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At least 217 records · Page 12

Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers

Histones belong to a family of highly conserved proteins in eukaryotes. They pack DNA into nucleosomes as functional units of chromatin. Post-translational modifications (PTMs) of histones, which are highly dynamic and can be added or removed by enzymes, play critical roles in regulating gene expression. In plants, epigenetic factors including histone PTMs are related to their adaptive responses to the environment. Understanding the molecular mechanisms of epigenetic control can bring unprecedented opportunities for engineering solutions to increase the resilience of crops to climate change. Herein, we describe a protocol to isolate the nuclei and purify histones from sorghum leaf tissue. The extracted histones can be analyzed as their intact forms by top-down mass spectrometry (MS) coupled to online reversed-phase (RP) liquid chromatography (LC). Combinations and stoichiometry of multiple PTMs on the same histone proteoform can be readily identified. In addition, histone tail clipping can be detected using the top-down LC-MS workflow thus yielding the global PTM profile of core histones (H4, H2A, H2B, H3). By comparing the PTM profile among samples corresponding to different conditions (e.g. drought vs. control), potential epigenetic marks can be discovered as targets for further characterization using approaches such as chromatin immunoprecipitation – sequencing (ChIP-seq).

59 BASIC BIOLOGICAL SCIENCES↗

Partial purification and characterization of a Ca(2+)-dependent protein kinase from pea nuclei

Almost all the Ca(2+)-dependent protein kinase activity in nuclei purified from etiolated pea (Pisum sativum, L.) plumules is present in a single enzyme that can be extracted from chromatin by 0.3 molar NaCl. This protein kinase can be further purified 80,000-fold by salt fractionation and high performance liquid chromatography, after which it has a high specific activity of about 100 picomoles per minute per microgram in the presence of Ca2+ and reaches half-maximal activation at about 3 x 10(-7) molar free Ca2+, without calmodulin. It is a monomer with a molecular weight near 90,000. It can efficiently use histone III-S, ribosomal S6 protein, and casein as artificial substrates, but it phosphorylates phosvitin only weakly. Its Ca(2+)-dependent kinase activity is half-maximally inhibited by 0.1 millimolar chlorpromazine, by 35 nanomolar K-252a and by 7 nanomolar staurosporine. It is insensitive to sphingosine, an inhibitor of protein kinase C, and to basic polypeptides that block other Ca(2+)-dependent protein kinases. It is not stimulated by exogenous phospholipids or fatty acids. In intact isolated pea nuclei it preferentially phosphorylates several chromatin-associated proteins, with the most phosphorylated protein band being near the same molecular weight (43,000) as a nuclear protein substrate whose phosphorylation has been reported to be stimulated by phytochrome in a calcium-dependent fashion.

NASA Discipline Number 40-50↗

An Inverse Modeling Approach to Estimating Phytoplankton Pigment Concentrations from Phytoplankton Absorption Spectra

Phytoplankton absorption spectra and High-Performance Liquid Chromatography (HPLC) pigment observations from the Eastern U.S. and global observations from NASA's SeaBASS archive are used in a linear inverse calculation to extract pigment-specific absorption spectra. Using these pigment-specific absorption spectra to reconstruct the phytoplankton absorption spectra results in high correlations at all visible wavelengths (r(sup 2) from 0.83 to 0.98), and linear regressions (slopes ranging from 0.8 to 1.1). Higher correlations (r(sup 2) from 0.75 to 1.00) are obtained in the visible portion of the spectra when the total phytoplankton absorption spectra are unpackaged by multiplying the entire spectra by a factor that sets the total absorption at 675 nm to that expected from absorption spectra reconstruction using measured pigment concentrations and laboratory-derived pigment-specific absorption spectra. The derived pigment-specific absorption spectra were further used with the total phytoplankton absorption spectra in a second linear inverse calculation to estimate the various phytoplankton HPLC pigments. A comparison between the estimated and measured pigment concentrations for the 18 pigment fields showed good correlations (r(sup 2) greater than 0.5) for 7 pigments and very good correlations (r(sup 2) greater than 0.7) for chlorophyll a and fucoxanthin. Higher correlations result when the analysis is carried out at more local geographic scales. The ability to estimate phytoplankton pigments using pigment-specific absorption spectra is critical for using hyperspectral inverse models to retrieve phytoplankton pigment concentrations and other Inherent Optical Properties (IOPs) from passive remote sensing observations.

