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155 records · Page 9

In vitro and in vivo protein phosphorylation in Avena sativa L. coleoptiles: effects of Ca2+, calmodulin antagonists, and auxin

In vitro and in vivo protein phosphorylations in oat (Avena sativa L.) coleoptile segments were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis and by two-dimensional gel electrophoresis. In vitro phosphorylation of several polypeptides was distinctly promoted at 1 to 15 micromolar free Ca2+ concentrations. Ca2(+)-stimulated phosphorylation was markedly reduced by trifluoperazine, chlorpromazine, and naphthalene sulfonamide (W7). Two polypeptides were phosphorylated both under in vitro and in vivo conditions, but the patterns of phosphorylation of several other polypeptides were different under the two conditions indicating that the in vivo phosphorylation pattern of proteins is not truly reflected by in vitro phosphorylation studies. Trifluoperazine, W7, or ethylene glycol-bis-(beta-aminoethyl ether)-N,N'-tetraacetic acid (EGTA) + calcium ionophore A23187 treatments resulted in reduced levels of in vivo protein phosphorylation of both control and auxin-treated coleoptile segments. Analysis by two-dimensional electrophoresis following in vivo phosphorylation revealed auxin-dependent changes of certain polypeptides. A general inhibition of phosphorylation by calmodulin antagonists suggested that both control and auxin-treated coleoptiles exhibited Ca2+, and calmodulin-dependent protein phosphorylation in vivo.

NASA Discipline Plant Biology↗

Soil developments in polar deserts: Implications for exobiology and future Mars missions

Chemical alterations, weathering, and diagenesis of soil profiles from the dry valleys of Antarctica were studied as analogs of regolith development for the Martian regolith. Chemical weathering processes play an important part in soil development within the dry valleys of Antarctica. A suite of core samples were studied which were taken within the valley floors in addition to samples taken in the vicinity of evaporite and brine ponds. Analysis of water soluable cations and anions from core samples were performed along with petrographic analysis of selected samples. It was shown that ionic transport processes operate primarily above the permafrost zone. Abundances of the water soluable ions reflect the nature of secondary minerals produced by evaporation and weathering. Chloride, calcium, and sodium abundances for soils from the cores within the North and South Forks of Wright Valley, reflect the secondary mineralogy of the soil columns. Calculations for Na, Ca, and Cl abundances reflect the appearance of halite and antarcticite. In areas where excess Ca is present, X-ray diffraction studies show the presence of gypsum. It is well known that the Martian surface conditions may be favorable for chemical weathering. Primary silicates would be expected to be reactive with any ground water. It seems likely that Martian subsurface water is available to assist in the weathering of the primary minerals. Such weathering could result in the formation of clays, sulfates, carbonates, hydrates, halides, and zeolites. The dry valley cores have shown that they maybe excellent analogs to weathering processes on the near-surface of Mars. Since movement of water within the near-surface region clearly results in chemical weathering, leaching, and salt formation in the dry valleys, similar processes are probably operating within the Martian regolith.

Gibson, Everett K., Jr.↗

A Diversity of Calcium-Rich Carbonates in EETA 79001

Carbonate minerals of martian origin are present in several martian meteorites in trace concentrations (less than 1 percent) and possess unique isotopic signatures that suggest that the martian environment and/or isotopic reservoirs are very different from the Earth’s. Carbonates are most common in the older martian meteorites (ALH 84001 and the nakhlites), however, there have been reports of carbonate in the younger shergottites including EETA 79001 (Mars meteorite Elephant Moraine 79001). Acidification studies of Zagami and Shergotty have shown that CO2 is released suggesting that carbonate phases are present in these meteorites, but the origin of these phases is controversial. The young ages of the shergottites makes them important samples for understanding the modern martian environment. The carbonates in EETA 79001 are the best-characterized secondary minerals in a shergottite, but their origin remains controversial. Gooding et al. argued that two types of carbonate occur with-in the glassy parts of the meteorite. One type, nearly pure CaCO3 associated with Ca-sulfate shows textural evidence for being present in the rock prior to it being shocked, suggesting formation on Mars. The second was more abundant and consists of Ca-rich carbonate, possibly with finely intergrown Mg-phosphate, but does not possess any textural relationships indicative of a martian origin. Carbon and oxygen isotopic studies of this carbonate yielded oxygen isotopes that potentially suggest a martian origin as well

Niles, P. B.↗

Thermo-chemo-mechanical understanding of damage development in porous cementitious materials exposed to sodium chloride under thermal cycling

Interactions between sodium chloride (NaCl) and cementitious materials have shown to facilitate premature deteriorations of concrete in cold environments. NaCl chemically interacts with tri‑calcium aluminate (C{sub 3}A) and monosulfate (AF{sub m}) resulting in a chemical phase change during thermal cycling. The chemical phase change can create damage in porous cementitious materials. Experimental and thermodynamic modeling were conducted in this study to understand the thermo-chemo-physical interactions between NaCl and cementitious materials and identify the source of the chemical phase change. Results indicates that the destructive chemical phase change is the formation of mirabilite (Na{sub 2}SO{sub 4}.10H{sub 2}O). It was found that the phase change temperature of mirabilite is strongly influenced by the concentration of NaCl in the solution. At high concentration NaCl solutions (>10% by mass), mirabilite is formed due to the release of a small amount of sulfate ions from the concrete matrix.

