Quantitative water mapping of cryosectioned cells by electron energy-loss spectroscopy

A comparative modeling study of the mitochondrial function of the proximal tubule and thick ascending limb cells in the rat kidney

To reabsorb >99% of the glomerular filtrate, the metabolic demand of the kidney is high. Interestingly, renal blood flow distribution exhibits marked inhomogeneity, with typical tissue oxygen tension (Po2) of 50-60 mmHg in the well-perfused cortex and 10-20 mmHg in the inner medulla. Cellular fluid composition and acidity also varies substantially. To understand how different renal epithelial cells adapt to their local environment, we have developed and applied computational models of mitochondrial function of proximal convoluted tubule cell (baseline Po2 = 50 mmHg, cytoplasmic pH = 7.20) and medullary thick ascending limb (mTAL) cell (baseline Po2 = 10 mmHg, cytoplasmic pH = 6.85). The models predict key cellular quantities, including ATP generation, P/O (phosphate/oxygen) ratio, proton motive force, electrical potential gradient, oxygen consumption, the redox state of key electron carriers, and ATP consumption. Model simulations predict that close to their respective baseline conditions, the proximal tubule and mTAL mitochondria exhibit qualitatively similar behaviors. Nonetheless, because the mTAL mitochondrion has adapted to a much lower Po2, it can sustain a sufficiently high ATP production at Po2 as low as 4-5 mmHg, whereas the proximal tubule mitochondria would not. Also, because the mTAL cytosol is already acidic under baseline conditions, the proton motive force (pmf) exhibits higher sensitivity to further acidification. Among the different pathways that lead to oxidative phosphorylation impairment, the models predict that both the proximal tubule and mTAL mitochondria are most sensitive to reductions in Complex III activity.NEW & NOTEWORTHY Tissue fluid composition varies substantially within the mammalian kidney. The renal cortex is well perfused and pH neutral, whereas some medullary regions are hypoxic and acidic. How do these environments affect the mitochondrial function of proximal convoluted tubule and medullary thick ascending limb cells, which reside in the cortex and medulla, respectively? This computational modeling study demonstrates that these mitochondria can adapt to their contrasting environments and exhibit different sensitivities to perturbations to local environments.

Reliable Characterization of Organic & Pharmaceutical Compounds with High Resolution Monochromated EEL Spectroscopy

Organic and biological compounds (especially those related to the pharmaceutical industry) have always been of great interest for researchers due to their importance for the development of new drugs to diagnose, cure, treat or prevent disease. As many new API (active pharmaceutical ingredients) and their polymorphs are in nanocrystalline or in amorphous form blended with amorphous polymeric matrix (known as amorphous solid dispersion—ASD), their structural identification and characterization at nm scale with conventional X-Ray/Raman/IR techniques becomes difficult. During any API synthesis/production or in the formulated drug product, impurities must be identified and characterized. Electron energy loss spectroscopy (EELS) at high energy resolution by transmission electron microscope (TEM) is expected to be a promising technique to screen and identify the different (organic) compounds used in a typical pharmaceutical or biological system and to detect any impurities present, if any, during the synthesis or formulation process. In this work, we propose the use of monochromated TEM-EELS, to analyze selected peptides and organic compounds and their polymorphs. In order to validate EELS for fingerprinting (in low loss/optical region) and by further correlation with advanced DFT, simulations were utilized.

Time-resolved cathodoluminescence of DNA triggered by picosecond electron bunches

Despite the tremendous importance of so-called ionizing radiations (X-rays, accelerated electrons and ions) in cancer treatment, most studies on their effects have focused on the ionization process itself, and neglect the excitation events the radiations can induce. Here, we show that the excited states of DNA exposed to accelerated electrons can be studied in the picosecond time domain using a recently developed cathodoluminescence system with high temporal resolution. Our study uses a table-top ultrafast, UV laser-triggered electron gun delivering picosecond electron bunches of keV energy. This scheme makes it possible to directly compare time-resolved cathodoluminescence with photoluminescence measurements. This comparison revealed qualitative differences, as well as quantitative similarities between excited states of DNA upon exposure to electrons or photons.