Moisan, John R.↗

Extraterrestrial Amino Acids in the C2 Ungrouped Carbonaceous Chondrite Tarda: A Unique Distribution

Introduction: Meteorites provide a record of the chemical processes that occurred in the early solar sys-tem. The delivery of organic matter by carbonaceous chondrites to the early Earth could have been an im-portant source of amino acids and other prebiotic or-ganic molecules required for the emergence of life [1]. To date, 96 amino acids have been named in meteor-ites, most of which are rare or absent in the biosphere [2]. The variability in amino acid concentrations and isomer distributions measured in carbonaceous chon-drites can be explained by differences in parent body chemistry and alteration conditions [3]. In addition, aqueous alteration was likely important in the amplifi-cation of some left-handed amino acids over their right-handed forms (L-excesses up to ~60%) in the Tagish Lake meteorite [3], suggesting that the origin of life on Earth and possibly elsewhere in the solar sys-tem was biased towards L-amino acids. On August 25, 2020, a fireball was witnessed in southern Morocco and the first pieces of the meteorite fall were recovered the following day near the town of Tarda [4]. Thousands of individual fragments were recovered from the strewn field totaling ~4 kg [4]. Based on petrographic observations, bulk mineralogy, and chemical and O-isotopic analyses, Tarda has been classified as a C2 ungrouped carbonaceous chondrite with similarities to Tagish Lake (though more primi-tive), as well as CI, CY, and CR chondrites [4,5]. The fall and rapid recovery of the Tarda stones provide an important opportunity to investigate a C-rich meteorite using the state-of-the-art techniques that will also be used to study the samples returned from asteroids Ryugu and Bennu by the Hayabusa2 and OSIRIS-REx missions, respectively. Here, we report the first amino acid analyses of the Tarda meteorite. The total concentrations, enantio-meric ratios and relative distributions of amino acids were determined using ultrahigh performance liquid chromatography with UV fluorescence and time-of-flight mass spectrometry (LC-FD/ToF-MS) at NASA GSFC. This analytical technique was employed on extracts from two different pre-rain Tarda meteorite fragments and a sample of sand collected from the Tarda fall site for the purpose of assessing potential terrestrial contamination. Bulk H, C, and N elemental and isotopic analyses were also conducted at the Car-negie Institution for Science (CIS) to assist with petro-logic type classification using elemental analysis iso-tope ratio mass spectrometry (EA-IRMS).

D P Glavin↗

Task 2.1: Adsorption-Based ISPR for BETO-Relevant Bioproducts

This task focuses on the development of adsorption-based in situ product recovery (ISPR) integrated with simulated moving bed chromatography for the recovery and purification of carboxylate products that are relevant to BETO. ISPR has been pursued previously in the Separations Consortium to recover carboxylic acids near or below their pKa values with liquid-liquid extraction coupled to downstream distillation. However, there are many acid products in the BETO portfolio that require neutralization well above their pKa values wherein ISPR could still be a major benefit to the bioprocess performance, including muconic acid, beta-ketoadipic acid, 3-hydroxypropionic acid, itaconic acid, butyric acid, and others. In this task, we are combining dynamic filtration with a rotating ceramic disk, resin capacity measurements, tailored resin synthesis, and simulated moving bed chromatography into an ISPR system that can be used to recover BETO-relevant carboxylates from bioreactor cultivations. We are working across process scales and using computational modeling where applicable alongside techno-economic analysis and life cycle assessment to understand major cost, energy, and GHG emissions drivers. The impact of this project will be a bench-scale integrated approach to recover carboxylate products in situ, which will reduce the waste generation from biological carboxylate production processes and improve the productivities of biological systems.

bio-based acid↗

Ultraviolet-photoproduced organic solids synthesized under simulated Jovian conditions - Molecular analysis

