Use of partial least squares regression to impute SNP genotypes in Italian Cattle breeds

Background

The objective of the present study was to test the ability of the partial least squares regression technique to impute genotypes from low density single nucleotide polymorphisms (SNP) panels i.e. 3K or 7K to a high density panel with 50K SNP. No pedigree information was used.

Methods

Data consisted of 2093 Holstein, 749 Brown Swiss and 479 Simmental bulls genotyped with the Illumina 50K Beadchip. First, a single-breed approach was applied by using only data from Holstein animals. Then, to enlarge the training population, data from the three breeds were combined and a multi-breed analysis was performed. Accuracies of genotypes imputed using the partial least squares regression method were compared with those obtained by using the Beagle software. The impact of genotype imputation on breeding value prediction was evaluated for milk yield, fat content and protein content.

Results

In the single-breed approach, the accuracy of imputation using partial least squares regression was around 90 and 94% for the 3K and 7K platforms, respectively; corresponding accuracies obtained with Beagle were around 85% and 90%. Moreover, computing time required by the partial least squares regression method was on average around 10 times lower than computing time required by Beagle. Using the partial least squares regression method in the multi-breed resulted in lower imputation accuracies than using single-breed data. The impact of the SNP-genotype imputation on the accuracy of direct genomic breeding values was small. The correlation between estimates of genetic merit obtained by using imputed versus actual genotypes was around 0.96 for the 7K chip.

Conclusions

Results of the present work suggested that the partial least squares regression imputation method could be useful to impute SNP genotypes when pedigree information is not available.     

Brain Gangliosides of Quaking and Shiverer Mutants: Qualitative and Quantitative Changes of Monosialogangliosides in the Quaking Brain

Ganglioside compositions in the brains of the mutant mice quaking and shiverer were compared with those of their littermate controls, C57BL/6 and C3HSWV. Neither ganglioside content nor composition of shiverer brains differed from those of the control brains. Change in the ganglioside composition of the mutant brain from that of the control was observed only in the quaking mutant brain, in which monosialoganglioside GM1 was significantly reduced and GM4 was completely absent. The structures of the gangliosides were determined by negative ion fast atom bombardment mass spectrometry, and the GM3 and GM4 gangliosides in the quaking brain were found to be altered in regard to their long-chain base and fatty acid compositions when compared to the normal C57BL/6 brain.     

Interaction of (dien)Pd(II) with cytidine and cytidine 5'-monophosphate. Influence of the phosphate group on the kinetics and mechanism

The kinetics and the equilibrium of (dien)PdCl+ interaction with cytidine (C) and cytidine 5'-monophosphate (CMP) were studied by spectrophotometry and by stopped-flow methods. In both cases, the mechanism implies a (dien)Pd(H2O)2+ intermediate with a significant contribution of the solvent path at low chloride concentrations. With CMP, the rate is affected due to the addition of a mechanistic path via an intermediate formed between (dien)Pd(II) and the phosphate group of CMP. The kinetic and thermodynamic parameters have been determined and reflect the favorable electrostatic interactions due to the presence of the phosphate group of CMP. Furthermore, these parameters are in agreement with a transient (dien)Pd(II)-phosphate complex of CMP leading to the formation of the thermodynamically favored (dien)Pd(II)-N3 complex as final product.     

Oral and parenteral immunization with HIV immunosome induce the secretion of IgA specific of HIV-1 in the salivary and the production of circulatory IgA in mice and rabbits]

Given the sexual transmission of HIV, the establishment of a genital mucosal immunity through secretory IgA may be necessary to achieve protection. We have investigated if repeated stimulations of oral mucosa with HIV-Immunosomes would lead to the production of secretory IgA in saliva and also, if such an oral immunization could prime the immune system to an early systemic immune response following a parenteral immunisation with a low dose of the antigen. HIV-1 gp 160-specific secretory IgA were detected in the saliva of all rabbits orally immunized with HIV-Immunosomes. As early as one week after the parenteral immunization, high titers of serum IgA, IgM and IgG were detected both in mice and rabbits that had been orally stimulated with the antigen. These antibodies could neutralize HIV infectivity in vitro. Animals that were immunized only parenterally showed a very weak humoral immune response.     

Selective inhibition of prostaglandin biosynthesis by gold salts and phenylbutazone

Gold salts and phenylbutazone selectively inhibit the synthesis of PGF_2α and PGE₂ respectively. Lowered production of one prostaglandin species is accompanied by an increased production of the other. Selective inhibition by these drugs was observed in the presence of adrenaline, reduced glutathione and copper sulphate under conditions when most anti-inflammatory compounds inhibited PGE₂ and PGF_2α syntheses equally. It is postulated that selective inhibitors may have a different mode of action in vivo and beneficial effects may be related to the endogenous ratio of PGE to PGF required for normal function.     

The succinate receptor GPR91 in neurons has a major role in retinal angiogenesis

Vascularization is essential for tissue development and in restoration of tissue integrity after an ischemic injury. In studies of vascularization, the focus has largely been placed on vascular endothelial growth factor (VEGF), yet other factors may also orchestrate this process. Here we show that succinate accumulates in the hypoxic retina of rodents and, via its cognate receptor G protein-coupled receptor-91 (GPR91), is a potent mediator of vessel growth in the settings of both normal retinal development and proliferative ischemic retinopathy. The effects of GPR91 are mediated by retinal ganglion neurons (RGCs), which, in response to increased succinate levels, regulate the production of numerous angiogenic factors including VEGF. Accordingly, succinate did not have proangiogenic effects in RGC-deficient rats. Our observations show a pathway of metabolite signaling where succinate, acting through GPR91, governs retinal angiogenesis and show the propensity of RGCs to act as sensors of ischemic stress. These findings provide a new therapeutic target for modulating revascularization.     

