Effect of inclusion or non-inclusion of short lactations and cow and/or dam genetic group on genetic evaluation of Girolando dairy cattle

The objective of this study was to evaluate the effects of inclusion or non-inclusion of short lactations and cow (CGG) and/or dam (DGG) genetic group on the genetic evaluation of 305-day milk yield (MY305), age at first calving (AFC), and first calving interval (FCI) of Girolando cows. Covariance components were estimated by the restricted maximum likelihood method in an animal model of single trait analyses. The heritability estimates for MY305, AFC, and FCI ranged from 0.23 to 0.29, 0.40 to 0.44, and 0.13 to 0.14, respectively, when short lactations were not included, and from 0.23 to 0.28, 0.39 to 0.43, and 0.13 to 0.14, respectively, when short lactations were included. The inclusion of short lactations caused little variation in the variance components and heritability estimates of traits, but their non-inclusion resulted in the re-ranking of animals. Models with CGG or DGG fixed effects had higher heritability estimates for all traits compared with models that consider these two effects simultaneously. We recommend using the model with fixed effects of CGG and inclusion of short lactations for the genetic evaluation of Girolando cattle

Lack of mutations of exon 2 of the MEN1 gene in endocrine and nonendocrine sporadic tumors

In addition to the mutations that underlie most cases of the multiple endocrine neoplasia type 1 (MEN1) syndrome, somatic mutations of the MEN1 gene have also been described in sporadic tumors like gastrinomas, insulinomas and bronchial carcinoid neoplasm. We examined exon 2 of this gene, where most of the mutations have been described, in 148 endocrine and nonendocrine sporadic tumors. DNA was obtained by phenol/chloroform extraction and ethanol precipitation from 92 formalin-fixed, paraffin-embedded samples, and from 40 fresh tumor tissue samples. We used 5 pairs of primers to encompass the complete coding sequence of exon 2 of the MEN1 gene that was screened by the polymerase chain reaction-single-stranded conformation polymorphism (PCR-SSCP) technique in 78 sporadic thyroid cancers: 28 follicular adenomas, 35 papillary carcinomas, 14 follicular carcinomas, and 1 anaplastic thyroid carcinoma. We also examined 46 adrenal lesions (3 hyperplasias, 3 adenomas and 35 adrenocortical carcinomas, 2 pheochromocytomas, 2 ganglioneuroblastomas, and 1 lymphoma) and 24 breast cancers (6 noninvasive, 16 infiltrating ductal, and 2 invasive lobular tumors). The PCR product of 5 tumors suspected to present band shifts by SSCP was cloned. Direct sense and antisense sequencing did not identify mutations. These results suggest that the MEN1 gene is not important in breast, thyroid or adrenal sporadic tumorigenesis. Because the frequency of mutations varies significantly among tumor subgroups and allelic deletions are frequently observed at 11q13 in thyroid and adrenal cancers, another tumor suppressor gene residing in this region is likely to be involved in the tumorigenesis of these neoplasms.86186

Comparison of dimensionality reduction methods to predict genomic breeding values for carcass traits in pigs

A significant contribution of molecular genetics is the direct use of DNA information to identify genetically superior individuals. With this approach, genome-wide selection (GWS) can be used for this purpose. GWS consists of analyzing a large number of single nucleotide polymorphism markers widely distributed in the genome; however, because the number of markers is much larger than the number of genotyped individuals, and such markers are highly correlated, special statistical methods are widely required. Among these methods, independent component regression, principal component regression, partial least squares, and partial principal components stand out. Thus, the aim of this study was to propose an application of the methods of dimensionality reduction to GWS of carcass traits in an F2 (Piau x commercial line) pig population. The results show similarities between the principal and the independent component methods and provided the most accurate genomic breeding estimates for most carcass traits in pigs

Fermion Zero Modes in the Presence of Fluxes and a Non-perturbative Superpotential

