Zooming in: a single-cell perspective on nitrogen fixation in the rhizosphere of rice

2020 ◽  
Author(s):  
Hannes Schmidt ◽  
Stefan Gorka ◽  
David Seki ◽  
Arno Schintlmeister ◽  
Dagmar Woebken
Keyword(s):  
Single Cell ◽  
Secondary Ion Mass Spectrometry ◽  
World Population ◽  
Hotspot Detection ◽  
Engineer Plant ◽  
The Individual ◽  
Root Surfaces ◽  
Secondary Ion ◽  
Microbial Hotspots

<p>Our current understanding of microbial hotspots such as the rhizosphere mainly stems from observations through measurements at the macroscopic scale, integrating a multitude of microbial cells and taxa into a few measured variables. Consequently, we still lack an understanding of the individual participants that actively contribute to processes. Identifying microorganisms and relating their activity to these processes within the soil-plant interface on a microscopic scale represent a missing link in understanding nutrient flux in agriculturally important ecosystems such as rice cultivation.</p><p>I will present a novel workflow for single-cell isotope imaging in the rhizosphere that combines fluorescence <em>in situ</em> hybridization, gold-targeted secondary electron microscopy, and nano-scale secondary ion mass spectrometry. Based on correlative microscopy and hotspot detection, this approach now allows to (i) identify single bacteria on root surfaces that actively incorporate stable isotopes, (ii) quantify their contribution to processes of interest within a given population, and (iii) potentially trace nutrient fluxes among plants and bacteria on a microscale.</p><p>Illuminating plant-microorganism interactions on a microscale provides the potential to evaluate the actual impact of bio-inoculants applied as fertilizers and to engineer plant-microorganism associations which may be essential to increase the production of major staple crops for a growing world population.</p>

Optics-Free Visualization of Proteins in Single Cells by Time of Flight-Secondary Ion Mass Spectrometry Coupled with Genetically Encoded Chemical Tags

2020 ◽  
Author(s):  
Feifei Jia ◽  
Jie Wang ◽  
Yanyan Zhang ◽  
Qun Luo ◽  
Luyu Qi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Secondary Ion Mass Spectrometry ◽  
Single Cells ◽  
Time Of Flight ◽  
E Coli ◽  
Tof Sims ◽  
Ion Mass Spectrometry ◽  
Chemical Tags ◽  
Secondary Ion

<p></p><p><i>In situ</i> visualization of proteins of interest at single cell level is attractive in cell biology, molecular biology and biomedicine, which usually involves photon, electron or X-ray based imaging methods. Herein, we report an optics-free strategy that images a specific protein in single cells by time of flight-secondary ion mass spectrometry (ToF-SIMS) following genetic incorporation of fluorine-containing unnatural amino acids as a chemical tag into the protein via genetic code expansion technique. The method was developed and validated by imaging GFP in E. coli and human HeLa cancer cells, and then utilized to visualize the distribution of chemotaxis protein CheA in E. coli cells and the interaction between high mobility group box 1 protein and cisplatin damaged DNA in HeLa cells. The present work highlights the power of ToF-SIMS imaging combined with genetically encoded chemical tags for <i>in situ </i>visualization of proteins of interest as well as the interactions between proteins and drugs or drug damaged DNA in single cells.</p><p></p>

scholarly journals Triple Oxygen Isotope Measurements by Multi-Collector Secondary Ion Mass Spectrometry

2021 ◽  
Vol 8 ◽  
Author(s):  
Nordine Bouden ◽  
Johan Villeneuve ◽  
Yves Marrocchi ◽  
Etienne Deloule ◽  
Evelyn Füri ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Oxygen Isotope ◽  
Spatial Resolution ◽  
Secondary Ion Mass Spectrometry ◽  
Small Radius ◽  
Large Radius ◽  
Ion Mass Spectrometry ◽  
Secondary Ion ◽  
Isotope Measurements

