Journal: Advanced materials (Deerfield Beach, Fla.)

Article Title: Self-Oxidation Resistance of the Curved Surface of Achromatic Copper.

doi: 10.1002/adma.202210564

Figure Lengend Snippet: Figure 3. Surface structure analysis and origin of strong oxidation resistance in ACF. a) (left) Low-magnification ADF-STEM image of a top part of B-ACF, (middle) composite elemental maps of Cu (Cu K = 8.04 keV, green) and oxygen (O K = 0.525 keV, red) for B-ACF sample, and (right) ADF-STEM image of the interface region between Cu film and Al2O3 substrate. The white dashed square in the elemental map of middle panel denotes the imaging region. b,c) (left) ADF-STEM images of parts (denoted by L and R in (a)) of Cu nanograin depicting atomic steps on the surface and (right) superposition of atomic model with A–B–C planar stacking on each structure image. d) Projected atomic distance (PAD) maps for left (L), right (R), and top (T) parts of chosen Cu nanograin (denoted in a) and histogram of the measured PADs. e) DFT results. (left) Relative total energy profile of the O atom penetrating from outside into inside of biatomic step edge of a curved surface (violet open square □), compared with the biatomic step edge of a flat surface (black open square □); (right) Compression of the interlayer distances in (001) direction near the biatom step edge of curved surface of ACF. Blue spheres represent Cu atoms in bulk and dark blue spheres represent Cu atoms in the steps.

Article Snippet: In combination with STEM imaging, elemental mapping of the Cu films grown on Al2O3 (0001) substrates was performed in the same STEM imaging mode using an EDX spectrometer (JED-2300T, JEOL) with a dual-type silicon drift detector and a large effective solid angle (≈1.2 sr).

Techniques: Imaging

Journal: Ultramicroscopy

Article Title: Application of EELS and EFTEM to the Life Sciences Enabled by the Contributions of Ondrej Krivanek

doi: 10.1016/j.ultramic.2017.01.002

Figure Lengend Snippet: STEM-EELS imaging of frozen hydrated specimens at a beam energy of 100 keV using a Gatan PEELS interfaced to a VG Microscopes HB501 STEM. (a) Low-loss spectra up to an energy loss of 30 eV from major chemical constituents of cells; these can be used to fit spectra from cryosectioned cells to give quantitative compositional information; (b) Low-dose dark-field STEM of frozen hydrated liver cryosection showing no contrast apart from deformation lines; scale bar = 1 μm; (c) Water map of hepatocytes generated by multiple least squares fitting of water and protein reference spectra at each pixel revealing: mitochondria (M), cytoplasm (C), red blood cells (R), plasma (P) and lipid droplets (L); (d) Water content histogram for 2700 pixels of cytoplasm (light bars) and 500 pixels of mitochondria (dark bars) in hepatocyte, showing approximately Gaussian peaks with half width ~5%. From S. Sun et al. [27].

Article Snippet: Other laboratories have also determined water distributions using this approach [ 28 , 29 ]. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 4 caption a7 STEM-EELS imaging of frozen hydrated specimens at a beam energy of 100 keV using a Gatan PEELS interfaced to a VG Microscopes HB501 STEM. (a) Low-loss spectra up to an energy loss of 30 eV from major chemical constituents of cells; these can be used to fit spectra from cryosectioned cells to give quantitative compositional information; (b) Low-dose dark-field STEM of frozen hydrated liver cryosection showing no contrast apart from deformation lines; scale bar = 1 μm; (c) Water map of hepatocytes generated by multiple least squares fitting of water and protein reference spectra at each pixel revealing: mitochondria (M), cytoplasm (C), red blood cells (R), plasma (P) and lipid droplets (L); (d) Water content histogram for 2700 pixels of cytoplasm (light bars) and 500 pixels of mitochondria (dark bars) in hepatocyte, showing approximately Gaussian peaks with half width ~5%.