36 MATERIALS SCIENCE↗

Dietary and Urinary Sulfur can Predict Changes in Bone Metabolism During Space Flight

Mitigating space flight-induced bone loss is critical for space exploration, and diet can play a major role in this effort. Previous ground-based studies provide evidence that dietary composition can influence bone resorption during bed rest. In this study we examined the role of dietary intake patterns as one factor that can influence bone mineral loss in astronauts during space flight. Crew members were asked to consume, for 4 days at a time, prescribed menus with either a low (0.3-0.6 g/mEq) or high (1.0-1.3 g/mEq) ratio of animal protein to potassium (APro:K). Menus were developed for each crewmember, and were designed to meet both crew preferences and study constraints. Intakes of energy, total protein, calcium, and sodium were held relatively constant between the two diets. The order of the menus was randomized, and crews completed each set (low and high) once before and twice during space flight, for a total of 6 controlled diet sessions. One inflight session and three postflight sessions (R+30, R+180, R+365) monitored typical dietary intake. As of this writing, data are available from 14 crew members. The final three subjects' inflight samples are awaiting return from the International Space Station via Space-X. On the last day of each of the 4-d controlled diet sessions, 24-h urine samples were collected, along with a fasting blood sample on the morning of the 5th day. Preliminary analyses show that urinary excretion of sulfate (normalized to lean body mass) is a significant predictor of urinary n-telopeptide (NTX). Dietary sulfate (normalized to lean body mass) is also a significant predictor of urinary NTX. The results from this study, will be important to better understand diet and bone interrelationships during space flight as well as on Earth. This study was funded by the Human Health Countermeasures Element of the NASA Human Research Program.

Zwart, Sara R.↗

Data and scripts associated with a manuscript investigating dissolved organic matter and microbial community linkages across seven globally distributed rivers

This data package is associated with the publication “Meta-metabolome ecology reveals that geochemistry and microbial functional potential are linked to organic matter development across seven rivers” submitted to Science of the Total Environment. This data package includes the data necessary to replicate the analyses presented within the manuscript to investigate dissolved organic matter (DOM) development across broad spatial distances and within divergent biomes. Specifically, we included the Fourier transform ion cyclotron mass spectrometry (FTICR-MS) data, geochemistry data, annotated metagenomic data, and results from ecological null modeling analyses in this data package. Additionally, we included the scripts necessary to generate the figures from the manuscript. Complete metagenomic data associated with this data package can be found at the National Center for Biotechnology (NCBI) under Bioproject PRJNA946291. This dataset consists of (1) four folders; (2) a file-level metadata (flmd) file; (3) a data dictionary (dd) file; (4) a factor sheet describing samples; and (5) a readme. The FTICR Data folder contains (1) the processed Fourier transform ion cyclotron mass spectrometry (FTICR-MS) data; (2) a transformation-weighted characteristics dendrogram generated from the FTICR-MS data; and (3) the script used to generate all FTICR-MS related figures. The Geochemical Data folder contains (1) the single geochemistry data file and (2) the R script responsible for generating associated figures. The Metagenomic Data folder contains (1) annotation information across different levels; (2) carbohydrate active enzyme (CAZyme) information from the dbCAN database (Yin et al., 2012); (3) phylogenetic tree data (FASTAs, alignments, and tree file); and (4) the scripts necessary to analyze all of these data and generate figures. The Null Modeling Data folder contains (1) data generated during null modeling for each river and all rivers combined and (2) the R scripts necessary to process the data. All files are .csv, .pdf, .tsv, .tre, .faa, .afa, .tree, or .R.

