Procedures for estimation of genetic persistency indices for milk production for the South African dairy industry

Procedures have been developed for calculation of a Persistency Index for South African dairy breeds. This index is based on the Canadian Persistency Index, which is simple and easy to understand. Data used in this study were test-day records of the first three lactations, as included in the National Dairy Genetic Evaluations of South Africa, of the Ayrshire, Guernsey, Holstein and Jersey breeds. Interpolation, using the Wilmink curve, was done on these test-day records to calculate 60-day and 280-day yields for each cow and lactation. Variance components have been estimated for these yields to be used in breeding value estimations, using bivariate evaluations and a repeatability model. To obtain independence of persistency from total milk yield, 305-day milk yield estimated breeding values were included as covariates in the genetic model for estimation of breeding values for 60- and 280-day yields. The Persistency Index will be released for sires with progeny following each national dairy genetic evaluation, allowing the South African dairy industry to select for changes in persistency in future. Keywords: Ayrshire, Guernsey, Holstein, Jersey, Repeatability model, test-day recordsSouth African Journal of Animal Science Vol. 38 (3) 2008: pp. 224-23

Characterization of the Covalently Bound Anionic Flavin Radical in Monoamine Oxidase A by Electron Paramagnetic Resonance

It was recently suggested that partially reduced monoamine oxidase (MAO) A contains an equilibrium mixture of an anionic flavin radical and a tyrosyl radical (Rigby, S. E.; et al. J. Biol. Chem. 2005, 280, 4627-4632). These observations formed the basis for a revised radical mechanism for MAO. In contrast, an earlier study of MAO B only found evidence for an anionic flavin radical (DeRose, V. J.; et al. Biochemistry 1996, 35, 11085-11091). To resolve the discrepancy, we have performed continuous-wave electron paramagnetic resonance at 94 GHz (W-band) on the radical form of MAO A. A comparison with D-amino acid oxidase (DAAO) demonstrates that both enzymes only contain anionic flavin radicals. Pulsed electron-nuclear double resonance spectra of the two enzymes recorded at 9 GHz (X-band) reveal distinct hyperfine coupling patterns for the two flavins. Density functional theory calculations show that these differences can be understood in terms of the difference at C8 of the isoalloxazine ring. DAAO contains a noncovalently bound flavin whereas MAO A contains a flavin covalently bound to a cysteinyl residue at C8. The similar electronic structures and hydrophobic environments of MAO and DAAO, and the similar structural motifs of their substrates suggest that a direct hydride transfer catalytic mechanism established for DAAO (Umhau, S.; et al. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 12463-12468) should be considered for MAO

Rate of inbreeding and effective population size in four major South African dairy cattle breeds

Pedigree information on the registered South African Ayrshire (n = 47 116), Guernsey (n = 18 766), Holstein (n = 892 458) and Jersey (n = 314 403) breeds was analyzed to determine the rate of inbreeding and effective population sizes for the period 1960 to 2003. Inbreeding coefficients were calculated using the Animal Breeder's Tool Kit. The mean inbreeding coefficients for 2003 were 2.02%, 2.04%, 2.30%, and 3.05% for the Ayrshire, Guernsey, Holstein and Jersey, respectively. The corresponding rates of inbreeding per year were 0.05%, 0.05%, 0.06%, and 0.07% indicating that inbreeding is accumulating at a slightly higher rate in Jersey compared to the other three breeds. However, the rates of inbreeding in the current study are still considerably lower than the acceptable rate of less than 0.5% per year. Estimates of effective population sizes were 148, 165, 137, and 108 for the Ayrshire, Guernsey, Holstein and Jersey, respectively. Results indicate that the impact of inbreeding on genetic variability is still minimal. However, the impact of inbreeding on phenotypic performance on traits of economic importance was not investigated in the current study and should therefore receive future consideration. South African Journal of Animal Science Vol. 36(1) 2006: 50-5

A complex pattern of post‐divergence expansion, contraction, introgression and asynchronous responses to Pleistocene climate changes in two Dipelta sister species from western China

The well-known vicariance and dispersal models dominate in understanding the allopatric pattern for related species and presume the simultaneous occurrence of speciation and biogeographic events. However, the formation of allopatry may postdate the species divergence. We examined this hypothesis using DNA sequence data from 3 chloroplast fragments and 5 nuclear loci of Dipelta floribunda and D. yunnanensis, two shrub species with the circum Sichuan Basin distribution, combining the climatic niche modeling approach. The best-fit model supported by the approximate Bayesian computation (ABC) analysis indicated that, D. floribunda and D. yunnanensis diverged during the mid-Pleistocene period, consistent with the largest glacial period in the Qinghai-Tibet Plateau (QTP). The historically inter-specific gene flow was identified but seemed to have ceased after the last interglacial period (LIG), when the range of D. floribunda moved northward from the south of the Sichuan Basin. Further, populations of D. floribunda had expanded obviously in the north of the Sichuan Basin after the last glacial maximum (LGM). Relatively, the range of D. yunnanensis expanded before the LGM, reduced during the post-LGM especially in the north of the Sichuan Basin, reflecting the asynchronous responses of related species to the contemporary climate changes. Our results suggested that complex topography should be considered in understanding the distributional patterns even for closely related species and their demographic responses

Non-Redundant Spectral Dimensionality Reduction

Spectral dimensionality reduction algorithms are widely used in numerous domains, including for recognition, segmentation, tracking and visualization. However, despite their popularity, these algorithms suffer from a major limitation known as the "repeated Eigen-directions" phenomenon. That is, many of the embedding coordinates they produce typically capture the same direction along the data manifold. This leads to redundant and inefficient representations that do not reveal the true intrinsic dimensionality of the data. In this paper, we propose a general method for avoiding redundancy in spectral algorithms. Our approach relies on replacing the orthogonality constraints underlying those methods by unpredictability constraints. Specifically, we require that each embedding coordinate be unpredictable (in the statistical sense) from all previous ones. We prove that these constraints necessarily prevent redundancy, and provide a simple technique to incorporate them into existing methods. As we illustrate on challenging high-dimensional scenarios, our approach produces significantly more informative and compact representations, which improve visualization and classification tasks

