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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 37 records · Page 2

Four Isotope-Labeled Recombination Pathways of Ozone Formation

A theoretical approach is developed for the description of all possible recombination pathways in the ozone forming reaction, without neglecting any process a priori, and without decoupling the individual pathways one from another. These pathways become physically distinct when a rare isotope of oxygen is introduced, such as 18 O, which represents a sensitive probe of the ozone forming reaction. Each isotopologue of O 3 contains two types of physically distinct entrance channels and two types of physically distinct product wells, creating four recombination pathways. Calculations are done for singly and doubly substituted isotopologues of ozone, eight rate coefficients total. Two pathways for the formation of asymmetric ozone isotopomer exhibit rather different rate coefficients, indicating large isotope effect driven by ΔZPE-difference. Rate coefficient for the formation of symmetric isotopomer of ozone (third pathway) is found to be in between of those two, while the rate of insertion pathway is smaller by two orders of magnitude. These trends are in good agreement with experiments, for both singly and doubly substituted ozone. The total formation rates for asymmetric isotopomers are found to be somewhat larger than those for symmetric isotopomers, but not as much as in the experiment. Altogether, the distribution of lifetimes is found to be very similar for the metastable states in symmetric and asymmetric ozone isotopomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Surface Functionalization of Black Phosphorus with Nitrenes: Identification of P=N Bonds by Using Isotopic Labeling

Abstract Surface functionalization of two‐dimensional crystals is a key path to tuning their intrinsic physical and chemical properties. However, synthetic protocols and experimental strategies to directly probe chemical bonding in modified surfaces are scarce. Introduced herein is a mild, surface‐specific protocol for the surface functionalization of few‐layer black phosphorus nanosheets using a family of photolytically generated nitrenes (RN) from the corresponding azides. By embedding spectroscopic tags in the organic backbone, a multitude of characterization techniques are employed to investigate in detail the chemical structure of the modified nanosheets, including vibrational, X‐ray photoelectron, solid state 31 P NMR, and UV‐vis spectroscopy. To directly probe the functional groups introduced on the surface, R fragments were selected such that in conjunction with vibrational spectroscopy, 15 N‐labeling experiments, and DFT methods, diagnostic P=N vibrational modes indicative of iminophosphorane units on the nanosheet surface could be conclusively identified.

Walz Mitra, Kendahl L.↗

Isotopically labelled inorganic carbon delivered to algalcultures via bubbler bottle

This protocol describes a method for delivering labelled inorganic carbon as 13 CO 2 to algal cultures by bubbling air through a solution of H 13 CO 3 - , and then into the culture. We developed this method to deliver label to cultures grown under continuous bubbling with air, without the use of 13 CO 2 labelled gas and the necessary equipment to mix labelled gas with air at near-atmospheric levels. Bubbling precludes the more common approach of adding H 13 CO 3 - label directly to the media, because dissolved HCO 3 - is in equilibrium with atmospheric CO 2 . Thus, excess HCO 3 - added to a solution will leave the solution as CO 2 gas as it equilibrates. Bubbling rapidly accelerates this equilibration which is typically diffusion limited. The method described here takes advantage of this aspect of carbonate chemistry, and uses a solution of H 13 CO 3 - —which is less expensive and more convenient than 13 CO 2 gas—to generate a flux of 13 CO 2 that can be bubbled into a culture.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular and mass spectroscopic analysis of isotopically labeled organic residues

Experimental studies aimed at understanding the evolution of complex organic molecules on interstellar grains were performed. The photolysis of frozen gas mixtures of various compositions containing H2O, CO, NH3, and CH4 was studied. These species were chosen because of their astrophysical importance as deducted from observational as well as theoretical studies of ice mantles on interstellar grains. These ultraviolet photolyzed ices were warmed up in order to produce refractory organic molecules like the ones formed in molecular clouds when the icy mantles are being irradiated and warmed up either by a nearby stellar source or impulsive heating. The laboratory studies give estimates of the efficiency of production of such organic material under interstellar conditions. It is shown that the gradual carbonization of organic mantles in the diffuse cloud phase leads to higher and higher visual absorptivity - yellow residues become brown in the laboratory. The obtained results can be applied to explaining the organic components of comets and their relevance to the origin of life.

