Soft X-ray spectromicroscopic proof of a reversible oxidation/reduction of microbial biofilm structures using a novel microfluidic in situ electrochemical device.

In situ electrochemistry on micron and submicron-sized individual particles and thin layers is a valuable, emerging tool for process understanding and optimization in a variety of scientific and technological fields such as material science, process technology, analytical chemistry, and environmental sciences. Electrochemical characterization and manipulation coupled with soft X-ray spectromicroscopy helps identify, quantify, and optimize processes in complex systems such as those with high heterogeneity in the spatial and/or temporal domain. Here we present a novel platform optimized for in situ electrochemistry with variable liquid electrolyte flow in soft X-ray scanning transmission X-ray microscopes (STXM).

Soft X-ray spectro-ptychography of boron nitride nanobamboos, carbon nanotubes and permalloy nanorods.

Spectro-ptychography offers improved spatial resolution and additional phase spectral information relative to that provided by scanning transmission X-ray microscopes. However, carrying out ptychography at the lower range of soft X-ray energies (e.g.

Chemical Structure and Distribution in Nickel-Nitrogen-Carbon Catalysts for CO Electroreduction Identified by Scanning Transmission X-ray Microscopy.

Atomically dispersed metal-nitrogen-carbon (M-N-C) materials are a class of electrocatalysts for fuel cell and electrochemical CO reduction (COR) applications. However, it is challenging to characterize the identity and concentration of catalytically active species owing to the structural heterogeneity of M-N-C materials. We utilize scanning transmission X-ray microscopy (STXM) as a correlative spectromicroscopy approach for spatially resolved imaging, identification, and quantification of structures and chemical species in mesoscale regions of nickel-nitrogen-carbon (Ni-N-C) catalysts, thereby elucidating the relationship between Ni content/speciation and COR activity/selectivity.

Calculating absorption dose when X-ray irradiation modifies material quantity and chemistry.

X-ray absorption is a sensitive and versatile tool for chemical speciation. However, when high doses are used, the absorbed energy can change the composition, amount and structure of the native material, thereby changing the aspects of the absorption process on which speciation is based. How can one calculate the dose when X-ray irradiation affects the chemistry and changes the amount of the material? This paper presents an assumption-free approach which can retrieve from the experimental data all dose-sensitive parameters - absorption coefficients, composition (elemental molecular units), material densities - which can then be used to calculate accurate doses as a function of irradiation.

Magnetosome magnetite biomineralization in a flagellated protist: evidence for an early evolutionary origin for magnetoreception in eukaryotes.

The most well-recognized magnetoreception behaviour is that of the magnetotactic bacteria (MTB), which synthesize membrane-bounded magnetic nanocrystals called magnetosomes via a biologically controlled process. The magnetic minerals identified in prokaryotic magnetosomes are magnetite (Fe O ) and greigite (Fe S ). Magnetosome crystals, regardless of composition, have consistent, species-specific morphologies and single-domain size range.

Misalignment between the magnetic dipole moment and the cell axis in the magnetotactic bacterium Magnetospirillum magneticum AMB-1.

While most quantitative studies of the motion of magnetotactic bacteria rely on the premise that the cells' magnetic dipole moment is aligned with their direction of motility, this assumption has so far rarely been challenged. Here we use phase contrast microscopy to detect the rotational diffusion of non-motile cells of Magnetospirillum magneticum AMB-1 around their magnetic moment, showing that in this species the magnetic dipole moment is, in fact, not exactly aligned with the cell body axis. From the cell rotational trajectories, we are able to infer the misalignment between cell magnetic moment and body axis with a precision of better than 1°, showing that it is, on average, 6°, and can be as high as 20°.

Electron beam damage of perfluorosulfonic acid studied by soft X-ray spectromicroscopy.

Scanning transmission X-ray microscopy (STXM) was used to study chemical changes to perfluorosulfonic acid (PFSA) spun cast thin films as a function of dose imparted by exposure of a 200 kV electron beam in a Transmission Electron Microscope (TEM). The relationship between electron beam fluence and absorbed dose was calibrated using a modified version of a protocol based on the positive to negative lithography transition in PMMA [Leontowich et al, J. Synchrotron Rad.

Electron beam damage of epoxy resin films studied by scanning transmission X-ray spectromicroscopy.

