevent pulmonary infection in adults. In this study, we leverage a synthetic biology approach to engineer BCG to produce more (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), an intermediate of bacterial—but not host—isoprenoid biosynthesis via the methylerythritol phosphate (MEP) pathway. HMBPP strongly activates and expands Vγ9Vδ2 T cells, which are unique to higher-order primates and protect against Mycobacterium tuberculosis infection. BCG has been engineered to produce specific ligands and antigens to some success; in contrast, our strategy exploits a self-nonself recognition mechanism in the host via HMBPP sensing, which has not been attempted before. To inform the design of our recombinant strains, we performed synteny analyses of >63 mycobacterial species and found that isoprenoid biosynthetic genes are not operonic across all the 356 surveyed genomes, but some genes are frequently found in pairs. Thus, we generated synthetic loci with the goal of specifically overproducing HMBPP and tested the ability of these engineered strains to induce human Vγ9Vδ2 expansion in an in vitro stimulation assay. We found that BCG expressing a synthetic MEP locus significantly enhanced Vγ9Vδ2 T cell expansion over the wild-type vaccine strain, and overexpression of the HMBPP synthase GcpE alone potently induced Vγ9Vδ2 T cell expansion with no downregulation of other pathway genes. Together these engineered strains present two successful strategies to accumulate HMBPP and overcome feedback inhibition of the MEP pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Variation of lead isotopic composition and atomic weight in terrestrial materials (IUPAC Technical Report)

The isotopic composition and atomic weight of lead are variable in terrestrial materials because its three heaviest stable isotopes are stable end-products of the radioactive decay of uranium ( 238 U to 206 Pb; 235 U to 207 Pb) and thorium ( 232 Th to 208 Pb). The lightest stable isotope, 204 Pb, is primordial. These variations in isotope ratios and atomic weights provide useful information in many areas of science, including geochronology, archaeology, environmental studies, and forensic science. While elemental lead can serve as an abundant and homogeneous isotopic reference, deviations from the isotope ratios in other lead occurrences limit the accuracy with which a standard atomic weight can be given for lead. In a comprehensive review of several hundred publications and analyses of more than 8000 samples, published isotope data indicate that the lowest reported lead atomic weight of a normal terrestrial materials is 206.1462 ± 0.0028 (k = 2), determined for a growth of the phosphate mineral monazite around a garnet relic from an Archean high-grade metamorphic terrain in north-western Scotland, which contains mostly 206 Pb and almost no 204 Pb. The highest published lead atomic weight is 207.9351 ± 0.0005 (k = 2) for monazite from a micro-inclusion in a garnet relic, also from a high-grade metamorphic terrain in north-western Scotland, which contains almost pure radiogenic 208 Pb. When expressed as an interval, the lead atomic weight is [206.14, 207.94]. It is proposed that a value of 207.2 be adopted for the single lead atomic-weight value for education, commerce, and industry, corresponding to previously published conventional atomic-weight values.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