Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip

Background

Among the European countries, Italy counts the largest number of local goat breeds. Thanks to the recent availability of a medium-density SNP (single nucleotide polymorphism) chip for goat, the genetic diversity of Italian goat populations was characterized by genotyping samples from 14 Italian goat breeds that originate from different geographical areas with more than 50 000 SNPs evenly distributed on the genome.

Results

Analysis of the genotyping data revealed high levels of genetic polymorphism and an underlying North–south geographic pattern of genetic diversity that was highlighted by both the first dimension of the multi-dimensional scaling plot and the Neighbour network reconstruction. We observed a moderate and weak population structure in Northern and Central-Southern breeds, respectively, with pairwise F_ST values between breeds ranging from 0.013 to 0.164 and 7.49 % of the total variance assigned to the between-breed level. Only 2.11 % of the variance explained the clustering of breeds into geographical groups (Northern, Central and Southern Italy and Islands).

Conclusions

Our results indicate that the present-day genetic diversity of Italian goat populations was shaped by the combined effects of drift, presence or lack of gene flow and, to some extent, by the consequences of traditional management systems and recent demographic history. Our findings may constitute the starting point for the development of marker-assisted approaches, to better address future breeding and management policies in a species that is particularly relevant for the medium- and long-term sustainability of marginal regions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0140-6) contains supplementary material, which is available to authorized users.     

Is the PRC for Dark Pulses in LL a Mirror Image of the PRC for Light Pulses in DD in Mice?

The phase-response curves (PRC) for light pulses in continuous darkness (DD) have been described in many mammals, especially in nocturnal rodents. The PRC for dark pulses in continuous light (LL), however, has been described in a few mammals only, in nocturnal for bat and for hamster and in diurnal for Octodon degus, suggesting that this PRC is mirror imaging the PRC for light pulses. Therefore, the effect of 1-h and 3-h lasting dark pulses on the circadian wheel-running activity rhythm of mice in continuous light was investigated and then the PRC for dark pulses in LL was drawn up. For comparison, the effect of 1-h lasting light pulses on the circadian wheel-running activity rhythm of mice in DD was examined and the PRC for light pulses in DD was constructed. It appeared that the PRC for dark pulses, to a certain degree, represents a mirror image of the PRC for light pulses in mice. However, the advance region of this PRC is longer than that of delay. The mechanism of dark pulses action is discussed.     

Effects of interaction between65Zn,cadmium, and copper in rats

Distribution and retention of zinc in the presence of cadmium and copper was studied in rats exposed repeatedly to these metals. The experiment was performed on white rats of the Wistar strain. The animals were divided into four groups/five rats each: 1)⁶⁵ZnCl₂; 2)⁶⁵ZnCl₂+CdCl₂; 3)⁶⁵ZnCl₂+CuCl₂; and 4) control group. Rats were administered sc every other day for two weeks:⁶⁵ZnCl₂−5 mg Zn/kg; CdCl₂−0,3 Cd/kg; and CuCl₂−2 mg Cu/kg. The zinc content was measured in rat tissues by γ-counting. Effect of Cd and Cu on subcellular distribution of zinc in the kidney and liver and on the level of metallothionein were also examined. Whole body retention of zinc under the influence of cadmium was lower than that observed in animals treated with zinc alone. However, copper increased twofold the whole body retention of zinc. Cadmium elevated the accumulation of zinc only in the kidneys nuclear fraction and liver soluble fraction. In the kidneys and liver, copper elevated the accumulation of zinc, in the nuclear, mitochondrial, and soluble fractions. The level of metallothionein-like proteins (MT) in the kidneys after a combined supply of zinc and copper was significantly increased with respect to the group of animals treated with zinc alone. These results indicated complex interactions between cadmium, copper, and zinc that can affect the metabolism of each of the metals.     

Disturbances in heme biosynthesis in rabbits after administrationper os of low doses of tin or lead

The experiment was performed on female rabbits that receivedper os equimolar doses (17 μM Me/kg) of SnCl₂×2H₂O or Pb (CH₃ COO)₂ every day for 5 d. The activity of δ-aminolevulinic acid dehydratase (ALA-D) in the whole blood, liver, kidneys, brain, spleen, and bone marrow, concentration of free erythrocyte protoporphyrins (FEP), activity of δ-aminolevulinic acid synthetase (ALA-S) in the liver and bone marrow, urine δ-aminolevulinic acid (ALA-U), and coproporphyrins (CP-U) were determined. Lead and tin concentrations in the blood were estimated. Lead caused a significant inhibition of ALA-D in the blood, increased FEP concentration, and ALA and CP excretion in urine of rabbits. Lead also decreased ALA-D activity in the bone marrow and in the liver, and did not change ALA-2 activity in the liver and bone marrow. Tin did not change any of the examined indices. Tin doses applied in the present study, maintained within the limits of permissible standards of metal levels in human diet, did not affect the process of heme biosynthesis in rabbits.     

