OMNY—A tOMography Nano crYo stage

Holler, Mirko; Raabe, Jörg; Díaz, Ana; Guizar‐Sicairos, Manuel; Wepf, Roger; Odstrčil, Michal; Shaik, Farooque Razvi; Panneels, Valérie; Menzel, Andreas; Sarafimov, B.; Maag, Stephan; Wang, X.; Thominet, Vincent; Walther, H.; Lachat, Thierry; Vitins, M.; Bunk, Oliver

doi:10.1063/1.5020247

Cited by 48 publications

(58 citation statements)

References 46 publications

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“…(b) OMNY instrument used in the cSAXS beamline (PSI) for the X-ray experiment. The sample was inserted into the OMNY cryogenic device 34 , which uses a Fresnel zone plate (FZP) to focus and define the coherent beam size. A combination of a central stop (CS) and an order sorting aperture (OSA) are used as filters, such that only the first diffraction order makes it to the sample.…”

Section: Morphology and Thickness Distribution Provided By Segmentatimentioning

confidence: 99%

“…5f. The pins containing the samples were transferred to the OMNY instrument through a modified commercial vacuum cryo transfer system (Leica EM VCT100) in liquid nitrogen 34 .…”

Section: Scanning Electron Microscopymentioning

confidence: 99%

“…The experiment was done at the cSAXS beamline of the Swiss Light Source (SLS) at the Paul Scherrer Institute (Villigen PSI, Switzerland). We use the "OMNY" ("tOMography Nano crYo") stage, an instrument that allows cryo-PXCT of biological materials 34 . The instrument comprises high-resolution 3D scanning setup, which allows nanometre precision positioning via differential interferometry and allows sample rotation over 360°.…”

Section: Scanning Electron Microscopymentioning

confidence: 99%

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Correlations between lignin content and structural robustness in plants revealed by X-ray ptychography

Polo

Pereira

Mazzafera

et al. 2020

Sci Rep

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Lignin is a heterogeneous aromatic polymer responsible for cell wall stiffness and protection from pathogen attack. However, lignin represents a bottleneck to biomass degradation due to its recalcitrance related to the natural cell wall resistance to release sugars for fermentation or further processing. A biological approach involving genetics and molecular biology was used to disrupt lignin pathway synthesis and decrease lignin deposition. Here, we imaged three-dimensional fragments of the petioles of wild type and C4H lignin mutant Arabidopsis thaliana plants by synchrotron cryoptychography. the three-dimensional images revealed the heterogeneity of vessels, parenchyma, and fibre cell wall morphologies, highlighting the relation between disturbed lignin deposition and vessel implosion (cell collapsing and obstruction of water flow). We introduce a new parameter to accurately define cell implosion conditions in plants, and we demonstrate how cryo-ptychographic X-ray computed tomography (cryo-PXCT) provides new insights for plant imaging in three dimensions to understand physiological processes. Lignin is a hydrophobic and heterogeneous biopolymer fundamental for the development of an efficient water transport system in plants, conferring structural robustness and impermeability to conduits, essential for plant stiffness 1,2. Lignin is found in the plant cell wall, mainly in vessels and fibres, forming chemical bonds with hemicellulose, which adheres to cellulose microfibrils. This polymer plays a fundamental physiological role during pathogen infection by inducing cell wall coarsening, impeding the action of fungal and bacterial cellulolytic enzymes and consequently inhibiting the pathogen invasion of surrounding tissues 3. On the other hand, for lignocellulosic biofuel production, lignin is among the molecules that limit the value of biomass crops, impacting the cellulose breakdown to glucose, which is used for further fermentation steps 4,5. Different pretreatment approaches have been developed to change the physical and chemical nanostructure of lignocellulosic biomass to alter its three-dimensional structure, interactions and composition to improve hydrolysis rates 6-10. As an alternative, genetic manipulations of the lignin biosynthetic pathway can alter the composition and reduce the content of lignin, thereby decreasing biomass recalcitrance related to the natural cell resistance to release sugars for fermentation or further processing. This effect has been largely elucidated for both Arabidopsis thaliana, a model organism for plants, and other species 1,11-15. However, the compromised growth of manipulated plants has made the commercial use of these crops a problematic issue, since the lack of cellular rigidity makes the vessels more susceptible to embolism formation 11,16,17 or collapse (i.e., conduit implosion) 18 , preventing the water transport along the plant. Therefore, it is crucial to determine the three-dimensional distribution of lignin in the cell walls and in different tissues to understand ...

