Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data

Citation: Tetreault, H. M., & Ungerer, M. C. (2016). Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data. G3-Genes Genomes Genetics, 6(8), 2299-2308. doi:10.1534/g3.116.029082/-/DC1The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia. Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius. We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny

Ecological Genomics: Understanding Gene and Genome Function in the Natural Environment

The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic variation. Likewise, genomic approaches are beginning to offer new insights into higher-level biological phenomena that previously occupied the realm of ecological investigation only. We discuss various approaches that are likely to be useful in ecological genomic studies and offer thoughts on where this field is headed in the future

Observational Constraints on Interstellar Grain Alignment

We present new multicolor photo-polarimetry of stars behind the Southern Coalsack. Analyzed together with multiband polarization data from the literature, probing the Chamaeleon I, Musca, rho Opiuchus, R CrA and Taurus clouds, we show that the wavelength of maximum polarization (lambda_max) is linearly correlated with the radiation environment of the grains. Using Far-Infrared emission data, we show that the large scatter seen in previous studies of lambda_max as a function of A_V is primarily due to line of sight effects causing some A_V measurements to not be a good tracer of the extinction (radiation field strength) seen by the grains being probed. The derived slopes in lambda_max vs. A_V, for the individual clouds, are consistent with a common value, while the zero intercepts scale with the average values of the ratios of total-to-selective extinction (R_V) for the individual clouds. Within each cloud we do not find direct correlations between lambda_max and R_V. The positive slope in consistent with recent developments in theory and indicating alignment driven by the radiation field. The present data cannot conclusively differentiate between direct radiative torques and alignment driven by H_2 formation. However, the small values of lambda_max(A_V=0), seen in several clouds, suggest a role for the latter, at least at the cloud surfaces. The scatter in the lambda_max vs. A_V relation is found to be associated with the characteristics of the embedded Young Stellar Objects (YSO) in the clouds. We propose that this is partially due to locally increased plasma damping of the grain rotation caused by X-rays from the YSOs.Comment: Accepted for publication in the Astrophysical Journa

Photon-mediated long range coupling of two Andreev level qubits

In a superconducting weak link, the supercurrent is carried by Andreev bound states (ABSs) formed by the phase-coherent reflection of electrons and their time-reversed partners. A single, highly transmissive ABS can serve as an ideal, compact two-level system, due to a potentially large energy difference to the next ABS. While the coherent manipulation of such Andreev levels qubits (ALQs) has been demonstrated, a long-range coupling between two ALQs, necessary for advanced qubit architectures, has not been achieved, yet. Here, we demonstrate a coherent remote coupling between two ALQs, mediated by a microwave photon in a novel superconducting microwave cavity coupler. The latter hosts two modes with different coupling rates to an external port. This allows us to perform fast readout of each qubit using the strongly coupled mode, while the weakly coupled mode is utilized to mediate the coupling between the qubits. When both qubits are tuned into resonance with the latter mode, we find excitation spectra with avoided-crossings, in very good agreement with the Tavis-Cummings model. Based on this model, we identify highly entangled two-qubit states for which the entanglement is mediated over a distance of six millimeters. This work establishes ALQs as compact and scalable solid-state qubits.Comment: 13 pages, 7 figure

Diversity of Flowering Responses in Wild Arabidopsis thaliana Strains

Although multiple environmental cues regulate the transition to flowering in Arabidopsis thaliana, previous studies have suggested that wild A. thaliana accessions fall primarily into two classes, distinguished by their requirement for vernalization (extended winter-like temperatures), which enables rapid flowering under long days. Much of the difference in vernalization response is apparently due to variation at two epistatically acting loci, FRI and FLC. We present the response of over 150 wild accessions to three different environmental variables. In long days, FLC is among those genes whose expression is most highly correlated with flowering. In short days, FRI and FLC are less important, although their contribution is still significant. In addition, there is considerable variation not only in vernalization response, but also in the response to differences in day length or ambient growth temperature. The identification of accessions that flower relatively early or late in specific environments suggests that many of the flowering-time pathways identified by mutagenesis, such as those that respond to day length, contribute to flowering-time variation in the wild. In contrast to differences in vernalization requirement, which are mainly mediated by FRI and FLC, it seems that variation in these other pathways is due to allelic effects at several different loci

In-situ Tuning of the Electric Dipole Strength of a Double Dot Charge Qubit: Charge Noise Protection and Ultra Strong Coupling

