Predicting haplotype carriers from SNP genotypes in Bos taurus through linear discriminant analysis

Background

SNP (single nucleotide polymorphisms) genotype data are increasingly available in cattle populations and, among other things, can be used to predict carriers of specific haplotypes. It is therefore convenient to have a practical statistical method for the accurate classification of individuals into carriers and non-carriers. In this paper, we present a procedure combining variable selection (i.e. the selection of predictive SNPs) and linear discriminant analysis for the identification of carriers of a haplotype on BTA19 (Bos taurus autosome 19) known to be associated with reduced cow fertility. A population of 3645 Brown Swiss cows and bulls genotyped with the 54K SNP-chip was available for the analysis.

Results

The overall error rate for the prediction of haplotype carriers was on average very low (∼≤1%). The error rate was found to depend on the number of SNPs in the model and their density around the region of the haplotype on BTA19. The minimum set of SNPs to still achieve accurate predictions was 5, with a total test error rate of 1.59.

Conclusions

The paper describes a procedure to accurately identify haplotype carriers from SNP genotypes in cattle populations. Very few misclassifications were observed, which indicates that this is a very reliable approach for potential applications in cattle breeding.     

Localization of stilbene synthase in Vitis vinifera L. during berry development

The localization of stilbene synthase (STS) (EC 2.3.1.95) in grape berry (Vitis vinifera L.) was investigated during fruit development. The berries were collected at 2, 4, 7, 11, and 15 weeks postflowering from the cultivar Nebbiolo during the 2005 and 2006 growing seasons. High-performance liquid chromatography analysis showed that berries accumulated cis- and trans-isomers of resveratrol mainly in the exocarp throughout fruit development. Immunodetection of STS protein was performed on berry extracts and sections with an antibody specifically developed against recombinant grape STS1. In agreement with resveratrol presence, STS was found in berry exocarp tissues during all stages of fruit development. The labeled epidermal cells were few and were randomly distributed, whereas nearly all the outer hypodermis cells were STS-positive. The STS signal decreased gradually from exocarp to mesocarp, where the protein was detected only occasionally. At the subcellular level, STS was found predominantly within vesicles (of varying size), along the plasma membrane and in the cell wall, suggesting protein secretion in the apoplast compartment. Despite the differences in fruit size and structure, the STS localization was the same before and after veraison, the relatively short developmental period during which the firm green berries begin to soften and change color. Nevertheless, the amount of protein detected in both exocarp and mesocarp decreased significantly in ripe berries, in agreement with the lower resveratrol content measured in the same tissues. The location of STS in exocarp cell wall is consistent with its role in synthesizing defense compounds and supports the hypothesis that a differential localization of phenylpropanoid biosynthetic machinery regulates the deposition of specific secondary products at different action sites within cells.     

Ouabain-induced hypertension is accompanied by increases in endothelial vasodilator factors

The involvement of nitric oxide (NO), prostaglandins, and calcium-dependent potassium channel (K(Ca)) activators on the negative modulation of phenylephrine-induced contractions was evaluated on the isolated aorta and caudal (CAU) artery obtained from rats treated with ouabain for 5 wk to induce hypertension. In ouabain-treated rats, the reactivity to phenylephrine was reduced in the endothelium-intact aorta but not the CAU segments. Endothelial modulation of phenylephrine contraction, as demonstrated by endothelium removal, NO synthase (NOS) inhibition with N(omega)-nitro-L-arginine methyl ester and aminoguanidine, as well as K(Ca) inhibition with tetraethylammonium, was more pronounced in segments from ouabain-treated animals, and here greater effects were seen in the aorta than in CAU. An increased expression of endothelial NOS and neuronal NOS was seen in the aorta after ouabain treatment. In CAU, only endothelial NOS was detected and ouabain treatment did not alter its expression. These results suggest that ouabain-induced hypertension is accompanied by increased NO release derived from endothelial NOS and neuronal NOS and increased release of an endothelial hyperpolarizing factor that presumably opens K(Ca), all of which contribute to the increased negative modulation of the phenylephrine contraction.     

The Putative Mevalonate Diphosphate Decarboxylase from Picrophilus torridus Is in Reality a Mevalonate-3-Kinase with High Potential for Bioproduction of Isobutene

Mevalonate diphosphate decarboxylase (MVD) is an ATP-dependent enzyme that catalyzes the phosphorylation/decarboxylation of (R)-mevalonate-5-diphosphate to isopentenyl pyrophosphate in the mevalonate (MVA) pathway. MVD is a key enzyme in engineered metabolic pathways for bioproduction of isobutene, since it catalyzes the conversion of 3-hydroxyisovalerate (3-HIV) to isobutene, an important platform chemical. The putative homologue from Picrophilus torridus has been identified as a highly efficient variant in a number of patents, but its detailed characterization has not been reported. In this study, we have successfully purified and characterized the putative MVD from P. torridus. We discovered that it is not a decarboxylase per se but an ATP-dependent enzyme, mevalonate-3-kinase (M3K), which catalyzes the phosphorylation of MVA to mevalonate-3-phosphate. The enzyme''s potential in isobutene formation is due to the conversion of 3-HIV to an unstable 3-phosphate intermediate that undergoes consequent spontaneous decarboxylation to form isobutene. Isobutene production rates were as high as 507 pmol min⁻¹ g cells⁻¹ using Escherichia coli cells expressing the enzyme and 2,880 pmol min⁻¹ mg protein⁻¹ with the purified histidine-tagged enzyme, significantly higher than reported previously. M3K is a key enzyme of the novel MVA pathway discovered very recently in Thermoplasma acidophilum. We suggest that P. torridus metabolizes MVA by the same pathway.     