Phage annealing proteins promote oligonucleotide-directed mutagenesis in <Emphasis Type="Italic">Escherichia coli</Emphasis> and mouse ES cells

Background

The phage protein pairs, RecE/RecT from Rac or Redα/Redβ from λ, initiate efficient double strand break repair (DSBR) in Escherichia coli that has proven very useful for DNA engineering. These phage pairs initiate DSBR either by annealing or by another mechanism that is not defined.

Results

Here we report that these proteins also mediate single strand oligonucleotide repair (ssOR) at high efficiencies. The ssOR activity, unlike DSBR, does not require a phage exonuclease (RecE or Redα) but only requires a phage annealing protein (RecT or Redβ). Notably, the P22 phage annealing protein Erf, which does not mediate the same DSBR reactions, also delivers ssOR activity. By altering aspects of the oligonucleotides, we document length and design parameters that affect ssOR efficiency to show a simple relationship to homologies either side of the repair site. Notably, ssOR shows strand bias. Oligonucleotides that can prime lagging strand replication deliver more ssOR than their leading complements. This suggests a model in which the annealing proteins hybridize the oligonucleotides to single stranded regions near the replication fork. We also show that ssOR is a highly efficient way to engineer BACs and can be detected in a eukaryotic cell upon expression of a phage annealing protein.

Conclusion

Phage annealing proteins can initiate the recombination of single stranded oligonucleotides into endogenous targets in Escherichia coli at very high efficiencies. This expands the repertoire of useful DNA engineering strategies, shows promise for applications in eukaryotic cells, and has implications for the unanswered questions regarding DSBR mediated by RecE/RecT and Redα/Redβ.

     

Redox-dependent effects of nitric oxide on microvascular integrity in oxygen-induced retinopathy

Opposing effects have been ascribed to nitric oxide (NO) on retinal microvascular survival. We investigated whether changes in the redox state may contribute to explain apparent conflicting actions of NO in a model of oxygen-induced retinal vasoobliteration. Retinal microvascular obliteration was induced by exposing 7-day-old rat pups (P7) for 2 or 5 days to 80% O(2). The redox state of the retina was assessed by measuring reduced glutathione and oxidative and nitrosative products malondialdehyde and nitrotyrosine. The role of NO on vasoobliteration was evaluated by treating animals with nitric oxide synthase (NOS) inhibitors (N-nitro-l-arginine; L-NA) and by determining NOS isoform expression and activity; the contribution of nitrosative stress was also determined in animals treated with the degradation catalyst of peroxynitrite FeTPPS or with the superoxide dismutase mimetic CuDIPS. eNOS, but not nNOS or iNOS, expression and activity were increased throughout the exposure to hyperoxia. These changes were associated with an early (2 days hyperoxia) decrease in reduced glutathione and increases in malondialdehyde and nitrotyrosine. CuDIPS, FeTPPS, and L-NA treatments for these 2 days of hyperoxia nearly abolished the vasoobliteration. In contrast, during 5 days exposure to hyperoxia when the redox state rebalanced, L-NA treatment aggravated the vasoobliteration. Interestingly, VEGFR-2 expression was respectively increased by NOS inhibition after short-term (2 days) exposure to hyperoxia and decreased during the longer hyperoxia exposure. Data disclose that the dual effects of NO on newborn retinal microvascular integrity in response to hyperoxia in vivo depend on the redox state and seem mediated at least in part by VEGFR-2.     

HEAVILY LICHENIZED PHYSOLINUM (CHLOROPHYTA) FROM A DIMLY LIT CAVE IN MISSOURI1

Heavily lichenized Physolinum monile (De Wildem.) Printz from damp limestone walls in a dimly lit cave located in Missouri was studied from fresh collections and specimens fixed in situ, and from cultures. The narrow (7-13 μm wide thallus), profusely branched plant consisted of filaments of the alga P. monile ensheathed by clear fungal cells (5-8 in a single layer) that adhered tightly to each other and completely covered the algal cells. Cells of P. monile filaments were uninucleate, each containing a single massive chloroplast with numerous tightly packed thylakoids and lipid droplets and surrounded by a thin layer of cytoplasm. No plasmodesmata occurred in the cellulosic crosswalls between adjacent cells. The ensheathing fungal cells contained concentric bodies, produced haustoria that penetrated the algal cells, and developed hyphae (the tips of which formed clusters of conidia). Ensheathing fungal cells were well situated and constructed to concentrate light on the algal cells. Colonies of blue-green algae were firmly attached to the surface of the fungal cells. The association was slow growing but frequently produced and released aplanospores from the algal cells. Aplanospores were single (not attached to each other) with smooth walls or united in groups of two or more. Structures resembling lichen soredia, composed of aplanospore-like cells attached to one or more comdia-like cells, commonly occurred among the lichenized Physolinum filaments. The single chloroplast that occupies most of the cell's volume, the numerous, tightly packed thylakoids, and light focusing by ensheathing fungus cells may enable the organism to survive in a dimly lit environment. Because the filamentous alga reproduces only by aplanospores, we propose resurrection of the genus Physolinum. The lichenized Physolinum somewhat resembles the lichens Coenogonium moniliforme Tuck. and Cystocoleus Thwaites.