In an earlier paper, Khare and Sagan reported the production of a brownish polymeric material from the near-ultraviolet irradiation of simulated jovian atmospheres with a low hydrogen abundance. Examination of this product indicates that hydrogen sulfide is the initial photon acceptor; the powder resulting after extraction with benzene is 84 percent sulfur, largely S8. In results reported here, the remaining 16 percent was pyrolyzed and then examined by gas chromatography-mass spectrometry. Pyrolysis at 450 C yielded a series of alkanes, alkenes, C3-alkylbenzenes, aromatics, thiophenes, alkylthiophenes, alkylmercaptans, alkyldisulfides, together with the nitrogenous compounds hydrogen cyanide, methyl cyanide, alkylisothiocyanates, acrylonitrile, and allylisothiocyanates. Some of these compounds might be sought on Jupiter and Saturn and their satellites by remote infrared and ultraviolet spectroscopy and directly by entry probes.

Khare, B. N.↗

Extracting trace substances from biological fluids

Apparatus is used as aid in extraction of trace amounts of volatile organics from biological fluids. "Transervaporator" makes it possible to prepare violate fraction for analysis by high-resolution gas chromatography.

Zlatkis, A.↗

New Insights into Prebiotic Chemistry from Old Archived Miller Extracts

Following the discovery of an archived set of samples from Stanley Miller's early experiments, analyses were undertaken to better understand the diversity of compounds produced from electric discharges acting on reducing gas mixtures. The paper chromatography methods that Miller used in the 1950s were only capable of detecting a few amino acids and were unable to provide substantial quantitative data relative to today's techniques. Current analytical techniques are much more sensitive and selective, and are capable of precisely quantifying a much larger range of amino acids and their enantiomeric abundances. In one study, preserved dried samples produced by Miller using a lesser-known volcanic apparatus which differed from Miller's classic apparatus in that it utilized an aspirator that injected steam into the electric discharge chamber, simulating a volcanic eruption. The volcanic apparatus produced a wider variety of amino acids than the classic configuration. Prebiotic compounds synthesized in these environments may have locally accumulated where they could have undergone further processing. An additional preserved set of samples from an experiment conducted in 1958 were also found in Miller's archived collection. These samples which had been generated using a mixture of CH4, NH3, H2S and CO2 were collected, catalogued, and stored by Miller, but for unknown reasons were never studied. In our analyses a total of 23 amino acids and 4 amines, including 7 organosulfur compounds, were detected in these samples. The major amino acids with chiral centers are racemic within the accuracy of the measurements, indicating that they are not contaminants introduced during sample storage. This experiment marks the first synthesis of sulfur amino acids from spark discharge experiments designed to imitate primordial environments. The relative yield of some amino acids, in particular the isomers of amino butyric acid, are the highest ever found in a spark discharge experiment. The simulated primordial conditions used by Miller in these experiments may serve as a model for early volcanic plume chemistry and provide insight to the possible roles such plumes may have played in abiotic organic synthesis. Additionally, the overall abundances of the synthesized amino acids in the presence of H2S are very similar to the abundances found in some carbonaceous meteorites, suggesting that H2S may have played an important role in prebiotic reactions in early solar system environments. Although experiments using a variety of gases as components of the primordial Earth's atmospheric composition and a spark discharge apparatus configured according to Miller's original or volcanic design can be readily carried out, the unique opportunity to investigate samples prepared by the pioneer in abiotic synthesis using state of the art analytical methods is of considerable historic interest.

Parker, Eric T.↗

MetFish: a Metabolomics Pipeline for Studying Microbial Communities in Chemically Extreme Environments

Metabolites have essential roles in microbial communities, including as mediators of nutrient and energy exchange, cell-to-cell communication, and antibiosis. However, detecting and quantifying metabolites and other chemicals in samples having extremes in salt or mineral content using liquid chromatography-mass spectrometry (LC-MS)-based methods remains a significant challenge. Here, we report a facile method based on in situ chemical derivatization followed by extraction for analysis of metabolites and other chemicals in hypersaline samples, enabling for the first time direct LC-MS-based exometabolomics analysis in sample matrices containing up to 2 M total dissolved salts. The method, MetFish, is applicable to molecules containing amine, carboxylic acid, carbonyl, or hydroxyl functional groups, and it can be integrated into either targeted or untargeted analysis pipelines. In targeted analyses, MetFish provided limits of quantification as low as 1 nM, broad linear dynamic ranges (up to 5 to 6 orders of magnitude) with excellent linearity, and low median interday reproducibility (e.g., 2.6%). MetFish was successfully applied in targeted and untargeted exometabolomics analyses of microbial consortia, quantifying amino acid dynamics in the exometabolome during community succession; in situ in a native prairie soil, whose exometabolome was isolated using a hypersaline extraction; and in input and produced fluids from a hydraulically fractured well, identifying dramatic changes in the exometabolome over time in the well.