Techniques: Imaging, Generated

Journal: Ultramicroscopy

Article Title: Application of EELS and EFTEM to the Life Sciences Enabled by the Contributions of Ondrej Krivanek

doi: 10.1016/j.ultramic.2017.01.002

Figure Lengend Snippet: Spectrum-imaging of two neuronal dendrites in the vicinity of the Ca L2,3 edge, together with dark-field images (A, E) obtained using the Gatan 666 Parallel EELS attached to a VG Microscopes HB501 STEM. Background-subtracted nitrogen K-edge maps (B, F) reveal location of mitochondria and membranes of endoplasmic reticulum. Very weak signals are detected when these nitrogen maps are segmented according to compartment: endoplasmic reticulum (C, G) and mitochondria (D, H); Bars = 200 nm. Spectra at each pixel were acquired in the difference mode with a 6 eV shift to reduce noise due to channel gain variations in the photodiode array. Multiple-least-squares fit (solid curves) of filtered reference spectra for segmented spectrum-image data (circles) in endoplasmic reticulum (J) and mitochondria (K). Analysis of the Ca L2,3 edge signal showed that the ER calcium concentration was 4.9±0.4 mmol/kg dry wt., and the mitochondrial calcium concentration was 1.4±0.4 mmol/kg dry wt. From R.D. Leapman et al. [35].

Article Snippet: Other laboratories have also determined water distributions using this approach [ 28 , 29 ]. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 4 caption a7 STEM-EELS imaging of frozen hydrated specimens at a beam energy of 100 keV using a Gatan PEELS interfaced to a VG Microscopes HB501 STEM. (a) Low-loss spectra up to an energy loss of 30 eV from major chemical constituents of cells; these can be used to fit spectra from cryosectioned cells to give quantitative compositional information; (b) Low-dose dark-field STEM of frozen hydrated liver cryosection showing no contrast apart from deformation lines; scale bar = 1 μm; (c) Water map of hepatocytes generated by multiple least squares fitting of water and protein reference spectra at each pixel revealing: mitochondria (M), cytoplasm (C), red blood cells (R), plasma (P) and lipid droplets (L); (d) Water content histogram for 2700 pixels of cytoplasm (light bars) and 500 pixels of mitochondria (dark bars) in hepatocyte, showing approximately Gaussian peaks with half width ~5%.

Techniques: Imaging, Concentration Assay

Journal: Ultramicroscopy

Article Title: Application of EELS and EFTEM to the Life Sciences Enabled by the Contributions of Ondrej Krivanek

doi: 10.1016/j.ultramic.2017.01.002

Figure Lengend Snippet: Application of scanning transmission electron microscope-electron energy-loss spectroscopy (STEM-EELS) to explain contrast observed in brain magnetic resonance images (MRI) in terms of iron concentrations. (a) Optical micrograph of post-mortem human visual cortex treated with Perl stain for iron, showing elevated iron in the region of the line of Gennari (arrows). (b) Corresponding MRI, also showing contrast in the line of Gennari (arrows). Image widths in (a) and (b) are the same, and asterisks indicate boundaries of region of visual cortex. (c) Phase-contrast transmission electron microscopy of unstained section in the region of the line of Gennari showing electron-dense particles. (d–f) STEM-EELS iron maps obtained from randomly selected areas of an unstained specimen in the vicinity of the line of Gennari, showing particles with high Fe content. (g) Typical EELS extracted from one of the Fe-containing particles reveals a strong Fe L2,3 edge; quantitative analysis showed that the particles contained on average 1740 ± 580 Fe atoms, consistent with the iron cores of ferritin molecules; dotted lines indicate extrapolated background intensity. From M. Fukunaga et al. [36].

Article Snippet: Other laboratories have also determined water distributions using this approach [ 28 , 29 ]. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 4 caption a7 STEM-EELS imaging of frozen hydrated specimens at a beam energy of 100 keV using a Gatan PEELS interfaced to a VG Microscopes HB501 STEM. (a) Low-loss spectra up to an energy loss of 30 eV from major chemical constituents of cells; these can be used to fit spectra from cryosectioned cells to give quantitative compositional information; (b) Low-dose dark-field STEM of frozen hydrated liver cryosection showing no contrast apart from deformation lines; scale bar = 1 μm; (c) Water map of hepatocytes generated by multiple least squares fitting of water and protein reference spectra at each pixel revealing: mitochondria (M), cytoplasm (C), red blood cells (R), plasma (P) and lipid droplets (L); (d) Water content histogram for 2700 pixels of cytoplasm (light bars) and 500 pixels of mitochondria (dark bars) in hepatocyte, showing approximately Gaussian peaks with half width ~5%.

