A Sustained Dietary Change Increases Epigenetic Variation in Isogenic Mice

Epigenetic changes can be induced by adverse environmental exposures, such as nutritional imbalance, but little is known about the nature or extent of these changes. Here we have explored the epigenomic effects of a sustained nutritional change, excess dietary methyl donors, by assessing genomic CpG methylation patterns in isogenic mice exposed for one or six generations. We find stochastic variation in methylation levels at many loci; exposure to methyl donors increases the magnitude of this variation and the number of variable loci. Several gene ontology categories are significantly overrepresented in genes proximal to these methylation-variable loci, suggesting that certain pathways are susceptible to environmental influence on their epigenetic states. Long-term exposure to the diet (six generations) results in a larger number of loci exhibiting epigenetic variability, suggesting that some of the induced changes are heritable. This finding presents the possibility that epigenetic variation within populations can be induced by environmental change, providing a vehicle for disease predisposition and possibly a substrate for natural selection.This work was supported by the Australian Research Council (DP0771859) and the National Health and Medical Research Council (#459412, #635510)

Photon Assisted Tunneling of Zero Modes in a Majorana Wire

Hybrid nanowires with proximity-induced superconductivity in the topological regime host Majorana zero modes (MZMs) at their ends, and networks of such structures can produce topologically protected qubits. In a double-island geometry where each segment hosts a pair of MZMs, inter-pair coupling mixes the charge parity of the islands and opens an energy gap between the even and odd charge states at the inter-island charge degeneracy. Here, we report on the spectroscopic measurement of such an energy gap in an InAs/Al double-island device by tracking the position of the microwave-induced quasiparticle (qp) transitions using a radio-frequency (rf) charge sensor. In zero magnetic field, photon assisted tunneling (PAT) of Cooper pairs gives rise to resonant lines in the 2e-2e periodic charge stability diagram. In the presence of a magnetic field aligned along the nanowire, resonance lines are observed parallel to the inter-island charge degeneracy of the 1e-1e periodic charge stability diagram, where the 1e periodicity results from a zero-energy sub-gap state that emerges in magnetic field. Resonant lines in the charge stability diagram indicate coherent photon assisted tunneling of single-electron states, changing the parity of the two islands. The dependence of resonant frequency on detuning indicates a sizable (GHz-scale) hybridization of zero modes across the junction separating islands

Radio-frequency methods for Majorana-based quantum devices: fast charge sensing and phase diagram mapping

Radio-frequency (RF) reflectometry is implemented in hybrid semiconductor-superconductor nanowire systems designed to probe Majorana zero modes. Two approaches are presented. In the first, hybrid nanowire-based devices are part of a resonant circuit, allowing conductance to be measured as a function of several gate voltages ~40 times faster than using conventional low-frequency lock-in methods. In the second, nanowire devices are capacitively coupled to a nearby RF single-electron transistor made from a separate nanowire, allowing RF detection of charge, including charge-only measurement of the crossover from 2e inter-island charge transitions at zero magnetic field to 1e transitions at axial magnetic fields above 0.6 T, where a topological state is expected. Single-electron sensing yields signal-to-noise exceeding 3 and visibility 99.8% for a measurement time of 1 {\mu}s

CpG Methylation of a Silent Controlling Element in the Murine Avy Allele Is Incomplete and Unresponsive to Methyl Donor Supplementation

Background: The viable yellow allele of agouti (A vy) is remarkable for its unstable and partially heritable epigenetic state, which produces wide variation in phenotypes of isogenic mice. In the A vy allele an inserted intracisternal A particle (IAP) acts as a controlling element which deregulates expression of agouti by transcription from the LTR of the IAP; the phenotypic state has been linked to CpG methylation of the LTR. Phenotypic variation between A vy mice indicates that the epigenetic state of the IAP is unstable in the germline. Principal Findings: We have made a detailed examination of somatic methylation of the IAP using bisulphite allelic sequencing, and find that the promoter is incompletely methylated even when it is transcriptionally silent. In utero exposure to supplementary methyl donors, which alters the spectrum of A vy phenotypes, does not increase the density of CpG methylation in the silent LTR. Conclusions: Our findings suggest that, contrary to previous supposition, methyl donor supplementation acts through an indirect mechanism to silence A vy. The incomplete cytosine methylation we observe at the somatically silent A vy allele ma

Dispersive sensing in hybrid InAs/Al nanowires

Dispersive charge sensing is realized in hybrid semiconductor-superconductor nanowires in gate-defined single- and double-island device geometries. Signal-to-noise ratios (SNRs) were measured both in the frequency and time domain. Frequency-domain measurements were carried out as a function of frequency and power and yield a charge sensitivity of $1 \times 10^{-3} e/\sqrt{\rm Hz}$ for an 11 MHz measurement bandwidth. Time-domain measurements yield SNR > 1 for 20 $\mu$s integration time. At zero magnetic field, photon-assisted tunneling was detected dispersively in a double-island geometry, indicating coherent hybridization of the two superconducting islands. At an axial magnetic field of 0.6 T, subgap states are detected dispersively, demonstrating the suitability of the method for sensing in the topological regime

Direct measurement of the Meissner screening profile in superconductor-superconductor bilayers using low-energy muon spin rotation