We study the effect of background fluxes of general Hodge type on the supersymmetry conditions and on the fermionic zero modes on the world-volume of a Euclidean M5/D3-brane in M-theory/type IIB string theory. Using the naive susy variation of the modulino fields to determine the number of zero modes in the presence of a flux of general Hodge type, an inconsistency appears. This inconsistency is resolved by a modification of the supersymmetry variation of the modulinos, which captures the back-reaction of the non-perturbative effects on the background flux and the geometry.Comment: 21 pages, revised version contains a new appendix on dimensional reduction of spinors and some changes in the spinor equation

String-Loop Corrected Magnetic Black Holes

We discuss the form of the string-loop-corrected effective action obtained by compactification of the heterotic string theory on the manifold $K3\times T^2$ or on its orbifold limit and the loop-corrected magnetic black hole solutions of the equations of motion. Effective 4D theory has N=2 local supersymmetry. Using the string-loop-corrected prepotential of the N=2 supersymmetric theory, which receives corrections only from the string world sheets of torus topology, we calculate the loop corrections to the tree-level gauge couplings and solve the loop-corrected equations of motion. At the string-tree level, the effective gauge couplings decrease at small distances from the origin, and in this region string-loop corrections to the gauge couplings become important. A possibility of smearing the singularity of the tree-level supersymmetric solution with partially broken supersymmetry by quantum corrections is discussed.Comment: Improved version. Mixing of the dilaton with other moduli properly taken into account. Explanatory notes adde

Higher Derivative Corrections to Eleven Dimensional Supergravity via Local Supersymmetry

In this paper we derive higher derivative corrections to the eleven dimensional supergravity by applying the Noether method with respect to the N=1 local supersymmetry. An ansatz for the higher derivative effective action, which includes quartic terms of the Riemann tensor, is parametrized by 132 parameters. Then we show that by the requirement of the local supersymmetry, the higher derivative effective action is essentially described by two parameters. The bosonic parts of these two superinvariants completely match with the known results obtained by the perturbative calculations in the type IIA superstring theory. Since the calculations are long and systematic, we build the computer programming to check the cancellation of the variations under the local supersymmetry. This is an extended version of our previous paper hep-th/0508204.Comment: 67 pages, no figure, references added, typos correcte

Genetic evaluation of age at first calving for Guzerá beef cattle using linear, threshold, and survival Bayesian models

Age at first calving (AFC) is characterized as a censored trait due to missing values provided by recording mistakes and nonoccur-rence or delay in calving communication. In this context, we aimed to compare several statistical methods for genetic evaluation of AFC in Guzerá beef cattle under a Bayesian approach. Seven different methods were used for this purpose. The traditional linear mixed model (LM), which considers only uncensored records; the LM with simulated records (SM), which is based on data augmentation framework; the penalty method, in which a constant of 21 d was added to censored records; the bivariate threshold-linear method considering (TLcens) or not (TLmiss) censored information; and the piecewise Weibull proportional hazards model considering (PWPHcens) or not (PWPH) censored records. Heritability estimates ranged from 0.19 (TLcens) to 0.28 (SM) in non-survival approaches; and 0.40 and 0.46 to PWPH and PWPHcens methods, respectively. In general, breeding values correlations between different methods and the percentage of selected bulls in common indicated reranking, with these correlation ranging from -0.28 (between SM and PWPH) to 0.99 (between TLmiss and LM). The traditional LM, which considers only uncensored records, should be preferred due to its robustness and simplicity. Based on cross-validation analyses, we conclude that the TLmiss could be also a suitable alternative for breeding value prediction, and censored methods did not improve the analysis

Estimating additive and dominance variances for complex traits in pigs combining genomic and pedigree information