Cyclosporin A, an Immunosuppressive Drug, Induces Programmed Cell Death in Rat C6 Glioma Cells by a Mechanism that Involves the AP-1 Transcription Factor

Abstract: Cyclosporin A (CsA) is a clinically important immunosuppressive drug widely used to prevent graft rejection following organ or bone marrow transplantation. Although there are reports of serious neurologic alterations associated with the use of the drug, the precise mechanism of its action on the CNS still remains unknown. We studied the effects of CsA on the growth of C6 glioma cells. We found that CsA inhibits the growth of C6 glioma cells in a dose-dependent manner and induces morphological changes such as shrinkage of the cell body and loss of extensions followed by cell death. The analysis of DNA from CsA-treated cells revealed a ladder-like pattern of fragmented DNA. Acridine orange staining showed the occurrence of apoptotic changes in nuclear morphology. Apoptotic morphological alterations were prevented by the treatment with cycloheximide. Altogether, our findings suggest that the CsA-induced cell death of C6 glioma cells bears all the features characteristic of programmed cell death. We also observed a significant increase in the DNA-binding activity of AP-1 during CsA-induced apoptosis. The AP-1 induction preceded the appearance of apoptotic, morphological changes and was accounted for by an increase in the expression of c-Jun protein. The occurrence of increased levels of AP-1 complex and c-Jun protein during CsA-induced programmed cell death suggests its involvement in the induction of apoptosis.     

Isolation of coliphage lambda ghosts able to adsorb onto bacterial cells

We have examined three methods of γ ghost production, starting with the [³H]eucine-labelled phage, purified by CsCl density gradient sedimentation. Ghosts obtained by the osmotic shock or by incubation in 5 M LiCl do not adsorb on bacteria. Ghosts obtained by the treatment with the chelating agent EDTA and purified by CsCl density gradient sedimentation posses well preserved adsorption properties and are virtually free of DNA and infectious phage particles.     

Purification and characterization of maize seedling casein kinase IIB, a monomeric enzyme immunologically related to the alpha subunit of animal casein kinase-2.

Casein kinase IIB (CKIIB), a protein kinase related to animal casein kinase-2 (CK2), has been purified to homogeneity. It appears to be a monomeric enzyme, composed by an individual 39 kDa subunit, homologous to the alpha/alpha' subunits of animal CK2 and devoid of the autophosphorylatable 25-kDa alpha subunit of animal CK2, which display an heterotetrameric alpha 2 beta 2/alpha alpha' beta 2 structure. Such a conclusion is supported by the following lines of evidence: (1) CKIIB displays an apparent 39,000 Mr by gel filtration on Ultrogel AcA 34 and it gives rise to a single prominent protein band of similar Mr (38,000) upon SDS/PAGE; (2) upon incubation of the enzyme with [32P]ATP, no radiolabeled bands are detectable which might be attributable to either canonical or atypical beta subunits; (3) the 39-kDa band immunoreacts with antisera that recognize the alpha subunit of rat and chicken CK2; (4) conversely, no component immunologically related with the beta subunit could be detected in CKIIB by Western-blot analyses with antisera that recognize animal beta subunits; (5) the recombinant beta subunit of human CK2 is readily phosphorylated by CKIIB, the reaction being prevented, rather than stimulated, by polylysine, a behaviour typical of animal CK2 autophosphorylation. While the responsiveness of CKIIB to either heparin inhibition or polylysine stimulation are reminiscent of those of animal CK2, its peptide substrate specificity is significantly different and its thermolability is increased. Altogether these data would indicate that maize seedling CKIIB represents a naturally occurring monomeric form of CK2 devoid of non-catalytic subunits. Its properties, compared to those of animal CK2, suggest that the beta subunits of animal CK2 may be responsible for structural modifications conferring an altered specificity and an increased stability to the catalytic subunit.