Secondary ion mass spectrometry (SIMS) is a powerful technique for in situ triple oxygen isotope measurements that has been used for more than 30 years. Since pioneering works performed on small-radius ion microprobes in the mid-80s, tremendous progress has been made in terms of analytical precision, spatial resolution and analysis duration. In this respect, the emergence in the mid-90s of the large-radius ion microprobe equipped with a multi-collector system (MC-SIMS) was a game changer. Further developments achieved on CAMECA MC-SIMS since then (e.g., stability of the electronics, enhanced transmission of secondary ions, automatic centering of the secondary ion beam, enhanced control of the magnetic field, 1012Ω resistor for the Faraday cup amplifiers) allow nowadays to routinely measure oxygen isotopic ratios (18O/16O and 17O/16O) in various matrices with a precision (internal error and reproducibility) better than 0.5‰ (2σ), a spatial resolution smaller than 10 µm and in a few minutes per analysis. This paper focuses on the application of the MC-SIMS technique to the in situ monitoring of mass-independent triple oxygen isotope variations.

Direct visualization of a vast cortical calcium compartment in Paramecium by secondary ion mass spectrometry (SIMS) microscopy: possible involvement in exocytosis

1995 ◽  
Vol 108 (5) ◽  
pp. 1895-1909 ◽  
Author(s):  
N. Stelly ◽  
S. Halpern ◽  
G. Nicolas ◽  
P. Fragu ◽  
A. Adoutte
Keyword(s):  
Mass Spectrometry ◽  
Secondary Ion Mass Spectrometry ◽  
Membrane Vesicles ◽  
Cell Periphery ◽  
A Value ◽  
External Reference ◽  
Ion Mass Spectrometry ◽  
First Time ◽  
Secondary Ion

The plasma membrane of ciliates is underlaid by a vast continuous array of membrane vesicles known as cortical alveoli. Previous work had shown that a purified fraction of these vesicles actively pumps calcium, suggesting that alveoli may constitute a calcium-storage compartment. Here we provide direct confirmation of this hypothesis using in situ visualization of total cell calcium on sections of cryofixed and cryosubstituted cells analyzed by SIMS (secondary ion mass spectrometry) microscopy a method never previously applied to protists. A narrow, continuous, Ca-emitting zone located all along the cell periphery was observed on sections including the cortex. In contrast, Na and K were evenly distributed throughout the cell. Various controls confirmed that emission was from the alveoli, in particular, the emitting zone was still seen in mutants totally lacking trichocysts, the large exocytotic organelles docked at the cell surface, indicating that they make no major direct contribution to the emission. Calcium concentration within alveoli was quantified for the first time in SIMS microscopy using an external reference and was found to be in the range of 3 to 5 mM, a value similar to that for sarcoplasmic reticulum. After massive induction of trichocyst discharge, this concentration was found to decrease by about 50%, suggesting that the alveoli are the main source of the calcium involved in exocytosis.

The distribution and abundance of halogens in eclogites: An in situ SIMS perspective of the Raspas Complex (Ecuador)

2020 ◽  
Vol 105 (3) ◽  
pp. 307-318 ◽  
Author(s):  
Benjamin M. Urann ◽  
Véronique Le Roux ◽  
Timm John ◽  
Grace M. Beaudoin ◽  
Jaime D. Barnes
Keyword(s):  
Upper Mantle ◽  
Subduction Zones ◽  
Secondary Ion Mass Spectrometry ◽  
Bulk Rock ◽  
Ocean Island Basalts ◽  
High Pressure Metamorphism ◽  
Southern Ecuador ◽  
And Behavior ◽  
Secondary Ion

