Catastrophic chromosomal restructuring during genome elimination in plants.

Genome instability is associated with mitotic errors and cancer. This phenomenon can lead to deleterious rearrangements, but also genetic novelty, and many questions regarding its genesis, fate and evolutionary role remain unanswered. Here, we describe extreme chromosomal restructuring during genome elimination, a process resulting from hybridization of Arabidopsis plants expressing different centromere histones H3. Shattered chromosomes are formed from the genome of the haploid inducer, consistent with genomic catastrophes affecting a single, laggard chromosome compartmentalized within a micronucleus. Analysis of breakpoint junctions implicates breaks followed by repair through non-homologous end joining (NHEJ) or stalled fork repair. Furthermore, mutation of required NHEJ factor DNA Ligase 4 results in enhanced haploid recovery. Lastly, heritability and stability of a rearranged chromosome suggest a potential for enduring genomic novelty. These findings provide a tractable, natural system towards investigating the causes and mechanisms of complex genomic rearrangements similar to those associated with several human disorders

On the role of the gas environment, electron-dose-rate, and sample on the image resolution in transmission electron microscopy

AbstractThe introduction of gaseous atmospheres in transmission electron microscopy offers the possibility of studying materials in situ under chemically relevant environments. The presence of a gas environment can degrade the resolution. Surprisingly, this phenomenon has been shown to depend on the electron-dose-rate. In this article, we demonstrate that both the total and areal electron-dose-rates work as descriptors for the dose-rate-dependent resolution and are related through the illumination area. Furthermore, the resolution degradation was observed to occur gradually over time after initializing the illumination of the sample and gas by the electron beam. The resolution was also observed to be sensitive to the electrical conductivity of the sample. These observations can be explained by a charge buildup over the electron-illuminated sample area, caused by the beam–gas–sample interaction, and by a subsequent sample motion induced by electrical capacitance in the sample.</jats:p

Analysis of Structure, Composition and Growth of Semiconductor Nanowires by Transmission Electron Microscopy

Nanowires have the potential to be a very flexible platform for the design of semiconductor devices. In nanowires it is possible to form crystal structures not found in the bulk materials under normal conditions, and to combine different III-V and group IV materials into axial or radial heterostructures. As quite complex structures can be formed, both intentionally and unintentionally, characterization of the crystal structure and composition is important. In this thesis, various transmission electron microscopy techniques are presented for this purpose. High resolution imaging can directly visualize the crystal structure, including twinning and stacking faults. The polar nature of the III-V materials leaves one more parameter to be determined. In order to determine polarity from high resolution images it is not only necessary to improve the resolution further by aberration correction, but in addition the local orientation of the sample must be determined. Convergent beam electron diffraction is an alternative method with much lower demands on the microscope and operator, and can be adapted to suit most materials and crystal structures. Transmission electron microscopy also provides several methods for determining and mapping the composition of the nanowires. It is important in all cases to avoid damaging the nanowires during the acquisition of the analytical signal. In the most commonly used method, energy dispersive X-ray spectroscopy, this can be achieved by spreading the electron dose over as large an area as possible. If there is only a single unknown parameter for the composition, alternative methods such as the shift in plasmon energy with composition can be used instead, as they have higher collection efficiencies. In order to improve the nanowires in terms of crystal structure and composition, these must be connected to the dynamic processes occurring during growth. Occasionally these processes can be inferred from the fully formed nanowires after growth, but ideally one would like to observe the growth in-situ in the microscope. This is usually possible only with highly specialized environmental microscopes. In this thesis, nanowire growth in much simpler closed cells is demonstrated. Although the growth conditions could neither be precisely measured nor controlled, the closed cells made it possible to observe for the first time growing InAs nanowires in-situ in a conventional transmission electron microscope