Methyl jasmonate affects phenolic metabolism and gene expression in blueberry (Vaccinium corymbosum)

Blueberry (Vaccinium corymbosum) is a fruit very much appreciated by consumers for its antioxidant potential and health‐promoting traits. Its beneficial potential properties are mainly due to a high content of anthocyanins and their amount can change after elicitation with methyl jasmonate. The aim of this work is to evaluate the changes in expression of several genes, accumulation of phenolic compounds and alterations in antioxidant potential in two different blueberry cultivars (‘Duke’ and ‘Blueray’) in response to methyl jasmonate (0.1 mM). Results showed that 9 h after treatment, the expression of phenylalanine ammonium lyase, chalcone synthase and anthocyanidin synthase genes was stimulated more in the ‘Blueray’ variety. Among the phenols measured an increase was recorded also for epicatechin and anthocyanin concentrations. ‘Duke’ is a richer sourche of anthocyanins compared to ‘Blueray’, treatment with methyl jasmonate promoted in ‘Blueray’ an increase in pigments as well as in the antioxidant potential, especially in fully ripe berries, but treated ‘Duke’ berries had greater levels, which were not induced by methyl jasmonate treatment. In conclusion, methyl jasmonate was, in some cases, an effective elicitor of phenolic metabolism and gene expression in blueberry, though with different intensity between cultivars.     

The influence of the polar head and the hydrophobic chain on the skin penetration enhancement effect of poly(ethylene glycol) derivatives

The effect of a homologue series of nonionic surfactants, namely poly(ethylene glycol) (PEG) fatty acid esters, differing in oxyethylene (PEG 8, PEG 12, and PEG 40) and fatty acid (stearate, mono and di-laurate, and mono and di-oleate) chain lengths, on in vitro skin permeability of ketoprofen (KTP) vehicled in plasters was investigated. The drug diffusion through hairless mouse skin as well as the effect of the surfactant type and strength was studied by Franz diffusion cells and ATR-FTIR spectroscopy. The use of PEG stearate series revealed that the surfactant with the largest polar head, namely PEG 40, was ineffective in enhancing the skin permeation of KTP, independently of the plaster concentrations. The effect of the hydrophobic chain was investigated only by using the shortest oxyethylene chains. The experimental results revealed that the oxyethylene chain length of surfactants appeared to be more influent than the alkyl chain. The prediction of the absorption enhancing capability of these PEG derivatives appeared related to the vehicle other than the proper combination of the number of ethylene oxide groups and alkyl groups.     

Autonomic innervation of salivary glands in the armadillo,anteater, and sloth (Edentata)

The intraglandular distribution of adrenergic and cholinergic nerve fibers was studied histochemically in the parotid, mandibular, and sublingual glands of six species of edentates belonging to the three families that comprise the order; namely, the Dasypodidae (armadillos), the Myrmecophagidae (anteaters), and the Bradipodidae (sloths). The following histochemical techniques were used: (a) acetylcholinesterase reaction for the demonstration of cholinergic fibers; (b) formaldehyde- and glyoxylic acid-induced fluorescence for the demonstration of adrenergic fibers. In addition, norepinephrine (NE) was assayed fluorimetrically in the mandibular and parotid glands of the armadillo. A network of acetylcholinesterase-positive nerve fibers surrounds the intra- and interlobular ducts and endpieces of all glands; it is of low density in the mandibular and sublingual gland of the sloth, of high density in the sublingual gland of the anteater and of moderate density in the remaining glands. A vascular cholinergic innervation occurs in all salivary glands. Although present around the vessels, adrenergic new fibers were virtually absent from the parenchyma of all glands, even after in vitro incubation of glandular tissue with NE, or after administration of NE to armadillos previously treated with a monoamine oxidase (MAO) inhibitor. Consistent with this fact, the amount of NE present in the parotid and mandibular gland of the armadillo was extremely low. These findings may indicate that the salivary secretion in the edentates is regulated by the parasympathetic rather than by the sympathetic nervous system.     

Post-transcriptional inhibition of ornithine decarboxylase induction by zinc in a difluoromethylornithine resistant cell line

Addition of Zn^2+_ to cell medium inhibited the induction of ornithine decarboxylase (ODC) activity in ODC overproducing L1210-DFMO^r cells. A significant effect was observed at a concentration as low as 0.01 mM, however a more marked inhibition was caused by the addition of 0.1 mM Zn²⁺. The inhibition of the induction of ODC activity was accompanied by a proportional decrease in the content of immunoreactive ODC protein, whereas the level of ODC mRNA, detemined by a solution hybridization RNase protection assay, was not affected signigicantly. Instead, some acceleration of ODC turnover was observed. the addition of 0.1 mM Co²⁺ or Mn²⁺, but not of other divalent metal ions, also inhibited ODC induction; differently from Zn²⁺ however, these metals affected cell viability and/or cell growth. Removal of endogenous Zn²⁺ by a chelator also provoked a strong decrease of ODC induction, which was reversed by Zn²⁺. However, addition of Zn²⁺ in excess of the chelator proved to be markedly inhibitory. These results indicate that both a restricted Zn²⁺ availability and an enhanced presence of the metal can inhibit the induction of ODC in L1210-DFMO^r cells.