59 BASIC BIOLOGICAL SCIENCES↗

Improved Characterization of Soil Organic Matter by Integrating FT-ICR MS, Liquid Chromatography Tandem Mass Spectrometry, and Molecular Networking: A Case Study of Root Litter Decay under Drought Conditions

Understanding of how soil organic matter (SOM) chemistry is altered in a changing climate has advanced considerably; however, most SOM components remain unidentified, impeding the ability to characterize a major fraction of organic matter and predict what types of molecules, and from which sources, will persist in soil. Here we present a novel approach to better characterize SOM extracts by integrating information from three types of analyses, and we deploy this method to characterize decaying root-detritus soil microcosms subjected to either drought or normal conditions. To observe broad differences in composition, we employed direct infusion Fourier-transform ion cyclotron resonance mass spectrometry (DI-FT-ICR MS). We complemented this with liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify components by library matching. Since libraries contain only a small fraction of SOM components, we also used fragment spectral cosine similarity scores to relate unknowns and library matches through molecular networks. This integrated approach allowed us to corroborate DI-FT-ICR MS molecular formulas using library matches, which included fungal metabolites and related polyphenolic compounds. We also inferred structures of unknowns from molecular networks and improved LC-MS/MS annotation rates from ~5 to 35% by considering DI-FT-ICR MS molecular formula assignments. Under drought conditions, we found greater relative amounts of lignin-like vs condensed aromatic polyphenol formulas and lower average nominal oxidation state of carbon, suggesting reduced decomposition of SOM and/or microbes under stress. Our integrated approach provides a framework for enhanced annotation of SOM components that is more comprehensive than performing individual data analyses in parallel.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Irradiated Benzene Ice Provides Clues to Meteoritic Organic Chemistry

Aromatic hydrocarbons account for a significant portion of the organic matter in carbonaceous chondrite meteorites, as a component of both the low molecular weight, solvent-extractable compounds and the insoluble organic macromolecular material. Previous work has suggested that the aromatic compounds in carbonaceous chondrites may have originated in the radiation-processed icy mantles of interstellar dust grains. Here we report new studies of the organic residue made from benzene irradiated at 19 K by 0.8 MeV protons. Polyphenyls with up to four rings were unambiguously identified in the residue by gas chromatography-mass spectrometry. Atmospheric pressure photoionization Fourier transform mass spectrometry was used to determine molecular composition, and accurate mass measurements suggested the presence of polyphenyls, partially hydrogenated polyphenyls, and other complex aromatic compounds. The profile of low molecular weight compounds in the residue compared well with extracts from the Murchison and Orgueil meteorites. These results are consistent with the possibility that solid phase radiation chemistry of benzene produced some of the complex aromatics found in meteorites.

benzene↗

Analysis of Membrane Lipids of Airborne Micro-Organisms

A method of characterization of airborne micro-organisms in a given location involves (1) large-volume filtration of air onto glass-fiber filters; (2) accelerated extraction of membrane lipids of the collected micro-organisms by use of pressurized hot liquid; and (3) identification and quantitation of the lipids by use of gas chromatography and mass spectrometry. This method is suitable for use in both outdoor and indoor environments; for example, it can be used to measure airborne microbial contamination in buildings ("sick-building syndrome"). The classical approach to analysis of airborne micro-organisms is based on the growth of cultureable micro-organisms and does not provide an account of viable but noncultureable micro-organisms, which typically amount to more than 90 percent of the micro-organisms present. In contrast, the present method provides an account of all micro-organisms, including cultureable, noncultureable, aerobic, and anaerobic ones. The analysis of lipids according to this method makes it possible to estimate the number of viable airborne micro-organisms present in the sampled air and to obtain a quantitative profile of the general types of micro-organisms present along with some information about their physiological statuses.

