High levels of gene flow and genetic diversity in Irish populations of Salix caprea L. inferred from chloroplast and nuclear SSR markers

peer-reviewedBackground Salix caprea is a cold-tolerant pioneer species that is ecologically important in Europe and western and central Asia. However, little data is available on its population genetic structure and molecular ecology. We describe the levels of geographic population genetic structure in natural Irish populations of S. caprea and determine the extent of gene flow and sexual reproduction using both chloroplast and nuclear simple sequence repeats (SSRs). Results A total of 183 individuals from 21 semi-natural woodlands were collected and genotyped. Gene diversity across populations was high for the chloroplast SSRs (H T  = 0.21-0.58) and 79 different haplotypes were discovered, among them 48% were unique to a single individual. Genetic differentiation of populations was found to be between moderate and high (mean G ST  = 0.38). For the nuclear SSRs, G ST was low at 0.07 and observed heterozygosity across populations was high (H O  = 0.32-0.51); only 9.8% of the genotypes discovered were present in two or more individuals. For both types of markers, AMOVA showed that most of the variation was within populations. Minor geographic pattern was confirmed by a Bayesian clustering analysis. Gene flow via pollen was found to be approximately 7 times more important than via seeds. Conclusions The data are consistent with outbreeding and indicate that there are no significant barriers for gene flow within Ireland over large geographic distances. Both pollen-mediated and seed-mediated gene flow were found to be high, with some of the populations being more than 200 km apart from each other. These findings could simply be due to human intervention through seed trade or accidental transportation of both seeds and pollen. These results are of value to breeders wishing to exploit natural genetic variation and foresters having to choose planting material.Teagasc Walsh Fellowship Programm

Surfactant-aided exfoliation of molydenum disulphide for ultrafast pulse generation through edge-state saturable absorption

We use liquid phase exfoliation to produce dispersions of molybdenum disulphide (MoS2) nanoflakes in aqueous surfactant solutions. The chemical structures of the bile salt surfactants play a crucial role in the exfoliation and stabilization of MoS2. The resultant MoS2 dispersions are heavily enriched in single and few (<6) layer flakes with large edge to surface area ratio. We use the dispersions to fabricate free-standing polymer composite wide-band saturable absorbers to develop mode-locked and Q- switched fibre lasers, tunable from 1535-1565 and 1030-1070 nm, respectively. We attribute this sub-bandgap optical absorption and its nonlinear saturation behaviour to edge-mediated states introduced within the material band-gap of the exfoliated MoS2 nanoflakes.Comment: 6 pages, 5 figure

Characterization of the second- and third-order nonlinear optical susceptibilities of monolayer MoS2_2 using multiphoton microscopy

We report second- and third-harmonic generation in monolayer MoS$_\mathrm{2}$ as a tool for imaging and accurately characterizing the material's nonlinear optical properties under 1560 nm excitation. Using a surface nonlinear optics treatment, we derive expressions relating experimental measurements to second- and third-order nonlinear sheet susceptibility magnitudes, obtaining values of $|\chi_s^{(2)}|=2.0\times10^{-20}$ m$^2$ V$^{-1}$ and for the first time for monolayer MoS$_\mathrm{2}$, $|\chi_s^{(3)}|=1.7\times10^{-28}$ m$^3$ V$^{-2}$. These sheet susceptibilities correspond to effective bulk nonlinear susceptibility values of $|\chi_{b}^{(2)}|=2.9\times10^{-11}$ m V$^{-1}$ and $|\chi_{b}^{(3)}|=2.4\times10^{-19}$ m$^2$ V$^{-2}$, accounting for the sheet thickness. Experimental comparisons between MoS$_\mathrm{2}$ and graphene are also performed, demonstrating $\sim$3.4 times stronger third-order sheet nonlinearity in monolayer MoS$_\mathrm{2}$, highlighting the material's potential for nonlinear photonics in the telecommunications C band.Comment: Accepted by 2D Materials, 28th Oct 201

Ultrafast Raman laser mode-locked by nanotubes

We demonstrate passive mode-locking of a Raman fiber laser using a nanotube-based saturable absorber coupled to a net normal dispersion cavity. This generates highly chirped 500 ps pulses. These are then compressed down to 2 ps , with 1.4 kW peak power, making it a simple wavelength-versatile source for various applications

Dairy Ingredients for Chocolate and Confectionery Products.