Application of EELS and EFTEM to the life sciences enabled by the contributions of Ondrej Krivanek

The pioneering contributions of Ondrej Krivanek to the development of electron energy loss spectrometers, energy filters, and detectors for transmission and scanning transmission electron microscopes have provided researchers with indispensible tools across a wide range of disciplines in the physical sciences, ranging from condensed matter physics, to chemistry, mineralogy, materials science, and nanotechnology. In addition, the same instrumentation has extended its reach into the life sciences, and it is this aspect of Ondrej Krivanek's influential contributions that will be surveyed here, together with some personal recollections. Traditionally, electron microscopy has given a purely morphological view of the biological structures that compose cells and tissues. However, the availability of high-performance electron energy loss spectrometers and energy filters offers complementary information about the elemental and chemical composition at the subcellular scale. Such information has proven to be valuable for applications in cell and structural biology, microbiology, histology, pathology, and more generally in the biomedical sciences.

Nanoscale Concentration Quantification of Pharmaceutical Actives in Amorphous Polymer Matrices by Electron Energy-Loss Spectroscopy

We demonstrated the use of electron energy-loss spectroscopy (EELS) to evaluate the composition of phenytoin:hydroxypropyl methylcellulose acetate succinate (HPMCAS) spin-coated solid dispersions (SDs). To overcome the inability of bright-field and high-angle annular dark-field TEM imaging to distinguish between glassy drug and polymer, we used the π-π* transition peak in the EELS spectrum to detect phenytoin within the HPMCAS matrix of the SD. The concentration of phenytoin within SDs of 10, 25, and 50 wt % drug loading was quantified by a multiple least-squares analysis. Evaluating the concentration of 50 different regions in each SD, we determined that phenytoin and HPMCAS are intimately mixed at a length scale of 200 nm, even for drug loadings up to 50 wt %. At length scales below 100 nm, the variance of the measured phenytoin concentration increases; we speculate that this increase is due to statistical fluctuations in local concentration and chemical changes induced by electron irradiation. We also performed EELS analysis of an annealed 25 wt % phenytoin SD and showed that the technique can resolve concentration differences between regions that are less than 50 nm apart. Our findings indicate that EELS is a useful tool for quantifying, with high accuracy and sub-100 nm spatial resolution, the composition of many pharmaceutical and soft matter systems.

Correlative electron and X-ray microscopy: probing chemistry and bonding with high spatial resolution

Two powerful and complementary techniques for chemical characterisation of nanoscale systems are electron energy-loss spectroscopy in the scanning transmission electron microscope, and X-ray absorption spectroscopy in the scanning transmission X-ray microscope. A correlative approach to spectro-microscopy may not only bridge the gaps in spatial and spectral resolution which exist between the two instruments, but also offer unique opportunities for nanoscale characterisation. This review will discuss the similarities of the two spectroscopy techniques and the state of the art for each microscope. Case studies have been selected to illustrate the benefits and limitations of correlative electron and X-ray microscopy techniques. In situ techniques and radiation damage are also discussed.

Development and application of STEM for the biological sciences

The design of the scanning transmission electron microscope (STEM), as conceived originally by Crewe and coworkers, enables the highly efficient and flexible collection of different elastic and inelastic signals resulting from the interaction of a focused probe of incident electrons with a specimen. In the present paper we provide a brief review for how the STEM today can be applied towards a range of different problems in the biological sciences, emphasizing four main areas of application. (1) For three decades, the most widely used STEM technique has been the mass determination of proteins and other macromolecular assemblies. Such measurements can be performed at low electron dose by collecting the high-angle dark-field signal using an annular detector. STEM mass mapping has proven valuable for characterizing large protein assemblies such as filamentous proteins with a well-defined mass per length. (2) The annular dark-field signal can also be used to image ultrasmall, functionalized nanoparticles of heavy atoms for labeling specific amino-acid sequences in protein assemblies. (3) By acquiring electron energy loss spectra (EELS) at each pixel in a hyperspectral image, it is possible to map the distributions of specific bound elements like phosphorus, calcium and iron in isolated macromolecular assemblies or in compartments within sectioned cells. Near single atom sensitivity is feasible provided that the specimen can tolerate a very high incident electron dose. (4) Electron tomography is a new application of STEM that enables three-dimensional reconstruction of micrometer-thick sections of cells. In this technique a probe of small convergence angle gives a large depth of field throughout the thickness of the specimen while maintaining a probe diameter of <2 nm; and the use of an on-axis bright-field detector reduces the effects of beam broadening and thus improves the spatial resolution compared to that attainable by STEM dark-field tomography.