MacNaughton, Sarah↗

Investigating the Variation in Solvation Interactions of Choline Chloride-Based Deep Eutectic Solvents Formed Using Different Hydrogen Bond Donors

Choline chloride-based deep eutectic solvents (DESs) have gained widespread recognition as green solvents in catalysis and separation science as their designer properties permit solvation properties to be modulated by the choice of the hydrogen bond donor (HBD) as well as its molar ratio. Despite being one of the most popular classes of DESs, very little is currently understood regarding how their solvation characteristics differ among themselves as well as from other classes of DESs. Previous studies have shown that the catalytic activity, extraction efficiency, and solubilities of natural compounds can be influenced by the type of choline salt and HBD, but no study has systematically related these parameters with its solvation properties. In this study, inverse gas chromatography was employed for the first time to study the individual solvation characteristics of a diverse range of choline chloride and acetate-based DESs composed of amides, diols, organic acids, and carbohydrates. Furthermore, hydrogen bond acidity was found to be a dominant interaction for all DESs, especially those composed of organic acid HBDs. DESs composed of isomers of butane diol and hexane diol as HBDs exhibited higher hydrogen bond basicity and dispersive-type interactions compared to those composed of urea, acetamide, and organic acids with the position of the hydroxyl functional group influencing their solvation interactions. Choline acetate-based DESs exhibited lower dipolarity and stronger hydrogen bond basicity and dispersive-type interactions compared to choline chloride DESs. The solvation models developed in this study were used to interpret and explain DES behavior in previously reported studies involving catalysis, organic synthesis, and extractions demonstrating that the measured solute–solvent interactions can serve to predict the performance of choline chloride-based DESs when used in various applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Purification and characterization of a casein kinase 2-type protein kinase from pea nuclei

Almost all the polyamine-stimulated protein kinase activity associated with the chromatin fraction of nuclei purified from etiolated pea (Pisum sativum L.) plumules is present in a single enzyme that can be extracted from chromatin by 0.35 molar NaCl. This protein kinase can be further purified over 2000-fold by salt fractionation and anion-exchange and casein-agarose column chromatography, after which it is more than 90% pure. The purified kinase has a specific activity of about 650 nanomoles per minute per milligram protein in the absence of polyamines, with either ATP or GTP as phosphoryl donor. Spermidine can stimulate its activity fourfold, with half-maximal activation at about 2 millimolar. Spermine and putrescine also stimulate activity, although somewhat less effectively. This kinase has a tetrameric alpha 2 beta 2 structure with a native molecular weight of 130,000, and subunit molecular weights of 36,000 for the catalytic subunit (alpha) and 29,000 for the regulatory subunit (beta). In western blot analyses, only the alpha subunit reacts strongly with polyclonal antibodies to a Drosophila casein kinase II. The pea kinase can use casein and phosvitin as artificial substrates, phosphorylating both the serine and threonine residues of casein. It has a pH optimum near 8.0, a Vmax of 1.5 micromoles per minute per milligram protein, and a Km for ATP of approximately 75 micromolar. Its activity can be almost completely inhibited by heparin at 5 micrograms per milliliter, but is relatively insensitive to concentrations of staurosporine, K252a, and chlorpromazine that strongly antagonize Ca(2+) -regulated protein kinases. These results are discussed in relation to recent findings that casein kinase 2-type kinases may phosphorylate trans-acting factors that bind to light-regulated promoters in plants.