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Section: Morphology and Thickness Distribution Provided By Segmentatimentioning

confidence: 99%

“…5f. The pins containing the samples were transferred to the OMNY instrument through a modified commercial vacuum cryo transfer system (Leica EM VCT100) in liquid nitrogen 34 .…”

Section: Scanning Electron Microscopymentioning

confidence: 99%

Section: Scanning Electron Microscopymentioning

confidence: 99%

See 1 more Smart Citation

Correlations between lignin content and structural robustness in plants revealed by X-ray ptychography

Polo

Pereira

Mazzafera

et al. 2020

Sci Rep

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show abstract

“…The cryo-PXCT measurements were performed at the cSAXS beamline at the SLS at the Paul Scherrer Institut (PSI), Switzerland, using the OMNY instrument (Holler et al , 2018). Samples were glued to OMNY pins (Holler et al , 2017) at room temperature and then frozen in liquid nitrogen.…”

Section: Imaging and Data Reconstructionmentioning

confidence: 99%

High-resolution synchrotron imaging studies of intact fresh roots reveal soil bacteria promoted bioremediation and bio-fortification

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Lusa

Honkanen

et al. 2019

Preprint

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Plant-microbe interactions can be utilized in bio-based processes such as bioremediation and biofortification, either to remove hazardous radionuclides and heavy metals from the soil, or to increase the accumulation of desired elements into crops to improve their quality. Optimizing such elegant plant-microbe interactions requires detailed understanding of the chemical element compositions of fresh plant tissues at cellular organelle resolution. However, such analyses remain challenging because conventional methods lack the required spatial resolution, contrast or sensitivity. Using a novel combination of nanoscaleresolution 3D cryogenic synchrotron-light ptychography, holotomography and fluorescence tomography, we show how soil bacteria interact with Arabidopsis thaliana and promote the uptake of various metals. Co-cultivation with Pseudomonas sp. strain T5-6-I alters root anatomy and increases levels of selenium (Se), iron (Fe) and other micronutrients in roots. Our approach highlights the interaction of plants and microbes in bioremediation and biofortification on the subcellular level.

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“…For some experiments, even micron sized Compound Refractive Lens (CRL) beams are used very efficiently [6]. Combined with piezo scanning sample towers and continuous 2D trajectories, large sample areas can be raster-scanned in short times [7]. Recently, a scanning micro-SAXS measurement of cardiac tissue slice in a 2 µm × 3µm CRL beam at a step size of 5 µm was performed [8].…”

Section: Introductionmentioning

confidence: 99%

STXM analysis: Preparing to go live @ 750 Hz

Osterhoff¹,

Goeman²,

Salditt³

et al. 2019

AIP Conference Proceedings

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Recent advances in detector technology, combined with continuous 2D Piezo scanning, are posing a significant challenge on data analysis. With the EigerX 4M detector by Dectris, for example, four million single-photon counting pixels can be read out at 750 Hz frame rate. Although compressed, this yields a data stream of roughly 100 MB per second. For analysis, data need to be uncompressed, yielding a data rate of more than 6 GB per second. To deal with the data obtained at such high rates in scanning transmission x-ray microscopy (STXM) measurements, we have developed a dedicated STXM analysis cluster, the "Heinzelmännchen system". With a special software, 24 computing nodes can process up to 3 500 EigerX frames per second, i.e. about four times as fast as the data is acquired. This allows for new algorithms to be developed, when datasets need to be processed multiple times in iterative schemes.

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OMNY—A tOMography Nano crYo stage

Cited by 48 publications

References 46 publications

Correlations between lignin content and structural robustness in plants revealed by X-ray ptychography

Correlations between lignin content and structural robustness in plants revealed by X-ray ptychography

High-resolution synchrotron imaging studies of intact fresh roots reveal soil bacteria promoted bioremediation and bio-fortification

STXM analysis: Preparing to go live @ 750 Hz

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