Development of Electron Energy Loss Spectroscopy in the Biological Sciences

The high sensitivity of electron energy loss spectroscopy (EELS) for detecting light elements at the nanoscale makes it a valuable technique for application to biological systems. In particular, EELS provides quantitative information about elemental distributions within subcellular compartments, specific atoms bound to individual macromolecular assemblies, and the composition of bionanoparticles. The EELS data can be acquired either in the fixed beam energy-filtered transmission electron microscope (EFTEM) or in the scanning transmission electron microscope (STEM), and recent progress in the development of both approaches has greatly expanded the range of applications for EELS analysis. Near single atom sensitivity is now achievable for certain elements bound to isolated macromolecules, and it becomes possible to obtain three-dimensional compositional distributions from sectioned cells through EFTEM tomography.

EELS characterization of radiolytic products in frozen samples

Electron energy loss spectroscopy (EELS) was used to obtain information about the radiation chemistry of frozen aqueous specimens in the electron microscope by observing the hydrogen and oxygen K-edges. Measurements on frozen solutions of 30% hydrogen peroxide revealed the presence of molecular oxygen identified by a distinct 531-eV peak at the O K-edge even for electron doses below 100 e/nm². The molecular oxygen content of irradiated H₂O₂ solution was determined by least squares fitting of O K-edge reference spectra from water and gas-phase oxygen. It was found that the fraction of molecular oxygen to water oxygen was in the range 0.03-0.05. EELS from pure frozen water showed no features attributable to molecular oxygen or molecular hydrogen (K edge at ~13 eV) even at high electron doses above 10⁵ e/nm². Spectra from frozen sucrose and protein solutions and their mixtures, however, did show evolution of a molecular hydrogen peak at ~13 eV for doses above 10⁵ e/nm², consistent with previous measurements and indicative of hydrogen bubble formation. Molecular oxygen was not observed in any of the frozen solutions of organic compounds indicating that oxygen is not a major product of free radical decay, in contrast to molecular hydrogen formation.

Nanoscale composition of biphasic polymer nanocolloids in aqueous suspension

The molecular distribution in nanocolloids of poly(dimethyl siloxane) (PDMS) and an organic copolymer (methyl acrylate co-methyl methacrylate co-vinyl acetate) preserved in a frozen aqueous solution was investigated using cryovalence electron energy-loss spectroscopy (EELS) coupled with a scanning transmission electron microscope. Low energy-loss spectra depend upon valence electron structure, and we show that they are substantially different for the PDMS, the copolymer, and the vitrified water studied here. Combining a high efficiency detection system and the use of high-signal low-loss spectra in EELS, we achieved a spatial resolution of 8 nm without serious beam-induced specimen damage in this radiation-sensitive soft-materials system. To obtain quantitative phase maps of silicone and copolymer composition within individual nanoparticles, spectrum datasets were processed via multiple least squares fitting. Quantitative line profiles from the resulting compositional maps indicate that the PDMS lobe of biphasic nanoparticles contained a significant amount of the copolymer and a diffuse interface was formed. Since the nanoparticle synthesis involves polymerization of acrylate monomer dissolved in PDMS nanoparticle precursors, these results suggest that the evolution of the nanocolloid morphology during synthesis is kinetically frozen as the acrylate copolymer achieves some critical molecular weight.