Focused ion beam coupled with scanning electron microscopy (FIB-SEM) is a popular technique for advanced electron microscopy with applications such as, high-precision site-specific lamella sample preparation for transmission electron microscopy (TEM) and slice-and-view FIB 3-dimensional tomography. Damage caused by the electron imaging component of FIB-SEM may be compounded with damage from the ions during the ion milling process. There are known strategies for mitigating damage from ions and electrons (cryo-SEM, dose-control, voltage control), but the electron damage on common embedding resins for EM has not been explored in detail beyond their resistance to shape-change.

Membrane-Modulating Drugs can Affect the Size of Amyloid-β Aggregates in Anionic Membranes.

The formation of amyloid-β plaques is one of the hallmarks of Alzheimer's disease. The presence of an amphiphatic cell membrane can accelerate the formation of amyloid-β aggregates, making it a potential druggable target to delay the progression of Alzheimer's disease. We have prepared unsaturated anionic membranes made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine (DMPS) and added the trans-membrane segment Aβ.

Instrumentation for in situ flow electrochemical Scanning Transmission X-ray Microscopy (STXM).

We report the design and performance of a 3-electrode device for real time in situ scanning transmission X-ray microscopy studies of electrochemical processes under both static (sealed, non-flow) conditions and with a continuous flow of electrolytes. The device was made using a combination of silicon microfabrication and 3D printing technologies. The performance is illustrated by results of a study of copper deposition and stripping at a gold working electrode.

Effect of UV radiation damage in air on polymer film thickness, studied by soft X-ray spectromicroscopy.

The thicknesses of thin films of polystyrene (PS), poly(methyl methacrylate) (PMMA), and perfluorosulfonic acid (PFSA) were measured by Ultraviolet Spectral Reflectance (UV-SR) and Scanning Transmission X-ray Microscopy (STXM). At high doses, the UV irradiation in air used in the UV-SR method was found to modify the chemical structures of PS and PMMA (but not PFSA), leading to thinning of these polymer films. The chemical changes caused by UV/air radiation damage were characterized by STXM.

First-principles X-ray absorption dose calculation for time-dependent mass and optical density.

A dose integral of time-dependent X-ray absorption under conditions of variable photon energy and changing sample mass is derived from first principles starting with the Beer-Lambert (BL) absorption model. For a given photon energy the BL dose integral D(e, t) reduces to the product of an effective time integral T(t) and a dose rate R(e). Two approximations of the time-dependent optical density, i.

Importance of the RpoE Regulon in Maintaining the Lipid Bilayer during Antimicrobial Treatment with the Polycationic Agent, Chlorhexidine.

The emergence of multidrug resistance in bacteria has reached alarming levels. To solve this growing problem, discovery of novel cellular targets or pathways important for antimicrobial resistance is urgently needed. In this study, we explored how the alternative sigma factor, RpoE, protects Escherichia coli O157 against the toxic effects of the polycationic antimicrobial agent, chlorhexidine (CHX).

Optimization of Three-Dimensional (3D) Chemical Imaging by Soft X-Ray Spectro-Tomography Using a Compressed Sensing Algorithm.

Soft X-ray spectro-tomography provides three-dimensional (3D) chemical mapping based on natural X-ray absorption properties. Since radiation damage is intrinsic to X-ray absorption, it is important to find ways to maximize signal within a given dose. For tomography, using the smallest number of tilt series images that gives a faithful reconstruction is one such method.

Iron Biochemistry is Correlated with Amyloid Plaque Morphology in an Established Mouse Model of Alzheimer's Disease.

A signature characteristic of Alzheimer's disease (AD) is aggregation of amyloid-beta (Aβ) fibrils in the brain. Nevertheless, the links between Aβ and AD pathology remain incompletely understood. It has been proposed that neurotoxicity arising from aggregation of the Aβ peptide can in part be explained by metal ion binding interactions.

X-ray Absorption Spectroscopy and Spectromicroscopy of Supported Lipid Bilayers.

The C 1s, O 1s, and N 1s X-ray absorption spectra of three lipid species, 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), and 1,2-dioleoyl-3-trimethylammonium-propane (chloride salt) (DOTAP), have been recorded using transmission detection in a scanning transmission X-ray microscope. The spectra are presented on an absolute intensity scale (i.e.

Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography.

Characterizing the chemistry and magnetism of magnetotactic bacteria (MTB) is an important aspect of understanding the biomineralization mechanism and function of the chains of magnetosomes (FeO nanoparticles) found in such species. Images and X-ray absorption spectra (XAS) of magnetosomes extracted from, and magnetosomes in, whole Magnetovibrio blakemorei strain MV-1 cells have been recorded using soft X-ray ptychography at the Fe 2p edge. A spatial resolution of 7 nm is demonstrated.

