Quantitative analysis of mammalian chromosome by scanning transmission soft X-ray microscopy

Differential electron yield imaging with STXM

Total electron yield (TEY) imaging is an established scanning transmission X-ray microscopy (STXM) technique that gives varying contrast based on a sample's geometry, elemental composition, and electrical conductivity. However, the TEY-STXM signal is determined solely by the electrons that the beam ejects from the sample. A related technique, X-ray beam-induced current (XBIC) imaging, is sensitive to electrons and holes independently, but requires electric fields in the sample. Here we report that multi-electrode devices can be wired to produce differential electron yield (DEY) contrast, which is also independently sensitive to electrons and holes, but does not require an electric field. Depending on whether the region illuminated by the focused STXM beam is better connected to one electrode or another, the DEY-STXM contrast changes sign. DEY-STXM images thus provide a vivid map of a device's connectivity landscape, which can be key to understanding device function and failure. To demonstrate an application in the area of failure analysis, we image a 100 nm, lithographically-defined aluminum nanowire that has failed after being stressed with a large current density.

Quantitative Distribution of DNA, RNA, Histone and Proteins Other than Histone in Mammalian Cells, Nuclei and a Chromosome at High Resolution Observed by Scanning Transmission Soft X-Ray Microscopy (STXM)

Soft X-ray microscopy was applied to study the quantitative distribution of DNA, RNA, histone, and proteins other than histone (represented by BSA) in mammalian cells, apoptotic nuclei, and a chromosome at spatial resolutions of 100 to 400 nm. The relative distribution of closely related molecules, such as DNA and RNA, was discriminated by the singular value decomposition (SVD) method using aXis2000 software. Quantities of nucleic acids and proteins were evaluated using characteristic absorption properties due to the 1s–π * transition of N=C in nucleic acids and amide in proteins, respectively, in the absorption spectra at the nitrogen K absorption edge. The results showed that DNA and histone were located in the nucleus. By contrast, RNA was clearly discriminated and found mainly in the cytoplasm. Interestingly, in a chromosome image, DNA and histone were found in the center, surrounded by RNA and proteins other than histone. The amount of DNA in the chromosome was estimated to be 0.73 pg, and the content of RNA, histone, and proteins other than histone, relative to DNA, was 0.48, 0.28, and 4.04, respectively. The method we present in this study could be a powerful approach for the quantitative molecular mapping of biological samples at high resolution.

Discrimination of DNA and RNA distribution in a mammalian cell by scanning transmission soft X-ray microscopy

Soft X-ray spectromicroscopy was applied to study the distribution of DNA and RNA in a mammalian cell at the spatial resolution of 400 nm. The relative distribution of DNA and RNA was examined by the SVD (singular value decomposition) method in aXis2000 program using combined full spectra of DNA and RNA at the absorption edge regions of carbon, nitrogen and oxygen. The absorption of nucleic acid was evaluated using 1s-π* transitions in the NEXAFS spectra at the nitrogen K absorption edge and distributed to DNA and RNA according to the relative level obtained above. The present results revealed the usefulness of the SVD method to discriminate closely related molecules such as DNA and RNA.