Superconducting radio frequency (SRF) cavities, which are critical components in many particle accelerators, need to be operated in the Meissner state to avoid strong dissipation from magnetic vortices. For a defect-free superconductor, the maximum attainable magnetic field for operation is set by the superheating field, $B_{\mathrm{sh}}$, which directly depends on the surface current. In heterostructures composed of different superconductors, the current in each layer depends not only on the properties of the individual material, but also on the electromagnetic response of the adjacent layers through boundary conditions at the interfaces. Three prototypical bilayers [$\mathrm{Nb_{1-x}Ti_xN}$(50 nm)/Nb, $\mathrm{Nb_{1-x}Ti_xN}$(80 nm)/Nb, and $\mathrm{Nb_{1-x}Ti_xN}$(160 nm)/Nb] are investigated here by depth-resolved measurements of their Meissner screening profiles using low-energy muon spin rotation (LE-$\mu$SR). From fits to a model based on London theory (with appropriate boundary and continuity conditions), a magnetic penetration depth for the thin $\mathrm{Nb_{1-x}Ti_xN}$ layers of $\lambda_\mathrm{Nb_{1-x}Ti_xN} =$ 182.5(31) nm is found, in good agreement with literature values for the bulk alloy. In contrast, a simple London model without appropriate boundary conditions overestimates $\lambda_\mathrm{Nb_{1-x}Ti_xN}$ by more than a factor of two, suggesting that it is inappropriate for quantifying $\lambda_\mathrm{Nb_{1-x}Ti_xN}$ here. Using the measured $\lambda_\mathrm{Nb_{1-x}Ti_xN}$, the maximum vortex-free field, $B_{\mathrm{max}}$, of the superconductor-superconductor (SS) bilayer structure was estimated to be 610(40) mT. The strong suppression of the surface current in the $\mathrm{Nb_{1-x}Ti_xN}$ layer suggests an optimal thickness of $\sim 1.4 \lambda_{\mathrm{Nb_{1-x}Ti_xN}} =$ 261(14) nm.Comment: 13 pages and 8 figure

Interlaboratory evaluation of rat hepatic gene expression changes induced by methapyrilene.

Several studies using microarrays have shown that changes in gene expression provide information about the mechanism of toxicity induced by xenobiotic agents. Nevertheless, the issue of whether gene expression profiles are reproducible across different laboratories remains to be determined. To address this question, several members of the Hepatotoxicity Working Group of the International Life Sciences Institute Health and Environmental Sciences Institute evaluated the liver gene expression profiles of rats treated with methapyrilene (MP). Animals were treated at one facility, and RNA was distributed to five different sites for gene expression analysis. A preliminary evaluation of the number of modulated genes uncovered striking differences between the five different sites. However, additional data analysis demonstrated that these differences had an effect on the absolute gene expression results but not on the outcome of the study. For all users, unsupervised algorithms showed that gene expression allows the distinction of the high dose of MP from controls and low dose. In addition, the use of a supervised analysis method (support vector machines) made it possible to correctly classify samples. In conclusion, the results show that, despite some variability, robust gene expression changes were consistent between sites. In addition, key expression changes related to the mechanism of MP-induced hepatotoxicity were identified. These results provide critical information regarding the consistency of microarray results across different laboratories and shed light on the strengths and limitations of expression profiling in drug safety analysis

Memory and relatedness of transcriptional activity in mammalian cell lineages

Phenotypically identical mammalian cells often display considerable variability in transcript levels of individual genes. How transcriptional activity propagates in cell lineages, and how this varies across genes is poorly understood. Here we combine live-cell imaging of short-lived transcriptional reporters in mouse embryonic stem cells with mathematical modelling to quantify the propagation of transcriptional activity over time and across cell generations in phenotypically homogenous cells. In sister cells we find mean transcriptional activity to be strongly correlated and transcriptional dynamics tend to be synchronous; both features control how quickly transcriptional levels in sister cells diverge in a gene-specific manner. Moreover, mean transcriptional activity is transmitted from mother to daughter cells, leading to multi-generational transcriptional memory and causing inter-family heterogeneity in gene expression

Complexity of murine cardiomyocyte miRNA biogenesis, sequence variant expression and function

microRNAs (miRNAs) are critical to heart development and disease. Emerging research indicates that regulated precursor processing can give rise to an unexpected diversity of miRNA variants. We subjected small RNA from murine HL-1 cardiomyocyte cells to next generation sequencing to investigate the relevance of such diversity to cardiac biology. ∼40 million tags were mapped to known miRNA hairpin sequences as deposited in miRBase version 16, calling 403 generic miRNAs as appreciably expressed. Hairpin arm bias broadly agreed with miRBase annotation, although 44 miR* were unexpectedly abundant (>20% of tags); conversely, 33 -5p/-3p annotated hairpins were asymmetrically expressed. Overall, variability was infrequent at the 5' start but common at the 3' end of miRNAs (5.2% and 52.3% of tags, respectively). Nevertheless, 105 miRNAs showed marked 5' isomiR expression (>20% of tags). Among these was miR-133a, a miRNA with important cardiac functions, and we demonstrated differential mRNA targeting by two of its prevalent 5' isomiRs. Analyses of miRNA termini and base-pairing patterns around Drosha and Dicer cleavage regions confirmed the known bias towards uridine at the 5' most position of miRNAs, as well as supporting the thermodynamic asymmetry rule for miRNA strand selection and a role for local structural distortions in fine tuning miRNA processing. We further recorded appreciable expression of 5 novel miR*, 38 extreme variants and 8 antisense miRNAs. Analysis of genome-mapped tags revealed 147 novel candidate miRNAs. In summary, we revealed pronounced sequence diversity among cardiomyocyte miRNAs, knowledge of which will underpin future research into the mechanisms involved in miRNA biogenesis and, importantly, cardiac function, disease and therapy.This work was supported by by the Victor Chang Cardiac Research Institute and grants 573726, 573731 and 514904 from the National Health & Medical Research Council awarded to TP