Mendoza-Gomez, Celia X.↗

Coupling Metabolic Source Isotopic Pair Labeling and Genome Wide Association for Metabolite and Gene Annotation in Plants (Final Technical Report)

In this project, we applied our labeling pipeline to Arabidopsis and sorghum by feeding tissues with isotopically labeled versions of commercially available amino acids to identify all metabolite features that incorporate the label. In sorghum, we fed five accessions, sampled across the diversity of sorghum, to identify the precursor-of-origin for metabolites that vary between accessions as well as those that may be missing from a single reference genotype. This provided us with precursor-of-origin annotation for thousands of unknown metabolites. We then used GWA to map genes responsible for the synthesis of precursor-of-origin classified metabolites. For sorghum leaf and root ducible metabolites, we performed untargeted metabolomics on leaf and root tissues from 300 diverse genotyped sorghum inbred lines. The amino acid precursor-of-origin metabolite library were then used to identify the corresponding metabolites in the GWA data sets and to identify novel gene-metabolite associations. Finally, we utilized existing and newly generated sequenced EMS mutants of sorghum to validate the predicted gene-metabolite relationships that our labelling analysis identified. In parallel, we conducted similar feeding experiments in Arabidopsis to categorize metabolites based on precursor-of-origin, identify those that vary across our existing Arabidopsis metabolite GWA dataset, and identify genes required for the synthesis of each metabolite. To provide an independent test of gene annotation and pathway involvement, we tested the GWA gene-metabolite associations in Arabidopsis by analyzing the metabolic phenotypes of gene knockouts. Genes of particular interest from both sorghum and Arabidopsis were studied in detail by directly measuring the activity of the corresponding enzymes following heterologous expression. In summary, this work classified as-yet-unknown amino acid-derived metabolites and identified genes involved in their production generated through “omics” technologies. This information was used to validate gene function and identify new metabolism in Arabidopsis and sorghum.

09 BIOMASS FUELS↗

Metabolic Source Isotopic Pair Labeling and Genome-Wide Association Are Complementary Tools for the Identification of Metabolite-Gene Associations in Plants

The optimal extraction of information from untargeted metabolomics analyses is a continuing challenge. Here, we describe an approach that combines stable isotope labeling, liquid chromatography– mass spectrometry (LC–MS), and a computational pipeline to automatically identify metabolites produced from a selected metabolic precursor. Here, we identified the subset of the soluble metabolome generated from phenylalanine (Phe) in Arabidopsis thaliana, which we refer to as the Phe-derived metabolome (FDM) In addition to identifying Phe-derived metabolites present in a single wild-type reference accession, the FDM was established in nine enzymatic and regulatory mutants in the phenylpropanoid pathway. To identify genes associated with variation in Phe-derived metabolites in Arabidopsis, MS features collected by untargeted metabolite profiling of an Arabidopsis diversity panel were retrospectively annotated to the FDM and natural genetic variants responsible for differences in accumulation of FDM features were identified by genome-wide association. Large differences in Phe-derived metabolite accumulation and presence/absence variation of abundant metabolites were observed in the nine mutants as well as between accessions from the diversity panel. Many Phe-derived metabolites that accumulated in mutants also accumulated in non-Col-0 accessions and was associated to genes with known or suspected functions in the phenylpropanoid pathway as well as genes with no known functions. Overall, we show that cataloguing a biochemical pathway’s products through isotopic labeling across genetic variants can substantially contribute to the identification of metabolites and genes associated with their biosynthesis.

09 BIOMASS FUELS↗

Analyzing Mass Spectrometry Imaging Data of 13C-Labeled Phospholipids in Camelina sativa and Thlaspi arvense (Pennycress) Embryos

The combination of 13C-isotopic labeling and mass spectrometry imaging (MSI) offers an approach to analyze metabolic flux in situ. However, combining isotopic labeling and MSI presents technical challenges ranging from sample preparation, label incorporation, data collection, and analysis. Isotopic labeling and MSI individually create large, complex data sets, and this is compounded when both methods are combined. Therefore, analyzing isotopically labeled MSI data requires streamlined procedures to support biologically meaningful interpretations. Using currently available software and techniques, here we describe a workflow to analyze 13C-labeled isotopologues of the membrane lipid and storage oil lipid intermediate―phosphatidylcholine (PC). Our results with embryos of the oilseed crops, Camelina sativa and Thlaspi arvense (pennycress), demonstrated greater 13C-isotopic labeling in the cotyledons of developing embryos compared with the embryonic axis. Greater isotopic enrichment in PC molecular species with more saturated and longer chain fatty acids suggest different flux patterns related to fatty acid desaturation and elongation pathways. The ability to evaluate MSI data of isotopically labeled plant embryos will facilitate the potential to investigate spatial aspects of metabolic flux in situ.

metabolomics↗

Escherichia coli amino acid auxotrophic expression host strains for investigating protein structure–function relationships

Abstract A set of C43(DE3) and BL21(DE3) Escherichia coli host strains that are auxotrophic for various amino acids is briefly reviewed. These strains require the addition of a defined set of one or more amino acids in the growth medium, and have been specifically designed for overproduction of membrane or water-soluble proteins selectively labelled with stable isotopes, such as 2H, 13C and 15N. The strains described here are available for use and have been deposited into public strain banks. Although they cannot fully eliminate the possibility of isotope dilution and mixing, metabolic scrambling of the different amino acid types can be minimized through a careful consideration of the bacterial metabolic pathways. The use of a suitable auxotrophic expression host strain with an appropriately isotopically labelled growth medium ensures high levels of isotope labelling efficiency as well as selectivity for providing deeper insight into protein structure–function relationships.