End of Project ReportHigh free-fat, spray-dried powders were successfully produced at a lower fat content (40% rather than 56%) using ultrafiltration. Chocolates made from these powders had improved flow properties and superior quality. The stability, viscosity and firmness of toffees were improved by optimising the casein, whey protein and lactose levels of skim milk powders used in their manufacture.Department of Agriculture, Food and the Marin

Development of an index to rank dairy females on expected lifetime profit

peer-reviewedThe objective of this study was to develop an index to rank dairy females on expected profit for the remainder of their lifetime, taking cognizance of both additive and nonadditive genetic merit, permanent environmental effects, and current states of the animal including the most recent calving date and cow parity. The cow own worth (COW) index is intended to be used for culling the expected least profitable females in a herd, as well as inform purchase and pricing decisions for trading of females. The framework of the COW index consisted of the profit accruing from (1) the current lactation, (2) future lactations, and (3) net replacement cost differential. The COW index was generated from estimated performance values (sum of additive genetic merit, nonadditive genetic merit, and permanent environmental effects) of traits, their respective net margin values, and transition probability matrices for month of calving, survival, and somatic cell count; the transition matrices were to account for predicted change in a cow’s state in the future. Transition matrices were generated from 3,156,109 lactation records from the Irish national database between the years 2010 and 2013. Phenotypic performance records for 162,981 cows in the year 2012 were used to validate the COW index. Genetic and permanent environmental effects (where applicable) were available for these cows from the 2011 national genetic evaluations and used to calculate the COW index and their national breeding index values (includes only additive genetic effects). Cows were stratified per quartile within herd, based on their COW index value and national breeding index value. The correlation between individual animal COW index value and national breeding index value was 0.65. Month of calving of the cow in her current lactation explained 18% of the variation in the COW index, with the parity of the cow explaining an additional 3 percentage units of the variance in the COW index. Females ranking higher on the COW index yielded more milk and milk solids and calved earlier in the calving season than their lower ranking contemporaries. The difference in phenotypic performance between the best and worst quartiles was larger for cows ranked on COW index than cows ranked on the national breeding index. The COW index is useful to rank females before culling or purchasing decisions on expected profit and is complementary to the national breeding index, which identifies the most suitable females for breeding replacements

Measurements of d(2)(n) and A(1)(n) : Probing the neutron spin structure

We report on the results of the E06-014 experiment performed at Jefferson Lab in Hall A, where a precision measurement of the twist-3 matrix element d(2) of the neutron (d(2)(n)) was conducted. The quantity d(2)(n) represents the average color Lorentz force a struck quark experiences in a deep inelastic electron scattering event off a neutron due to its interaction with the hadronizing remnants. This color force was determined from a linear combination of the third moments of the He-3 spin structure functions, g(1) and g(2), after nuclear corrections had been applied to these moments. The structure functions were obtained from a measurement of the unpolarized cross section and of double-spin asymmetries in the scattering of a longitudinally polarized electron beam from a transversely and a longitudinally polarized He-3 target. The measurement kinematics included two average Q(2) bins of 3.2 GeV2 and 4.3 GeV2, and Bjorken-x 0.25 = 3.2 GeV2, and even smaller for \u3c Q(2)\u3e = 4.3 GeV2, consistent with the results of a lattice QCD calculation. The twist-4 matrix element f(2)(n) was extracted by combining our measured d(2)(n) with the world data on the first moment in x of g(1)(n), Gamma(n)(1). We found f(2)(n) to be roughly an order of magnitude larger than d(2)(n). Utilizing the extracted d(2)(n) and f(2)(n) data, we separated the Lorentz color force into its electric and magnetic components, F-E(y,n) and F-B(y,n), and found them to be equal and opposite in magnitude, in agreement with the predictions from an instanton model but not with those from QCD sum rules. Furthermore, using the measured double-spin asymmetries, we have extracted the virtual photon-nucleon asymmetry on the neutron A(1)(n), the structure function ratio g(1)(n)/F-1(n), and the quark ratios (Delta u + Delta(u) over bar)/(u + (u) over bar) and (Delta d + Delta(d) over bar)/(d + (d) over bar). These results were found to be consistent with deep-inelastic scattering world data and with the prediction of the constituent quark model but at odds with the perturbative quantum chromodynamics predictions at large x