Techniques: Transmission Assay, Microscopy, Spectroscopy, Staining, Electron Microscopy

Journal: Ultramicroscopy

Article Title: Application of EELS and EFTEM to the Life Sciences Enabled by the Contributions of Ondrej Krivanek

doi: 10.1016/j.ultramic.2017.01.002

Figure Lengend Snippet: Spatially resolved element STEM-EELS analysis of hybrid silica nanoparticles containing quantum dots and coated with lipid that bind gadolinium; HAADF image of the lipid-coated nanoparticles (a); composite color map showing the location of different elements: red, blue and green indicate gadolinium (N4,5 edge), silicon (L2,3 edge) and carbon atoms (C K edge), respectively. From M.M. van Schooneveld et al. [39].

Article Snippet: Other laboratories have also determined water distributions using this approach [ 28 , 29 ]. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 4 caption a7 STEM-EELS imaging of frozen hydrated specimens at a beam energy of 100 keV using a Gatan PEELS interfaced to a VG Microscopes HB501 STEM. (a) Low-loss spectra up to an energy loss of 30 eV from major chemical constituents of cells; these can be used to fit spectra from cryosectioned cells to give quantitative compositional information; (b) Low-dose dark-field STEM of frozen hydrated liver cryosection showing no contrast apart from deformation lines; scale bar = 1 μm; (c) Water map of hepatocytes generated by multiple least squares fitting of water and protein reference spectra at each pixel revealing: mitochondria (M), cytoplasm (C), red blood cells (R), plasma (P) and lipid droplets (L); (d) Water content histogram for 2700 pixels of cytoplasm (light bars) and 500 pixels of mitochondria (dark bars) in hepatocyte, showing approximately Gaussian peaks with half width ~5%.

Techniques:

Journal: Nature Communications

Article Title: Disruption of tubulin-alpha4a polyglutamylation prevents aggregation of hyper-phosphorylated tau and microglia activation in mice

doi: 10.1038/s41467-022-31776-5

Figure Lengend Snippet: A – C Soluble-tubulin extraction assay using DIV15 neurons derived from Tuba4aΔpolyGlu (+/+) and (p/p) mice. A Western blot. Soluble fraction (S): un-polymerized tubulin and dissociated MAPs. Insoluble fraction (Ins): polymerized tubulin (microtubules) and associated MAPs. Fractions were probed for pan Tau, MAP2a/b, total alpha-tubulin, and polyglutamylated tubulin (polyGlu). Quantification of pan Tau ( B ) and MAP2a/b (C) in-soluble/soluble levels. Ratios smaller than 1 indicate higher protein abundance in the soluble fraction. n = 6 independent cultures per genotype. D – F Microtubule pelleting assay after repolymerization of hippocampal tubulin derived from adult mice. D Western blot. Supernatant (SN): un-polymerized tubulin and dissociated MAPs. Pellet (P): polymerized tubulin (microtubules) and associated MAPs. Fractions were probed for pan Tau, MAP2a/b, total alpha-tubulin and polyGlu. Quantification of pan Tau ( E ) and MAP2a/b ( F ) pellet/supernatant levels. Ratios smaller than 1 indicate higher protein abundance in the supernatant fraction. n = 3 mice per genotype. G – J Representative western blot analysis depicting Tau ( G ) and MAP2a/b ( H ) normalized to γ-Adaptin protein expression levels in the hippocampus. Respective quantifications are shown in ( I , J ). (+/+) set to 1. n = 5–7 experiments. K Representative super-resolution STED images of microtubules in axonal regions from DIV14 hippocampal neurons, derived from three independent experiments. Tuba4a (red), pan Tau (green). L , M Line scans: relative intensities of signals along 1 μm of microtubule length (boxed regions in ( K )). Scale bar, 500 nm. Arbitrary units (arb. units). N Mean pan Tau signal intensities normalized to Tuba4a. n = 45(+/+), 60(p/p) axonal regions. O Total Tuba4a signal intensities. n = 45(+/+), 60(p/p) axonal regions. Two-sided unpaired Student´s t-test ( B , C , E , F , I , J ) and Mann–Whitney test ( N , O ) were used to assess statistical significance. * p < 0.05, ** p < 0.01, *** p < 0.001. Data represent mean ± SEM. Source data, including exact p -values, are provided as a Source Data file.

Article Snippet: Briefly, STED images were acquired in gating mode by mean of an Abberior expert line laser scanning STED microscope.

Techniques: Extraction, Derivative Assay, Western Blot, Quantitative Proteomics, Expressing, MANN-WHITNEY