Biochemistry & Molecular Biology↗

Data for Selected Ion Monitoring for Orbitrap-Based Metabolomics

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage.f

Mass Spectrometry↗

Developing a peptide concatemer (PepCon) as a process control for LC-MS based proteomics

Quantitative concatenated peptide (QconCAT) technology is currently used for the absolute quantification of proteins of interest in a biological sample. It relies on artificially created proteins that are concatenations of different, isotopically labeled peptides. Because these isotopically labeled peptides are at a 1:1 ratio and correspond to naturally occurring peptides in the biological sample, each peptide can be used as a standard for the absolute quantitation of all proteins of interest at once. Although the QconCAT technology has utility for quantitation of known peptides in a mixture, it is not helpful for scientists who need a proteomics standard (1) that can be spiked into a protein mixture at an extremely low level, (2) that can be co-purified during sample fractionation, and (3) that is optimized for ESI used in mass spectrometry. Thus, there exists a need for an ideal standard protein that is large enough to behave as a protein but consists of multiple, concatenated copies of the same peptide, which, upon digestion, amplifies (e.g., >10-fold) into a detectable peptide species. Here, this technical report describes the development of “PepCon”, a peptide concatemer that fulfills this unmet need.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Selected Ion Monitoring for Orbitrap-Based Metabolomics

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage.

59 BASIC BIOLOGICAL SCIENCES↗

Using 14 C-acetate Pulse-chase Labeling to Study Fatty Acid and Glycerolipid Metabolism in Plant Leaves

Lipids metabolism is comprised of networks of reactions occurred in different subcellular compartments. Isotopic labeling is a good way to track the transformations and movements of metabolites without perturbing overall cellular metabolism. Fatty acids, the building blocks of membrane lipids and storage triacylglycerols, are synthesized in plastids. The immediate precursor for fatty acid synthesis is acetyl-CoA. Exogenous acetate is rapidly incorporated into fatty acids in leaves and isolated plastids because it can diffuse freely through cellular membranes, enter the plastid where it is rapidly metabolized to acetyl-CoA. Therefore, isotope-labeled acetate is often used as a tracer for the investigation of fatty acid synthesis and complex lipid metabolism in plants and other organisms. The basic principle of isotope labeling and its recent technical advances have been reviewed (Allen et al., 2015). The present protocol describes the use of 14C-labeled acetate to determine rates of fatty acid synthesis and degradation and to track the metabolism of glycerolipids in leaves. This method, which is often referred to as acetate pulse-chase labeling, has been widely used to probe various aspects of lipid metabolism (Allen et al., 2015), including the role of autophagy in membrane lipid turnover (Fan et al., 2019) and the interplay between lipid and starch metabolism pathways (Yu et al., 2018).

14C-acetate pulse-chase↗

Simulating metagenomic stable isotope probing datasets with MetaSIPSim

DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, ‘MetaSIPSim,’ to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment. Through simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G + C content impacted the assembly of labeled genomes and subsequent binning, where high community G + C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance. Metagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.

59 BASIC BIOLOGICAL SCIENCES↗

Unraveling the convoluted and dynamic interphasial mechanisms on Li metal anode

Accurate understanding of the chemistry of solid-electrolyte interphase (SEI) is key to developing new electrolytes for high-energy batteries using lithium metal (Li-0) anodes(1). SEI is generally believed to be formed by the reactions between Li-0 and electrolyte(2,3). However, our new study shows this is not the whole story. Through synchrotron-based X-ray diffraction and pair distribution function analysis, we reveal a much more convoluted formation mechanism of SEI, which receives considerable contributions from electrolyte, cathode, moisture and native surface species on Li-0, with highly dynamic nature during cycling. Using isotope labelling, we traced the origin of LiH to electrolyte solvent, moisture and a new source: the native surface species (LiOH) on pristine Li-0. When lithium accessibility is very limited as in the case of anode-free cells, LiOH develops into plate-shaped large crystals during cycling. Alternatively, when the lithium source is abundant, as in the case of Li||NMC811 cells, LiOH reacts with Li-0 to form LiH and Li2O. While the desired anion-derived LiF-rich SEI is typically found in the concentrated electrolytes or their derivatives, we found it can also be formed in low-concentration electrolyte via the crosstalk effect, emphasizing the importance of formation cycle protocol and opening up opportunities for low-cost electrolyte development.

Polzin, Bryant J.↗

MassIVE MSV000094084 - Data files for manuscript - Selected ion monitoring for orbitrap-based metabolomics: Please open README-data-for-SIM-paper-20240210.doc for details.

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage. Please open README-data-for-SIM-paper-20240210.doc for details. [doi:10.25345/C5JH3DD3K] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Rabinowitz, Joshua↗