NASA Program Space Biology↗

Total Synthesis of Ionic Liquid Systems for Dissolution of Lunar Simulant

For purposes of Space Resource Utilization, work in the total synthesis of a new ionic liquid system for the extraction of oxygen and metals from lunar soil is studied and described. Reactions were carried out according to procedures found in the chemical literature, analyzed via Thin-Layer Chromatography and 1H Nuclear Magnetic Resonance Spectroscopy and purified via vacuum distillation and rotary evaporation. Upon final analysis via 1H NMR, it was found that while the intermediates of the synthesis had been achieved, unexpected side products were also present. The mechanisms and constraints of the synthesis are described as well as the final results of the project and recommendations for continued study

Sharpe, Robert J.↗

Distinct Purine Distribution in Carbonaceous Chondrites

Carbonaceous chondrite meteorites are known to contain a diverse suite of organic compounds, many of which are essential components of biochemistry. Amino acids, which are the monomers of proteins, have been extensively studied in such meteorites (e.g. Botta and Bada 2002; Pizzarello et aI., 2006). The origin of amino acids in meteorites has been firmly established as extraterrestrial based on their detection typically as racemic mixtures of amino acids, the presence of many non-protein amino acids, and non-terrestrial values for compound-specific deuterium, carbon, and nitrogen isotopic measurements. In contrast to amino acids, nucleobases in meteorites have been far less studied. Nucleobases are substituted one-ring (pyrimidine) or two-ring (purine) nitrogen heterocyclic compounds and serve as the information carriers of nucleic acids and in numerous coenzymes. All of the purines (adenine, guanine, hypoxanthine, and xanthine) and pyrimidines (uracil) previously reported in meteorites are biologically common and could be interpreted as the result of terrestrial contamination (e.g. van del' Velden and Schwartz, 1974.) Unlike other meteoritic organics, there have been no observations of stochastic molecular diversity of purines and pyrimidines in meteorites, which has been a criterion for establishing extraterrestrial origin. Maltins et al. (2008) performed compound-specific stable carbon isotope measurements for uracil and xanthine in the Murchison meteorite. They assigned a non-terrestrial origin for these nucleobases; however, the possibility that interfering indigenous molecules (e.g. carboxylic acids) contributed to the 13C-enriched isotope values for these nucleobases cannot be completely ruled out. Thus, the origin of these meteoritic nucleobases has never been established unequivocally. Here we report on our investigation of extracts of II different carbonaceous chondrites covering various petrographic types (Cl, CM, and CR) and degrees of aqueous alteration (l, 2, and 3) and one ureilite. Analysis via liquid chromatography coupled with electrospray triple-stage mass spectrometry or orbitrap mass spectrometry employed a targeted approach for analysis focused on the five canonical RNA/DNA nucleobases as well as 14 non-canonical pyrimidines and purines, which have bcen observed under plausible prebiotic reactions.

Callahan, Michael P.↗

Extraterrestrial Amino Acids Identified in Metal-Rich CH and CB Carbonaceous Chondrites from Antarctica

Carbonaceous chondrites contain numerous indigenous organic compounds and could have been an important source of prebiotic compounds required for the origin of life on Earth or elsewhere. Extraterrestrial amino acids have been reported in five of the eight groups of carbonaceous chondrites and are most abundant in CI, CM, and CR chondritesbut are also present in the more thermally altered CV and CO chondrites. We report the abundance, distribution, and enantiomeric and isotopic compositions of simple primary amino acids in six metal-rich CH and CB carbonaceous chondrites that have not previously been investigated for amino acids: Allan Hills (ALH) 85085 (CH3), Pecora Escarpment(PCA) 91467 (CH3), Patuxent Range (PAT) 91546 (CH3), MacAlpine Hills (MAC) 02675(CBb), Miller Range (MIL) 05082 (CB), and Miller Range (MIL) 07411 (CB). Amino acid abundances and carbon isotopic values were obtained by using both liquid chromatography time-of-flight mass spectrometry and fluorescence, and gas chromatography isotope ratiomass spectrometry. The (delta D, delta C-13, delta N-15) ratios of multiple amino acids fall outside of the terrestrial range and support their extraterrestrial origin. Extracts of CH chondrites were found to be particularly rich in amino acids (1316 parts per million, ppm) while CB chondrite extracts had much lower abundances (0.22 ppm). The amino acid distributions of the CH and CB chondrites were distinct from the distributions observed in type 2 and 3 CM and CR chondrites and contained elevated levels of beta-, gamma-, and delta-amino acids compared to the corresponding alpha-amino acids, providing evidence that multiple amino acid formation mechanisms were important in CH and CB chondrites.

Burton, Aaron S.↗