Context dependent substitution biases vary within the human genome

Background: Models of sequence evolution typically assume that different nucleotide positions evolve independently. This assumption is widely appreciated to be an over-simplification. The best known violations involve biases due to adjacent nucleotides. There have also been suggestions that biases exist at larger scales, however this possibility has not been systematically explored. Results: To address this we have developed a method which identifies over- and under-represented substitution patterns and assesses their overall impact on the evolution of genome composition. Our method is designed to account for biases at smaller pattern sizes, removing their effects. We used this method to investigate context bias in the human lineage after the divergence from chimpanzee. We examined bias effects in substitution patterns between 2 and 5 bp long and found significant effects at all sizes. This included some individual three and four base pair patterns with relatively large biases. We also found that bias effects vary across the genome, differing between transposons and non-transposons, between different classes of transposons, and also near and far from genes. Conclusions: We found that nucleotides beyond the immediately adjacent one are responsible for substantial context effects, and that these biases vary across the genome

Influence of Dibble Shape and Depth on the Germination and Seedling Establishment of Burley Tobacco in the Float System

Direct seeding of pelleted tobacco seed into the float transplant system has become common in Kentucky. Direct seeding reduces labor compared to the plug and transfer method, but it increases the risk involved and requires more management by the producer. Uniform germination, and ultimately a high percentage of useable transplants are the keys to success with direct seeding

Extensive infrared spectroscopic study of CuO: signatures of strong spin-phonon interaction and structural distortion

Optical properties of single-crystal monoclinic CuO in the range 70 - 6000 \cm were studied at temperatures from 7 to 300 K. Normal reflection spectra were obtained from the (001) and (010) crystal faces thus giving for the first time separate data for the $A_{u}$ and $B_{u}$ phonon modes excited in the purely transverse way (TO modes). Mode parameters, including polarizations of the $B_{u}$ modes not determined by the crystal symmetry, were extracted by the dispersion analysis of reflectivity curves as a function of temperature. Spectra of all the components of the optical conductivity tensor were obtained using the Kramers-Kronig method recently extended to the case of the low-symmetry crystals. The number of strong phonon modes is in agreement with the factor-group analysis for the crystal structure, currently accepted for the CuO. However, several "extra" modes of minor intensity are detected. Comparison of frequencies of "extra" modes with the available phonon dispersion curves points to possible "diagonal" doubling of the unit cell \{{\bf a}, {\bf b}, {\bf c}\} $\to$ \{{\bf a}+{\bf c}, {\bf b}, {\bf a}-{\bf c}\} and formation of the superlattice. The previously reported softening of the $A^{3}_{u}$ mode ($\sim$ 400 \cm) with cooling at $T_{N}$ is found to be $\sim$ 10 % for the TO mode. The mode is very broad at high temperatures and strongly narrows in the AFM phase. We attribute this effect to strong resonance coupling of this mode to optical or acoustic bi-magnons and reconstruction of the magnetic excitations spectrum at the N\'eel point. A significant anisotropy of $\epsilon^{\infty}$ is observed: it was found to be 5.9 along the {\bf b}-axis, 6.2 along the {[}101{]} chains and 7.8 the {[}10$\bar{1}${]} chains. The "transverse" effective charge is value is about 2 electrons.Comment: 23 pages, 14 figures, REVTeX, submitted to PR

Anisotropic Exchange in LiCu2O2{\bf LiCu_2O_2}

We investigate the magnetic properties of the multiferroic quantum-spin system LiCu$_2$O$_2$ by electron spin resonance (ESR) measurements at $X$- and $Q$-band frequencies in a wide temperature range $(T_{\rm N1} \leq T \leq 300$\,K). The observed anisotropies of the $g$ tensor and the ESR linewidth in untwinned single crystals result from the crystal-electric field and from local exchange geometries acting on the magnetic Cu$^{2+}$ ions in the zigzag-ladder like structure of LiCu$_2$O$_2$. Supported by a microscopic analysis of the exchange paths involved, we show that both the symmetric anisotropic exchange interaction and the antisymmetric Dzyaloshinskii-Moriya interaction provide the dominant spin-spin relaxation channels in this material.Comment: 10 pages, 10 Figure

NMR evidence for inhomogeneous glassy behavior driven by nematic fluctuations in iron arsenide superconductors

We present $^{75}$As nuclear magnetic resonance spin-lattice and spin-spin relaxation rate data in Ba(Fe$_{1-x}$Co$_x$)$_2$As$_2$ and Ba(Fe$_{1-x}$Cu$_x$)$_2$As$_2$ as a function of temperature, doping and magnetic field. The relaxation curves exhibit a broad distribution of relaxation rates, consistent with inhomogeneous glassy behavior up to 100 K. The doping and temperature response of the width of the dynamical heterogeneity is similar to that of the nematic susceptibility measured by elastoresistance measurements. We argue that quenched random fields which couple to the nematic order give rise to a nematic glass that is reflected in the spin dynamics.Comment: Accepted to Physical Review

B-T phase diagram of CoCr2O4 in magnetic fields up to 14 T

We have measured the magnetization and specific heat of multiferroic CoCr2O4 in magnetic fields up to 14 T. The high-field magnetization measurements indicate a new phase transition at T* = 5 - 6 K. The phase between T* and the lock-in transition at 15 K is characterized by magnetic irreversibility. At higher magnetic fields, the irreversibility increases. Specific-heat measurements confirm the transition at T*, and also show irreversible behavior. We construct a field-temperature phase diagram of CoCr2O4.Comment: 4 page

Antifungal activity of some alternative control against mango anthracnose in Senegal

Mango production in the South of Senegal is exposed to intensive rainfall from late May to October, with high temperature and moisture levels. These conditions are conducive for the development of anthracnose caused by Colletotrichum gloeosporioides (sensu lato) and leading to an absolute necessity for adequate control measures for good quality mango production. Anthracnose disease causes both pre- and postharvest fruit spots and fruit rot as well as premature fruit drop. The purpose of this study was to test the efficacy of several fungicide alternatives (fertilizers and biological control agents) against mango anthracnose in Senegal comparatively to standard fungicides. Field trials were set up in contrasting climates conditions and involved three orchards in the Northern part of the country with a short rainy season and dry climate over 9 to 10 months a year and three other orchards in the Southern part of Senegal with in a humid tropic environment. No anthracnose was recorded in the orchards in northern Senegal. In the south, in contrast, the disease was actual. Among the treatments tested for the control of anthracnose, Sodium molybdate were found effective after fungicides (azoxystrobin and thiophanate methyl). All the alternative treatments to fungicides provided a statistically significant control to the disease as compared to the contro