Spectromicroscopy of C and azafullerene CN: Identifying surface adsorbed water.

C fullerene crystals may serve as important catalysts for interstellar organic chemistry. To explore this possibility, the electronic structures of free-standing powders of C and (CN) azafullerenes are characterized using X-ray microscopy with near-edge X-ray adsorption fine structure (NEXAFS) spectroscopy, closely coupled with density functional theory (DFT) calculations. This is supported with X-ray photoelectron spectroscopy (XPS) measurements and associated core-level shift DFT calculations.

Magnetic Field Landscapes Guiding the Chemisorption of Diamagnetic Molecules.

It is shown that the self-assembly of diamagnetic molecule submonolayers on a surface can be influenced by magnetic stray field landscapes emerging from artificially fabricated magnetic domains and domain walls. The directed local chemisorption of diamagnetic subphthalocyaninatoboron molecules in relation to the artificially created domain pattern is proved by a combination of surface analytical methods: ToF-SIMS, X-PEEM, and NEXAFS imaging. Thereby, a new method to influence self-assembly processes and to produce patterned submonolayers is presented.

Introduction of soft X-ray spectromicroscopy as an advanced technique for plant biopolymers research.

Soft X-ray absorption spectroscopy coupled with nano-scale microscopy has been widely used in material science, environmental science, and physical sciences. In this work, the advantages of soft X-ray absorption spectromicroscopy for plant biopolymer research were demonstrated by determining the chemical sensitivity of the technique to identify common plant biopolymers and to map the distributions of biopolymers in plant samples. The chemical sensitivity of soft X-ray spectroscopy to study biopolymers was determined by recording the spectra of common plant biopolymers using soft X-ray and Fourier Transform mid Infrared (FT-IR) spectroscopy techniques.

Spectromicroscopy and coherent diffraction imaging: focus on energy materials applications.

Current and future capabilities of X-ray spectromicroscopy are discussed based on coherence-limited imaging methods which will benefit from the dramatic increase in brightness expected from a diffraction-limited storage ring (DLSR). The methods discussed include advanced coherent diffraction techniques and nanoprobe-based real-space imaging using Fresnel zone plates or other diffractive optics whose performance is affected by the degree of coherence. The capabilities of current systems, improvements which can be expected, and some of the important scientific themes which will be impacted are described, with focus on energy materials applications.

Microscopic and spectroscopic analyses of chlorhexidine tolerance in Delftia acidovorans biofilms.

The physicochemical responses of Delftia acidovorans biofilms exposed to the commonly used antimicrobial chlorhexidine (CHX) were examined in this study. A CHX-sensitive mutant (MIC, 1.0 μg ml(-1)) was derived from a CHX-tolerant (MIC, 15.

Characterization of polymer monoliths containing embedded nanoparticles by scanning transmission X-ray microscopy (STXM).

The structural and chemical homogeneity of monolithic columns is a key parameter for high efficiency stationary phases in liquid chromatography. Improved characterization techniques are needed to better understand the polymer morphology and its optimization. Here the analysis of polymer monoliths by scanning transmission X-ray microscopy (STXM) is presented for the first time.

Synchrotron-based chemical nano-tomography of microbial cell-mineral aggregates in their natural, hydrated state.

Chemical nano-tomography of microbial cells in their natural, hydrated state provides direct evidence of metabolic and chemical processes. Cells of the nitrate-reducing Acidovorax sp. strain BoFeN1 were cultured in the presence of ferrous iron.

Anomalous magnetic orientations of magnetosome chains in a magnetotactic bacterium: Magnetovibrio blakemorei strain MV-1.

There is a good deal of published evidence that indicates that all magnetosomes within a single cell of a magnetotactic bacterium are magnetically oriented in the same direction so that they form a single magnetic dipole believed to assist navigation of the cell to optimal environments for their growth and survival. Some cells of the cultured magnetotactic bacterium Magnetovibrio blakemorei strain MV-1 are known to have relatively wide gaps between groups of magnetosomes that do not seem to interfere with the larger, overall linear arrangement of the magnetosomes along the long axis of the cell. We determined the magnetic orientation of the magnetosomes in individual cells of this bacterium using Fe 2p X-ray magnetic circular dichroism (XMCD) spectra measured with scanning transmission X-ray microscopy (STXM).