Abstract We present in situ secondary ion mass spectrometry (SIMS) and electron microprobe analyses of coexisting garnet, omphacite, phengite, amphibole, and apatite, combined with pyrohydrolysis bulk-rock analyses to constrain the distribution, abundance, and behavior of halogens (F and Cl) in six MORB-like eclogites from the Raspas Complex (Southern Ecuador). In all cases concerning lattice-hosted halogens, F compatibility decreases from apatite (1.47–3.25 wt%), to amphibole (563–4727 μg/g), phengite (610–1822 μg/g), omphacite (6.5–54.1 μg/g), and garnet (1.7–8.9 μg/g). The relative compatibility of Cl in the assemblage is greatest for apatite (192–515 μg/g), followed by amphibole (0.64–82.7 μg/g), phengite (1.2–2.1 μg/g), omphacite (&lt;0.05–1.0 μg/g), and garnet (&lt;0.05 μg/g). Congruence between SIMS-reconstructed F bulk abundances and yield-corrected bulk pyrohydrolysis analyses indicates that F is primarily hosted within the crystal lattice of eclogitic minerals. However, SIMS-reconstructed Cl abundances are a factor of five lower, on average, than pyrohydrolysis-derived bulk concentrations. This discrepancy results from the contribution of fluid inclusions, which may host at least 80% of the bulk rock Cl. The combination of SIMS and pyrohydrolysis is highly complementary. Whereas SIMS is well suited to determine bulk F abundances, pyrohydrolysis better quantifies bulk Cl concentrations, which include the contribution of fluid inclusion-hosted Cl. Raspas eclogites contain 145–258 μg/g F and at least 7–11 μg/g Cl. We estimate that ~95% of F is retained in the slab through eclogitization and returned to the upper mantle during subduction, whereas at least 95% of subducted Cl is removed from the rock by the time the slab equilibrates at eclogite facies conditions. Our calculations provide further evidence for the fractionation of F from Cl during high-pressure metamorphism in subduction zones. Although the HIMU (high U/Pb) mantle source (dehydrated oceanic crust) is often associated with enrichments in Cl/K and F/Nd, Raspas eclogites show relatively low halogen ratios identical within uncertainty to depleted MORB mantle (DMM). Thus, the observed halogen enrichments in HIMU ocean island basalts require either further fractionation during mantle processing or recycling of a halogen-enriched carrier lithology such as serpentinite into the mantle.

Characteristics and Recovery of SI Surfaces Plasma Etching in CHF3 / C2F6

1992 ◽  
Vol 259 ◽  
Author(s):  
H.-H. Park ◽  
K.-H. Kwon ◽  
B.-H. Koak ◽  
S.-M. Lee ◽  
O.-J. Kwon ◽  
...  
Keyword(s):  
Photoelectron Spectroscopy ◽  
Silicon Surface ◽  
Secondary Ion Mass Spectrometry ◽  
High Vacuum ◽  
Silicon Layer ◽  
Ultra High Vacuum ◽  
Rapid Thermal Anneal ◽  
Condition C ◽  
Secondary Ion

ABSTRACTThe effects of SiO2 reactive ion etching (RIE) in CHF3 / C2F6 on the surface properties of the underlying Si substrate have been studied by X-ray photoelectron spectroscopy (XPS) and secondary ion mass spectrometry (SIMS) techniques. The observed two major modifications are (i) a ∼50nm thick silicon layer which contains carbon and fluorine and (ii) 2∼3nm thick residue layer composed entirely of carbon, fluorine, oxygen and hydrogen on the silicon surface. The thermal behaviors of attributed peaks for C 1s, Si 2p, O 1s and F 1s of residue film have been analyzed after in-situ resistive anneal under ultra high vacuum (UHV) condition. C-F1, C-F2 and C-F3 bonds decompose and form C-CFx (x≤3) bonds above 200°C. Above 400°C, C-CFx bonds also decompose to C-C/H bonds. For recovery of the modified silicon surface, reactive ion etched specimens have been exposed to an oxygen plasma. By XPS analysis, the effect of an O2 plasma treatment has been revealed to be completed within 20min. With an O2 plasma pre-treated, a rapid thermal anneal (RTA) treatment as low as 500°2 is found to be effective for removal of impurities in the silicon.

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