4D STEM: high efficiency phase contrast imaging using a fast pixelated detector

Phase contrast imaging is widely used for imaging beam sensitive and weak phase objects in electron microscopy. In this work we demonstrate the achievement of high efficient phase contrast imaging in STEM using the pnCCD, a fast direct electron pixelated detector, which records the diffraction patterns at every probe position with a speed of 1000 to 4000 frames per second, forming a 4D STEM dataset simultaneously with the incoherent Z-contrast imaging. Ptychographic phase reconstruction has been applied and the obtained complex transmission function reveals the phase of the specimen. The results using GaN and Ti, Nd- doped BiFeO3 show that this imaging mode is especially powerful for imaging light elements in the presence of much heavier elements

Spectroscopic imaging of single atoms within a bulk solid

The ability to localize, identify and measure the electronic environment of individual atoms will provide fundamental insights into many issues in materials science, physics and nanotechnology. We demonstrate, using an aberration-corrected scanning transmission microscope, the spectroscopic imaging of single La atoms inside CaTiO3. Dynamical simulations confirm that the spectroscopic information is spatially confined around the scattering atom. Furthermore we show how the depth of the atom within the crystal may be estimated.Comment: 4 pages and 3 figures. Accepted in Phys.Rev.Let

Identification of a region required for TSC1 stability by functional analysis of TSC1 missense mutations found in individuals with tuberous sclerosis complex

Background: Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterised by the development of hamartomas in a variety of organs and tissues. The disease is caused by mutations in either the TSC1 gene on chromosome 9q34, or the TSC2 gene on chromosome 16p13.3. The TSC1 and TSC2 gene products, TSC1 and TSC2, form a protein complex that inhibits signal transduction to the downstream effectors of the mammalian target of rapamycin (mTOR). Recently it has been shown that missense mutations to the TSC1 gene can cause TSC. Methods: We have used in vitro biochemical assays to investigate the effects on TSC1 function of TSC1 missense variants submitted to the Leiden Open Variation Database. Results: We identified specific substitutions between amino acids 50 and 190 in the N-terminal region of TSC1 that result in reduced steady state levels of the protein and lead to increased mTOR signalling. Conclusion: Our results suggest that amino acid residues within the N-terminal region of TSC1 are important for TSC1 function and for maintaining the activity of the TSC1-TSC2 complex

Increasing Spatial Fidelity and SNR of 4D-STEM using Multi-frame Data Fusion

4D-STEM, in which the 2D diffraction plane is captured for each 2D scan position in the scanning transmission electron microscope (STEM) using a pixelated detector, is complementing and increasingly replacing existing imaging approaches. However, at present the speed of those detectors, although having drastically improved in the recent years, is still 100 to 1,000 times slower than the current PMT technology operators are used to. Regrettably, this means environmental scanning-distortion often limits the overall performance of the recorded 4D data. Here we present an extension of existing STEM distortion correction techniques for the treatment of 4D-data series. Although applicable to 4D-data in general, we use electron ptychography and electric-field mapping as model cases and demonstrate an improvement in spatial-fidelity, signal-to-noise ratio (SNR), phase-precision and spatial-resolution

Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, isolated from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families, and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of clade 1a and clade 1c. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from clade 1 and, will facilitate effector informed breeding strategies in other crops

Functional characterisation of the TSC1–TSC2 complex to assess multiple TSC2 variants identified in single families affected by tuberous sclerosis complex

BACKGROUND: Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterised by seizures, mental retardation and the development of hamartomas in a variety of organs and tissues. The disease is caused by mutations in either the TSC1 gene on chromosome 9q34, or the TSC2 gene on chromosome 16p13.3. The TSC1 and TSC2 gene products, TSC1 and TSC2, interact to form a protein complex that inhibits signal transduction to the downstream effectors of the mammalian target of rapamycin (mTOR). METHODS: We have used a combination of different assays to characterise the effects of a number of pathogenic TSC2 amino acid substitutions on TSC1-TSC2 complex formation and mTOR signalling. RESULTS: We used these assays to compare the effects of 9 different TSC2 variants (S132C, F143L, A196T, C244R, Y598H, I820del, T993M, L1511H and R1772C) identified in individuals with symptoms of TSC from 4 different families. In each case we were able to identify the pathogenic mutation. CONCLUSION: Functional characterisation of TSC2 variants can help identify pathogenic changes in individuals with TSC, and assist in the diagnosis and genetic counselling of the index cases and/or other family members

Imaging and Dynamics of Light Atoms and Molecules on Graphene

Observing the individual building blocks of matter is one of the primary goals of microscopy. The invention of the scanning tunneling microscope [1] revolutionized experimental surface science in that atomic-scale features on a solid-state surface could finally be readily imaged. However, scanning tunneling microscopy has limited applicability due to restrictions, for example, in sample conductivity, cleanliness, and data aquisition rate. An older microscopy technique, that of transmission electron microscopy (TEM) [2, 3] has benefited tremendously in recent years from subtle instrumentation advances, and individual heavy (high atomic number) atoms can now be detected by TEM [4 - 7] even when embedded within a semiconductor material [8, 9]. However, detecting an individual low atomic number atom, for example carbon or even hydrogen, is still extremely challenging, if not impossible, via conventional TEM due to the very low contrast of light elements [2, 3, 10 - 12]. Here we demonstrate a means to observe, by conventional transmision electron microscopy, even the smallest atoms and molecules: On a clean single-layer graphene membrane, adsorbates such as atomic hydrogen and carbon can be seen as if they were suspended in free space. We directly image such individual adatoms, along with carbon chains and vacancies, and investigate their dynamics in real time. These techniques open a way to reveal dynamics of more complex chemical reactions or identify the atomic-scale structure of unknown adsorbates. In addition, the study of atomic scale defects in graphene may provide insights for nanoelectronic applications of this interesting material.Comment: 9 pages manuscript and figures, 9 pages supplementary informatio