Development of a Next-Generation NIL Library in Arabidopsis Thaliana for Dissecting Complex Traits

The identification of the loci and specific alleles underlying variation in quantitative traits is an important goal for evolutionary biologists and breeders. Despite major advancements in genomics technology, moving from QTL to causal alleles remains a major challenge in genetics research. Near-isogenic lines are the ideal raw material for QTL validation, refinement of QTL location and, ultimately, gene discovery. Results: In this study, a population of 75 Arabidopsis thaliana near-isogenic lines was developed from an existing recombinant inbred line (RIL) population derived from a cross between physiologically divergent accessions Kas-1 and Tsu-1. First, a novel algorithm was developed to utilize genome-wide marker data in selecting RILs fully isogenic to Kas-1 for a single chromosome. Seven such RILs were used in 2 generations of crossing to Tsu-1 to create BC1 seed. BC1 plants were genotyped with SSR markers so that lines could be selected that carried Kas-1 introgressions, resulting in a population carrying chromosomal introgressions spanning the genome. BC1 lines were genotyped with 48 genome-wide SSRs to identify lines with a targeted Kas-1 introgression and the fewest genomic introgressions elsewhere. 75 such lines were selected and genotyped at an additional 41 SNP loci and another 930 tags using 2b-RAD genotyping by sequencing. The final population carried an average of 1.35 homozygous and 2.49 heterozygous introgressions per line with average introgression sizes of 5.32 and 5.16 Mb, respectively. In a simple case study, we demonstrate the advantage of maintaining heterozygotes in our library whereby fine-mapping efforts are conducted simply by self-pollination. Crossovers in the heterozygous interval during this single selfing generation break the introgression into smaller, homozygous fragments (sub-NILs). Additionally, we utilize a homozygous NIL for validation of a QTL underlying stomatal conductance, a low heritability trait. Conclusions: The present results introduce a new and valuable resource to the Brassicaceae research community that enables rapid fine-mapping of candidate loci in parallel with QTL validation. These attributes along with dense marker coverage and genome-wide chromosomal introgressions make this population an ideal starting point for discovery of genes underlying important complex traits of agricultural and ecological significance.NSF DEB-1022196, DEB-0618302, DEB-0618347, IOS-09221457Integrative Biolog

Contrasting xylem vessel constraints on hydraulic conductivity between native and non-native woody understory species

We examined the hydraulic properties of 82 native and non-native woody species common to forests of Eastern North America, including several congeneric groups, representing a range of anatomical wood types. We observed smaller conduit diameters with greater frequency in non-native species, corresponding to lower calculated potential vulnerability to cavitation index. Non-native species exhibited higher vessel-grouping in metaxylem compared with native species, however, solitary vessels were more prevalent in secondary xylem. Higher frequency of solitary vessels in secondary xylem was related to a lower potential vulnerability index. We found no relationship between anatomical characteristics of xylem, origin of species and hydraulic conductivity, indicating that non-native species did not exhibit advantageous hydraulic efficiency over native species. Our results confer anatomical advantages for non-native species under the potential for cavitation due to freezing, perhaps permitting extended growing seasons

Digital literacy linked to engagement and psychological benefits among breast cancer survivors in Internet-based peer support groups

© 2019 John Wiley & Sons Ltd Objective: Internet-based peer support groups (ISGs) represent an innovative, scalable approach to addressing information and support needs of cancer survivors. However, this innovation may not benefit survivors equally due to population variance in digital literacy. This study examined how digital literacy influences level of engagement in and psychological benefits from participating in ISGs for breast cancer (N = 183). Methods: Secondary analysis of data from a randomised trial of ISGs that included behavioural measures of engagement, subjective ratings and psychological distress symptoms. Results: Digital literacy was positively related to education level (p =.005). Relative to women with high digital literacy, those with lower digital literacy were more likely to report difficulties using the ISG and to value the user's guide and facilitator assistance (all p's <.05). Digital literacy was negatively correlated with computer anxiety pre-intervention, distress before and after online chat during the intervention and post-intervention depressive symptoms (all p's <.05). Conclusion: Low digital literacy is associated with computer anxiety and barriers to ISG use, as well as distress during and after ISG use. Digital literacy must be taken into account when designing or delivering innovative digital interventions for cancer survivors

Evaporation of a packet of quantized vorticity

A recent experiment has confirmed the existence of quantized turbulence in superfluid He3-B and suggested that turbulence is inhomogenous and spreads away from the region around the vibrating wire where it is created. To interpret the experiment we study numerically the diffusion of a packet of quantized vortex lines which is initially confined inside a small region of space. We find that reconnections fragment the packet into a gas of small vortex loops which fly away. We determine the time scale of the process and find that it is in order of magnitude agreement with the experiment.Comment: figure 1a,b,c and d, figure2, figure

Optical interconnect with densely integrated plasmonic modulator and germanium photodetector arrays

We demonstrate the first chip-to-chip interconnect utilizing a densely integrated plasmonic Mach-Zehnder modulator array operating at 3 x 10 Gbit/s. A multicore fiber provides a compact optical interface, while the receiver consists of germanium photodetectors