Diffuse Polymer Interfaces in Lobed Nanoemulsions Preserved in Aqueous Media

Using valence electron energy loss spectroscopy (EELS) in the cryo-scanning transmission electron microscopy (STEM), we found that the polymer-polymer interface in two-phase nanocolloids of polydimethyl siloxane (PDMS) and copolymer (methyl acrylate (MA)-methyl methacrylate (MMA)-vinyl acetate (VA)) preserved in water was diffuse despite the fact that equilibrium thermodynamics indicates it should only be on the order of a few nanometers. The diffuse interface is a result of the kinetic trapping of the copolymer within the PDMS phase, and this finding suggests new nonequilibrium pathways to control interfaces during the synthesis of multicomponent polymeric nanostructures.

Water mapping in hydrated soft materials

We present a method based on spatially resolved electron energy-loss spectroscopy in the cryo-STEM to map the spatial distribution of water in frozen-hydrated polymers. The spatial resolution is limited by the dose constraints imposed by radiation damage, and to stay within these constraints, the use of fine electron-probe sizes comes at the cost of reduced counts in the energy-loss spectra. Thus, at the resolution limit, the detection of isolated water-rich pixels or the identification of minor variations in water content across the specimen is complicated because one must distinguish significant fluctuations from noise. Here we develop a criterion with which to guide such a distinction. We characterize the intrinsic noise associated with spectral measurements under given illumination and acquisition conditions. We then use that noise in combination with scatter diagrams to threshold spectrum images and objectively identify statistically significant compositional fluctuations. We illustrate these ideas using a simulated spectrum dataset for a hypothetical blend of hydrophilic and hydrophobic homopolymers. We show that while a direct inspection of the water map may not allow any meaningful conclusions to be drawn, after applying the thresholding approach we can clearly identify the regions of the specimen that are rich in water. We also experimentally study a model blend system comprised of hydrophilic poly(vinyl pyrrolidone) (PVP) dispersed in a hydrophobic matrix of poly(styrene) (PS). By MLS fitting using damaged and undamaged PVP reference spectra, we determine that the critical dose characteristic of dry PVP is approximately 8000 e/nm2 using 200 keV incident electrons. Irradiating frozen-hydrated PVP gives rise to noticeable hydrogen evolution at doses of approximately 1500 e/nm2. To stay within this constraint we use doses of 400 e/nm2 and a pixel spacing in the spectrum imaging of 100 nm. In order to quantitatively map the water, PVP, and PS compositions, we measure their total inelastic scattering cross-sections. Direct inspection of the composition maps reveals the presence of large water-rich domains of the order of approximately 1 microm and the scatter-diagram thresholding approach identifies small water-rich domains one pixel in size.

Organization of interphase chromatin

The organization of interphase chromatin spans many topics, ranging in scale from the molecular level to the whole nucleus, and its study requires a concomitant range of experimental approaches. In this review, we examine these approaches, the results they have generated, and the interfaces between them. The greatest challenge appears to be the integration of information on whole nuclei obtained by light microscopy with data on nucleosome-nucleosome interactions and chromatin higher-order structures, obtained in vitro using biophysical characterization, atomic force microscopy, and electron microscopy. We consider strategies that may assist in the integration process, and we review emerging technologies that promise to reduce the "resolution gap."

The distribution of light elements in biological cells measured by electron probe X-ray microanalysis of cryosections

The intracellular distribution of the elements carbon, nitrogen, and oxygen was measured in cultured rat hepatocytes by energy dispersive electron probe X-ray microanalysis of 100-nm-thick freeze-dried cryosections. Electron irradiation with a dose up to 106 e/nm2 caused no or merely negligible mass loss in mitochondria and in cytoplasm. Cell nuclei lost carbon, nitrogen, and-to a clearly higher extent-oxygen with increasing electron irradiation. Therefore, electron doses less than 3 x 105 e/nm2 were used to measure the subcellular compartmentation of carbon, nitrogen, and oxygen in cytoplasm, mitochondria, and nuclei of the cells. The subcellular distribution of carbon, nitrogen, and oxygen reflects the intracellular compartmentation of various biomolecules. Cells exposed to inorganic mercury before cryofixation showed an increase of oxygen in nuclei and cytoplasm. Concomitantly the phosphorus/nitrogen ratio decreased in mitochondria. The data suggest mercury-induced production of ribonucleic acid (RNA) and decrease of adenosine triphosphate (ATP). Although biomolecules cannot be identified by X-ray microanalysis, measurements of the whole element spectrum including the light elements carbon, nitrogen, and oxygen can be useful to study specific biomolecular activity in cellular compartments depending on the functional state of the cell.