Knowledge of dominance effects should improve ge-netic evaluations, provide the accurate selection of purebred animals, and enable better breeding strategies, including the exploitation of het-erosis in crossbreeds. In this study, we combined genomic and pedi-gree data to study the relative importance of additive and dominance genetic variation in growth and carcass traits in an F2 pig population. Two GBLUP models were used, a model without a polygenic effect (ADM) and a model with a polygenic effect (ADMP). Additive effects played a greater role in the control of growth and carcass traits than did dominance effects. However, dominance effects were important for all traits, particularly in backfat thickness. The narrow-sense and broad-sense heritability estimates for growth (0.06 to 0.42, and 0.10 to 0.51, respectively) and carcass traits (0.07 to 0.37, and 0.10 to 0.76, respec-tively) exhibited a wide variation. The inclusion of a polygenic effect in the ADMP model changed the broad-sense heritability estimates only for birth weight and weight at 21 days of age

Use of multivariate analysis to evaluate genetic groups of pigs for dry-cured ham production

AbstractRecords of a pig population used for dry-cured ham production were used to evaluate genetic groups by multivariate analysis. The investigated genetic groups were as follows: DULL=Duroc×(Landrace×Large White), DULA=Duroc×Landrace, DUWI=Duroc×Large White, WIWI=Large White and DUDU=Duroc. Two groups were obtained for the carcass traits hot carcass weight (HCW), backfat thickness (BT) and loin depth (LD), with the groups including 597 and 341 animals harvested at 130kg and at 160kg weights, respectively. Two groups were also found for ham traits gross ham weight (GHW), trimmed ham weight (THW), ham inner layer fat thickness (HIFT), ham outer layer fat thickness (HOFT), pH (PH), and Göfo value, with 393 and 91 animals harvested at 130kg and 160kg weights, respectively. The analysis was performed within each group of traits and harvest weights, and the animals without records were excluded. The first and the second canonical variables explained 97.5% and 93.6% of the total variation for the carcass traits at 130kg and 160kg, respectively, and 88.8% of ham traits at 130kg. In the dispersion graph concerning the canonical means, a significant distance was observed between the genetic groups DUDU and WIWI for the carcass traits at 130kg and 160kg and the ham traits at 130kg. The 50% Duroc animals exhibited little dispersion regarding the carcass traits at 130kg and 160kg and were not divergent from the DUDU genetic group for the ham traits at 130kg. In a cluster analysis using the single linkage method, DULL, DULA and DUWI were grouped with a high similarity level for the carcass traits at 130kg and 160kg and ham traits at 130kg. Using the Tocher optimization method, 50% Duroc crossbred and 100% Duroc purebred animals were grouped for the ham traits at 130kg, suggesting that for ham traits, 50% Duroc animals were similar to 100% Duroc purebred animals. In this context, the genetic groups Duroc×Large White, Duroc×Landrace and Duroc×(Landrace×Large White) are recommended for use in producing dry-cured ham

Censored Bayesian models for genetic evaluation of age at first calving in Brazilian Brahman cattle

We compared different Bayesian models to handle censored data for genetic parameters estimation of age at first calving (AFC) in Brazilian Brahman cattle. Data from females with AFC above 1825 days of age were assumed to have failed to calve and were considered as censored records. Data including information of 53, 703 cows were analyzed through the following methods: conventional linear model method (LM), which consider only uncensored records; simulation method (SM), in which the data were augmented by drawing random samples from positive truncated normal distributions; penalty method (PM), in which a constant of 21 days was added to censored records; and the bivariate threshold-linear method (TLcens). The LM was the most suited for genetic evaluation of AFC in Brazilian Brahman cattle based on the predictive ability evaluation through cross-validation analysis. The similar results for LM and PM regarding Spearman correlations, and the higher percentages of selected animals in common, indicated that there was not relevant reranking of animals when censored records were used. In summary, the heritability estimates for AFC ranged from 0.09 (TLcens) to 0.20 (LM). Given its poor predictive performance, the SM is not recommended for handling censored records for genetic evaluation of AFC