Dynamics of Quantum Phase Transition in an Array of Josephson Junctions

We study the dynamics of the Mott insulator-superfluid quantum phase transition in a periodic 1D array of Josephson junctions. We show that crossing the critical point diabatically i.e. at a finite rate with a quench time $\tau_Q$ induces finite quantum fluctuations of the current around the loop proportional to $\tau_Q^{-1/6}$. This scaling could be experimentally verified with in array of weakly coupled Bose-Einstein condensates or superconducting grains.Comment: 4 pages in RevTex, 3 .eps figures; 2 references added; accepted for publication in Phys.Rev.Let

Spontaneous symmetry breaking in a quenched ferromagnetic spinor Bose condensate

A central goal in condensed matter and modern atomic physics is the exploration of many-body quantum phases and the universal characteristics of quantum phase transitions in so far as they differ from those established for thermal phase transitions. Compared with condensed-matter systems, atomic gases are more precisely constructed and also provide the unique opportunity to explore quantum dynamics far from equilibrium. Here we identify a second-order quantum phase transition in a gaseous spinor Bose-Einstein condensate, a quantum fluid in which superfluidity and magnetism, both associated with symmetry breaking, are simultaneously realized. $^{87}$Rb spinor condensates were rapidly quenched across this transition to a ferromagnetic state and probed using in-situ magnetization imaging to observe spontaneous symmetry breaking through the formation of spin textures, ferromagnetic domains and domain walls. The observation of topological defects produced by this symmetry breaking, identified as polar-core spin-vortices containing non-zero spin current but no net mass current, represents the first phase-sensitive in-situ detection of vortices in a gaseous superfluid.Comment: 6 pages, 4 figure

Testing the Kibble-Zurek Scenario with Annular Josephson Tunnel Junctions

In parallel with Kibble's description of the onset of phase transitions in the early universe, Zurek has provided a simple picture for the onset of phase transitions in condensed matter systems, strongly supported by agreement with experiments in He3. In this letter we show how experiments with annular Josephson tunnel Junctions can and do provide further support for this scenario.Comment: Revised version with correct formula for the Swihart velocity. The results are qualitatively the same as with the previous version but differ quantitatively. 4 pages, RevTe

Charge Delocalization in Self-Assembled Mixed-Valence Aromatic Cation Radicals

The spontaneous assembly of aromatic cation radicals (D+•) with their neutral counterpart (D) affords dimer cation radicals (D2+•). The intermolecular dimeric cation radicals are readily characterized by the appearance of an intervalence charge-resonance transition in the NIR region of their electronic spectra and by ESR spectroscopy. The X-ray crystal structure analysis and DFT calculations of a representative dimer cation radical (i.e., the octamethylbiphenylene dimer cation radical) have established that a hole (or single positive charge) is completely delocalized over both aromatic moieties. The energetics and the geometrical considerations for the formation of dimer cation radicals is deliberated with the aid of a series of cyclophane-like bichromophoric donors with drastically varied interplanar angles between the cofacially arranged aryl moieties. X-ray crystallography of a number of mixed-valence cation radicals derived from monochromophoric benzenoid donors established that they generally assemble in 1D stacks in the solid state. However, the use of polychromophoric intervalence cation radicals, where a single charge is effectively delocalized among all of the chromophores, can lead to higher-order assemblies with potential applications in long-range charge transport. As a proof of concept, we show that a single charge in the cation radical of a triptycene derivative is evenly distributed on all three benzenoid rings and this triptycene cation radical forms a 2D electronically coupled assembly, as established by X-ray crystallography

Defect Formation and Critical Dynamics in the Early Universe

We study the nonequilibrium dynamics leading to the formation of topological defects in a symmetry-breaking phase transition of a quantum scalar field with \lambda\Phi^4 self-interaction in a spatially flat, radiation-dominated Friedmann-Robertson-Walker Universe. The quantum field is initially in a finite-temperature symmetry-restored state and the phase transition develops as the Universe expands and cools. We present a first-principles, microscopic approach in which the nonperturbative, nonequilibrium dynamics of the quantum field is derived from the two-loop, two-particle-irreducible closed-time-path effective action. We numerically solve the dynamical equations for the two-point function and we identify signatures of topological defects in the infrared portion of the momentum-space power spectrum. We find that the density of topological defects formed after the phase transition scales as a power law with the expansion rate of the Universe. We calculate the equilibrium critical exponents of the correlation length and relaxation time for this model and show that the power law exponent of the defect density, for both overdamped and underdamped evolution, is in good agreement with the "freeze-out" scenario of Zurek. We introduce an analytic dynamical model, valid near the critical point, that exhibits the same power law scaling of the defect density with the quench rate. By incorporating the realistic quench of the expanding Universe, our approach illuminates the dynamical mechanisms important for topological defect formation. The observed power law scaling of the defect density with the quench rate, observered here in a quantum field theory context, provides evidence for the "freeze-out" scenario in three spatial dimensions.Comment: 31 pages, RevTex, 8 figures in EPS forma