Valence excitations in electron microscopy: resolved and unresolved issues

Recent progress in the interpretation of spatially localized valence loss spectra is outlined. For a well-defined geometry of dielectric interfaces, detailed and quantitative analysis is now possible. In other cases, useful results may still be available although the common assumption that the spectrum at each point should be directly related to that from a uniform reference sample of appropriate composition may not always be valid.

Detecting single atoms of calcium and iron in biological structures by electron energy-loss spectrum-imaging

As techniques for electron energy-loss spectroscopy (EELS) reach a higher degree of optimization, experimental detection limits for analysing biological structures are approaching values predicted by the physics of the electron scattering. Theory indicates that it should be possible to detect a single atom of certain elements like calcium and iron contained in a macromolecular assembly using a finely focused probe in the scanning transmission electron microscope (STEM). To test this prediction, EELS elemental maps have been recorded with the spectrum-imaging technique in a VG Microscopes HB501 STEM coupled to a Gatan Enfina spectrometer, which is equipped with an efficient charge-coupled device (CCD) array detector. By recording spectrum-images of haemoglobin adsorbed onto a thin carbon film, it is shown that the four heme groups in a single molecule can be detected with a signal-to-noise ratio of approximately 10 : 1. Other measurements demonstrate that calcium adsorbed onto a thin carbon film can be imaged at single atom sensitivity with a signal-to-noise ratio of approximately 5 : 1. Despite radiation damage due to the necessarily high electron dose, it is anticipated that mapping single atoms of metals and other bound elements will find useful applications in characterizing large protein assemblies.

Electron tomographic analysis of frozen-hydrated tissue sections

Electron tomography of frozen-hydrated tissue sections enables analysis of the 3-D structure of cell organelles in situ and in a near-native state. In this study, 160-200-nm-thick sections were cut from high-pressure frozen rat liver, and improved methods were used for handling and mounting the sections. Automated data collection facilitated tilt-series recording at low electron dose (approximately 4000 e(-)/nm(2) at 400 keV). Higher doses (up to 10,000 e(-)/nm(2)) were found to increase contrast and smooth out surface defects, but caused section distortion and movement, with likely loss of high-resolution information. Tomographic reconstruction showed that knife marks were 10-40 nm deep and located on the "knife face" of the section, while crevices were 20-50 nm deep and found on the "block face." The interior of the section was normally free of defects, except for compression, and contained useful structural information. For example, the topology of mitochondrial membranes in tissue was found to be very similar to that in frozen-hydrated whole mounts of isolated mitochondria. In rare cases, a 15-nm banding pattern perpendicular to the cutting direction was observed in the interior of the section, most evident in the uniformly dense, protein-rich material of the mitochondrial matrix.

Structure and mass analysis by scanning transmission electron microscopy

In the scanning transmission electron microscope (STEM) an electron beam of a few angstroms diameter is raster scanned over a thin sample and the scattered electrons are sequentially measured for each sample element irradiated. The mass, the elemental composition and the structure of a protein can be simultaneously assessed if all detector systems of the STEM are used. Aspects affecting the accuracy of the mass measurement technique and the demands placed on the instrument's dark-field detector system are outlined. In addition, the influences of some sample preparation techniques are noted and the mass-loss induced at ambient temperatures by the incidence of 80kV electrons on various biological samples is reported. Finally, the importance of the STEM for the structural analysis of proteins is documented by examples.