Semiconductor quantum dots, where electrons or holes are isolated via electrostatic potentials generated by surface gates, are promising building blocks for semiconductor-based quantum technology. Here, we investigate double quantum dot (DQD) charge qubits in GaAs, capacitively coupled to high-impedance SQUID array and Josephson junction array resonators. We tune the strength of the electric dipole interaction between the qubit and the resonator in-situ using surface gates. We characterize the qubit-resonator coupling strength, qubit decoherence, and detuning noise affecting the charge qubit for different electrostatic DQD configurations. We find that all quantities can be tuned systematically over more than one order of magnitude, resulting in reproducible decoherence rates $\Gamma_2/2\pi<~5$ MHz in the limit of high interdot capacitance. Conversely, by reducing the interdot capacitance, we can increase the DQD electric dipole strength, and therefore its coupling to the resonator. By employing a Josephson junction array resonator with an impedance of $\sim4$ k$\Omega$ and a resonance frequency of $\omega_r/2\pi \sim 5.6$ GHz, we observe a coupling strength of $g/2\pi \sim 630$ MHz, demonstrating the possibility to achieve the ultrastrong coupling regime (USC) for electrons hosted in a semiconductor DQD. These results are essential for further increasing the coherence of quantum dot based qubits and investigating USC physics in semiconducting QDs.Comment: 24 pages, 13 figure

Banking union in historical perspective: the initiative of the European Commission in the 1960s-1970s

This article shows that planning for the organization of EU banking regulation and supervision did not just appear on the agenda in recent years with discussions over the creation of the eurozone banking union. It unveils a hitherto neglected initiative of the European Commission in the 1960s and early 1970s. Drawing on extensive archival work, this article explains that this initiative, however, rested on a number of different assumptions, and emerged in a much different context. It first explains that the Commission's initial project was not crisis-driven; that it articulated the link between monetary integration and banking regulation; and finally that it did not set out to move the supervisory framework to the supranational level, unlike present-day developments

Potentiation of thrombus instability: a contributory mechanism to the effectiveness of antithrombotic medications

© The Author(s) 2018The stability of an arterial thrombus, determined by its structure and ability to resist endogenous fibrinolysis, is a major determinant of the extent of infarction that results from coronary or cerebrovascular thrombosis. There is ample evidence from both laboratory and clinical studies to suggest that in addition to inhibiting platelet aggregation, antithrombotic medications have shear-dependent effects, potentiating thrombus fragility and/or enhancing endogenous fibrinolysis. Such shear-dependent effects, potentiating the fragility of the growing thrombus and/or enhancing endogenous thrombolytic activity, likely contribute to the clinical effectiveness of such medications. It is not clear how much these effects relate to the measured inhibition of platelet aggregation in response to specific agonists. These effects are observable only with techniques that subject the growing thrombus to arterial flow and shear conditions. The effects of antithrombotic medications on thrombus stability and ways of assessing this are reviewed herein, and it is proposed that thrombus stability could become a new target for pharmacological intervention.Peer reviewedFinal Published versio

Embodied militarism and the process of disengagement from foreign fighter networks

With the collapse of the Islamic State in Syria and Iraq, international governments are scrambling to understand the process of leaving violent networks as large numbers of former fighters return to their home countries. Studies of foreign fighters have tended to emphasize the importance of ideology or trans-national identity in explaining the desire to travel across borders to participate in war. This paper looks to move beyond these accounts and investigates how embodied attachments to militarism shapes foreign fighters enduring involvement in jihadi networks. Feminist studies of militarism and armed violence have emphasized the importance of gendered forms of attachment and desire in making war possible. While this research has paid increasing attention to attachment and embodiment in shaping military personnel’s identities, far less attention has been paid to those involved in foreign fighter networks. Based on life-history research with three generations of former foreign fighters from Java (Afghanistan 1980s, Philippines 2000s, Syria/Iraq 2014-ongoing) this paper explores the complex and contradictory forms of attachment that shape their attempted transition to in civilian life. Focusing on the embodied practices of these former fighters, the article highlights the role of structural factors play in recrafting attachment and belonging

Mixing thermodynamics and electronic structure of the Pt1−xNix (0 ≤ x ≤ 1) bimetallic alloy

The development of affordable bifunctional platinum alloys as electrode materials for the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) remains one of the biggest challenges for the transition towards renewable energy sources. Yet, there is very little information on the optimal ratio between platinum and the transition metal used in the alloy and its impact on the electronic properties. Here, we have employed spin-polarised density functional simulations with long-range dispersion corrections [DFT–D3–(BJ)], to investigate the thermodynamics of mixing, as well as the electronic and magnetic properties of the Pt1−xNix solid solution. The Ni incorporation is an exothermic process and the alloy composition Pt0.5Ni0.5 is the most thermodynamically stable. The Pt0.5Ni0.5 solid solution is highly ordered as it is composed mainly of two symmetrically inequivalent configurations of homogeneously distributed atoms. We have obtained the atomic projections of the electronic density of states and band structure, showing that the Pt0.5Ni0.5 alloy has metallic character. The suitable electronic properties of the thermodynamically stable Pt0.5Ni0.5 solid solution shows promise as a sustainable catalyst for future regenerative fuel cells