54 ENVIRONMENTAL SCIENCES↗

Pyrogenic Organic Matter Laboratory Experiment: Aerobic Respiration and Geochemistry from Variably Inundated Stream Sediments (v3)

This dataset supports a broader study examining the effects of variable inundation and pyrogenic organic matter on ecosystem respiration. The dataset provides data generated from a laboratory batch experiment investigating the interaction between variable inundation conditions (wet and dry sediment) and pyrogenic organic matter (burned and unburned treatments). The contents include time series dissolved oxygen, sediment geochemistry data, and field metadata (including qualitative information on instream and river corridor characteristics). This data package was originally published in November 2025. It was updated in April 2026 (v2; new and modified files) and May 2026 (v3; modified files). See the change history section in the readme for more details For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) international generic sample number (IGSN) mapping file; (5) readme; (6) field protocol; (7) sample name metadata; (8) an environmental context picture for the dry and inundated sampling locations; and (9) a subfolder with sample data from the sediment incubation experiment. The sample data subfolder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC); (2) total nitrogen (TN); (3) gravimetric moisture; (4) partial pressure and production rates of carbon dioxide, methane, and nitrous oxide; (5) field wet sediment mass, dry sediment mass, water mass, and field wet sediment volume in incubation and sediment NPOC/TN vials; (6) methods codes; (7) respiration rates, pH, and temperature from after the incubation, raw time series dissolved oxygen and temperature, and a subfolder containing associated plots and scripts; (8) ions; (9) FTICR-MS methods; and (10) a subfolder of 12 Tesla (12T) FTICR-MS data. This folder contains the CoreMS processed data and three subfolders, one containing the .xml files, one containing the CoreMS output files, and the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .xml, .html, .Rmd, .py, .cal, .json, or .jpg.

54 ENVIRONMENTAL SCIENCES↗

Depth-resolved soil data from DOE-LM Riverton Wyoming site, April-September 2017

Averaged (from 3 to 5 replicates) and QA/QC:d data for soil cores taken roughly every month in the period April 5 to September 13 in 2017 at a location close to DOE Legacy Management well 855 at the Riverton, Wyoming floodplain site. The groundwater at this site exhibits persistent U, Mo, and sulfate plumes and is one of the field sites in focus for the SLAC Groundwater Quality SFA program. Cores were separated into 5-20 cm segments based on soil horizonation and each segment was subsampled for microbial analyses (data available at the NCBI Single Read Archive (SRA) Database, https://www.ncbi.nlm.nih.gov/sra/, BioProject ID# PRJNA626616) in addition to the soil analyses included in this dataset. The soil analyses dataset includes aerobic and anaerobic respiration rate estimates (MicroResp method), water content estimates (on collected samples, not in situ), total C, N, S, Ca, K, Mg, Na, Fe, As, Mo, U, and organic-C concentrations, water extractable concentrations of the same elements, and HCl-extractable Fe(II) concentrations.There are four files included in this data package: metadataFile.csv, avgDataFile.csv, methodFile.csv, and RVT2017soilData.xlsx. The excel file contains the same information as the individual csv-files (in separate tabs).

54 ENVIRONMENTAL SCIENCES↗

Temporal Study 2021-2022: Sample-Based Surface Water Chemistry and Organic Matter Characterization across Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of temporal variability in sediment respiration rates in the Yakima River Basin. The dataset provides geochemistry and organic matter characterization data generated from samples collected at weekly or bi-weekly intervals at six sites across the Yakima River Basin in Washington, USA. Related sensor data will be published separately and can be used to link sediment respiration rates to biogeochemical processing rates. The data package was originally published in November 2022. It was updated in November 2023 (v2; modified files) and April 2025 (new and modified files). See the change history section in readme for more details. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved inorganic carbon (DIC), dissolved organic carbon (DOC; reported as non-purgeable organic carbon; NPOC), total nitrogen (TN), total suspended solids (TSS), and ions; (5) averaged values from water chemistry data; (6) surface water sampling protocol; (7) sensor protocol; (8) readme; (9) methods codes; (10) international generic sample number (IGSN) mapping file; and (11) folder of high resolution characterization of organic via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). This folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected our data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

Spatial Study 2021: Sample-Based Surface Water Chemistry and Organic Matter Characterization across Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of spatial variability in sediment respiration rates in the Yakima River Basin. The dataset provides geochemistry and organic matter characterization data generated from samples collected during the same two-week period at 47 sites within multiple rivers throughout the Yakima River Basin in Washington, USA. Related sensor data are published at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1892054. This data package was originally published September 2022. It was updated May 2023 (modified files) and November 2024 (new and modified files). See the change history section in the readme for more details. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved inorganic carbon (DIC), dissolved organic carbon (DOC; reported as non-purgeable organic carbon; NPOC), total nitrogen (TN), total suspended solids (TSS), ions, and benzene polycarboxylic acid (BPCA) concentration and stable isotope data; (5) averaged values from water chemistry data; (6) surface water sampling protocol; (7) sensor protocol (8) readme; (9) methods codes; (10) international generic-sample number (IGSN) mapping file; and (11) folder of high resolution characterization of organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). This folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formultitude (https://github.com/PNNL-Comp-Mass-Spec/Formultitude) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml. We thank the United States Forest Service, Washington Department of Natural Resources, Washington Department of Fish and Wildlife, Washington State Parks, Confederated Tribes and Bands of the Yakama Nation, and Cowiche Canyon Conservancy for access to field locations where these samples were collected. We also thank the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