Low energy loss electron microscopy of chromophores

A novel prism-mirror-prism imaging electron spectrometer with 1 eV energy resolution for a transmission electron microscope permits imaging with spectral energies corresponding to light-optical colour absorptions. The instrument selects the molecular orbital excitations of natural chromophores or of specific dyes normally used in biological light microscopy for delineation and chemical identification, but images them with electron microscopic detail. Heavy atom contrast agents customarily used in electron microscopy are not required. The first results exploit the intrinsic red colour of hematin molecules to demonstrate the potential of the technique and address its spatial resolution. Glycosaminoglycans in cartilage stained with Alcian blue are selectively depicted in situ by means of the electron-induced molecular absorption of this chromophore. Thus, with the use of specific colours the direct or indirect analysis of local chemistry by electron microscopy is possible, and can be carried out with a depiction of spatial detail as small as 16 A, or at least 100-fold finer than observed by light microscopy.

Intracellular mapping of 4'-deoxy-4'-iododoxorubicin in sensitive and multidrug resistant cells by electron spectroscopic imaging

Electron spectroscopic imaging (ESI) was employed to study, with high spatial resolution, the intracellular distribution of the halogenated derivative of doxorubicin 4'-deoxy-4'-iododoxorubicin (IDX) in sensitive and multidrug resistant human breast carcinoma cells. Both ESI and electron energy loss spectroscopy (EELS) observations confirmed results obtained with flow cytometry (FC), laser scanning confocal microscopy (LSCM) and secondary ion mass spectrometry (SIMS). Moreover, ESI allowed us to obtain a more detailed intracellular localization of IDX. Our results confirm that nuclear DNA represents the main intracellular target for IDX and that the Golgi apparatus is involved in the intracellular transport of the drug.

Thickness measurement of hydrated and dehydrated cryosections by EELS

Electron energy-loss spectroscopy (EELS) provides a useful method for determining the thickness of frozen-hydrated and dehydrated cryosections in terms of the inelastic mean free path. Cryosection thickness is an important parameter because plural inelastic scattering limits the sensitivity of elemental microanalysis based on core-loss EELS, and because overlapping structures can affect interpretation of microanalytical data as well as the quality of electron images. The purpose of this work was to establish the minimum practical thickness for cutting cryosections and to explain the measured values for hydrated and dehydrated specimens. Hydrated sections were typically found to be between 1.5-2.5 times thicker than expected from the nominal microtome setting; this difference can be largely explained by compression during cutting. Comparison of micrographs from hydrated and dehydrated cryosections of rapidly-frozen, vitrified liver revealed a lateral shrinkage of approximately 20% on drying. The measured compression and shrinkage factors are consistent with dark-field scanning transmission electron microscopy (STEM) mass measurements on freeze-dried sections. Freeze-dried cryosections, cut to a nominal thickness of 90 nm and supported on thin Formvar/carbon films, had a relative thickness t/lambda i in the range of 0.5 for cytoplasm to 0.9 for mitochondria when analyzed at 100 keV beam energy. Mass loss of approximately 30% occurring at high electron dose enabled useful core-loss spectra to be recorded even from high-mass compartments such as mitochondria without excessive plural scattering.

Cryo-electron energy loss spectroscopy: observations on vitrified hydrated specimens and radiation damage

Valence electron energy loss spectroscopy (EELS) has been used to characterize the composition of frozen-hydrated specimens in the electron microscope. Fine structure in the energy range up to 30 eV provides a means of distinguishing between vitreous and crystalline ice. Some features of the ice spectrum can be understood in terms of transitions between molecular orbitals in the water molecule and by the existence of excitons in the solid. Spectra from hydrated biological specimens can be analyzed to obtain quantitative estimates of the water content by fitting contributions from the ice and organic components. EELS also provides information about the radiation chemistry that occurs when hydrated specimens are exposed to the electron beam. From the observation of the hydrogen K-edge at approximately 13 eV, it can be deduced that bubbles of molecular hydrogen are evolved during irradiation at doses of > 10(4) nm-2, and that these bubbles contain gas at pressures in excess of one thousand atmospheres.