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The fibroblast mitogen platelet-derived growth factor -BB (PDGF-BB) induces a transient expression of the orphan nuclear receptor NR4A1 (also named Nur77, TR3 or NGFIB). The aim of the present study was to investigate the pathways through which NR4A1 is induced by PDGF-BB and its functional role. We demonstrate that in PDGF-BB stimulated NIH3T3 cells, the MEK1/2 inhibitor CI-1040 strongly represses NR4A1 expression, whereas Erk5 downregulation delays the expression, but does not block it. Moreover, we report that treatment with the NF-κB inhibitor BAY11-7082 suppresses NR4A1 mRNA and protein expression. The majority of NR4A1 in NIH3T3 was found to be localized in the cytoplasm and only a fraction was translocated to the nucleus after continued PDGF-BB treatment. Silencing NR4A1 slightly increased the proliferation rate of NIH3T3 cells; however, it did not affect the chemotactic or survival abilities conferred by PDGF-BB. Moreover, overexpression of NR4A1 promoted anchorage-independent growth of NIH3T3 cells and the glioblastoma cell lines U-105MG and U-251MG. Thus, whereas NR4A1, induced by PDGF-BB, suppresses cell growth on a solid surface, it increases anchorage-independent growth

In situ etching for total control over axial and radial nanowire growth

We report a method using in situ etching to decouple the axial from the radial nanowire growth pathway, independent of other growth parameters. Thereby a wide range of growth parameters can be explored to improve the nanowire properties without concern of tapering or excess structural defects formed during radial growth. We demonstrate the method using etching by HCl during InP nanowire growth. The improved crystal quality of etched nanowires is indicated by strongly enhanced photoluminescence as compared to reference nanowires obtained without etching

Sisyphus cooling and amplification by a superconducting qubit

Laser cooling of the atomic motion paved the way for remarkable achievements in the fields of quantum optics and atomic physics, including Bose-Einstein condensation and the trapping of atoms in optical lattices. More recently superconducting qubits were shown to act as artificial two-level atoms, displaying Rabi oscillations, Ramsey fringes, and further quantum effects. Coupling such qubits to resonators brought the superconducting circuits into the realm of quantum electrodynamics (circuit QED). It opened the perspective to use superconducting qubits as micro-coolers or to create a population inversion in the qubit to induce lasing behavior of the resonator. Furthering these analogies between quantum optical and superconducting systems we demonstrate here Sisyphus cooling of a low frequency LC oscillator coupled to a near-resonantly driven superconducting qubit. In the quantum optics setup the mechanical degrees of freedom of an atom are cooled by laser driving the atom's electronic degrees of freedom. Here the roles of the two degrees of freedom are played by the LC circuit and the qubit's levels, respectively. We also demonstrate the counterpart of the Sisyphus cooling, namely Sisyphus amplification. Parallel to the experimental demonstration we analyze the system theoretically and find quantitative agreement, which supports the interpretation and allows us to estimate system parameters.Comment: 7 pages, 4 figure

Gene set of nuclear-encoded mitochondrial regulators is enriched for common inherited variation in obesity

There are hints of an altered mitochondrial function in obesity. Nuclear-encoded genes are relevant for mitochondrial function (3 gene sets of known relevant pathways: (1) 16 nuclear regulators of mitochondrial genes, (2) 91 genes for oxidative phosphorylation and (3) 966 nuclear-encoded mitochondrial genes). Gene set enrichment analysis (GSEA) showed no association with type 2 diabetes mellitus in these gene sets. Here we performed a GSEA for the same gene sets for obesity. Genome wide association study (GWAS) data from a case-control approach on 453 extremely obese children and adolescents and 435 lean adult controls were used for GSEA. For independent confirmation, we analyzed 705 obesity GWAS trios (extremely obese child and both biological parents) and a population-based GWAS sample (KORA F4, n = 1,743). A meta-analysis was performed on all three samples. In each sample, the distribution of significance levels between the respective gene set and those of all genes was compared using the leading-edge-fraction-comparison test (cut-offs between the 50(th) and 95(th) percentile of the set of all gene-wise corrected p-values) as implemented in the MAGENTA software. In the case-control sample, significant enrichment of associations with obesity was observed above the 50(th) percentile for the set of the 16 nuclear regulators of mitochondrial genes (p(GSEA,50) = 0.0103). This finding was not confirmed in the trios (p(GSEA,50) = 0.5991), but in KORA (p(GSEA,50) = 0.0398). The meta-analysis again indicated a trend for enrichment (p(MAGENTA,50) = 0.1052, p(MAGENTA,75) = 0.0251). The GSEA revealed that weak association signals for obesity might be enriched in the gene set of 16 nuclear regulators of mitochondrial genes