High-efficiency GaAs and GaInP solar cells grown by all solid-state molecular-beam-epitaxy

We report the initial results of GaAs and GaInP solar cells grown by all solid-state molecular-beam-epitaxy (MBE) technique. For GaAs single-junction solar cell, with the application of AlInP as the window layer and GaInP as the back surface field layer, the photovoltaic conversion efficiency of 26% at one sun concentration and air mass 1.5 global (AM1.5G) is realized. The efficiency of 16.4% is also reached for GaInP solar cell. Our results demonstrate that the MBE-grown phosphide-contained III-V compound semiconductor solar cell can be quite comparable to the metal-organic-chemical-vapor-deposition-grown high-efficiency solar cell

The complete linkage disequilibrium test: a test that points to causative mutations underlying quantitative traits

<p>Abstract</p> <p>Background</p> <p>Genetically, SNP that are in complete linkage disequilibrium with the causative SNP cannot be distinguished from the causative SNP. The Complete Linkage Disequilibrium (CLD) test presented here tests whether a SNP is in complete LD with the causative mutation or not. The performance of the CLD test is evaluated in 1000 simulated datasets.</p> <p>Methods</p> <p>The CLD test consists of two steps i.e. analysis I and analysis II. Analysis I consists of an association analysis of the investigated region. The log-likelihood values from analysis I are next ranked in descending order and in analysis II the CLD test evaluates differences in log-likelihood ratios between the best and second best markers. Under the null-hypothesis distribution, the best SNP is in greater LD with the QTL than the second best, while under the alternative-CLD-hypothesis, the best SNP is alike-in-state with the QTL. To find a significance threshold, the test was also performed on data excluding the causative SNP. The 5^th, 10^thand 50^thhighest T_CLDvalue from 1000 replicated analyses were used to control the type-I-error rate of the test at p = 0.005, p = 0.01 and p = 0.05, respectively.</p> <p>Results</p> <p>In a situation where the QTL explained 48% of the phenotypic variance analysis I detected a QTL in 994 replicates (p = 0.001), where 972 were positioned in the correct QTL position. When the causative SNP was excluded from the analysis, 714 replicates detected evidence of a QTL (p = 0.001). In analysis II, the CLD test confirmed 280 causative SNP from 1000 simulations (p = 0.05), i.e. power was 28%. When the effect of the QTL was reduced by doubling the error variance, the power of the test reduced relatively little to 23%. When sequence data were used, the power of the test reduced to 16%. All SNP that were confirmed by the CLD test were positioned in the correct QTL position.</p> <p>Conclusions</p> <p>The CLD test can provide evidence for a causative SNP, but its power may be low in situations with closely linked markers. In such situations, also functional evidence will be needed to definitely conclude whether the SNP is causative or not.</p

Gate-controlled Guiding of Electrons in Graphene

Ballistic semiconductor structures have allowed the realization of optics-like phenomena in electronics, including magnetic focusing and lensing. An extension that appears unique to graphene is to use both n and p carrier types to create electronic analogs of optical devices having both positive and negative indices of refraction. Here, we use gate-controlled density with both p and n carrier types to demonstrate the analog of the fiber-optic guiding in graphene. Two basic effects are investigated: (1) bipolar p-n junction guiding, based on the principle of angle-selective transmission though the graphene p-n interface, and (2) unipolar fiber-optic guiding, using total internal reflection controlled by carrier density. Modulation of guiding efficiency through gating is demonstrated and compared to numerical simulations, which indicates that interface roughness limits guiding performance, with few-nanometer effective roughness extracted. The development of p-n and fiber-optic guiding in graphene may lead to electrically reconfigurable wiring in high-mobility devices.Comment: supplementary materal at http://marcuslab.harvard.edu/papers/OG_SI.pd

Compensated right ventricular function of the onset of pulmonary hypertension in a rat model depends on chamber remodeling and contractile augmentation.

Right-ventricular function is a good indicator of pulmonary arterial hypertension (PAH) prognosis; however, how the right ventricle (RV) adapts to the pressure overload is not well understood. Here, we aimed at characterizing the time course of RV early remodeling and discriminate the contribution of ventricular geometric remodeling and intrinsic changes in myocardial mechanical properties in a monocrotaline (MCT) animal model. In a longitudinal study of PAH, ventricular morphology and function were assessed weekly during the first four weeks after MCT exposure. Using invasive measurements of RV pressure and volume, heart performance was evaluated at end of systole and diastole to quantify contractility (end-systolic elastance) and chamber stiffness (end-diastolic elastance). To distinguish between morphological and intrinsic mechanisms, a computational model of the RV was developed and used to determine the level of prediction when accounting for wall masses and unloaded volume measurements changes. By four weeks, mean pulmonary arterial pressure and elastance rose significantly. RV pressures rose significantly after the second week accompanied by significant RV hypertrophy, but RV stroke volume and cardiac output were maintained. The model analysis suggested that, after two weeks, this compensation was only possible due to a significant increase in the intrinsic inotropy of RV myocardium. We conclude that this MCT-PAH rat is a model of RV compensation during the first month after treatment, where geometric remodeling on EDPVR and increased myocardial contractility on ESPVR are the major mechanisms by which stroke volume is preserved in the setting of elevated pulmonary arterial pressure. The mediators of this compensation might themselves promote longer-term adverse remodeling and decompensation in this animal model