Design of reference populations for genomic selection in crossbreeding programs

Background

In crossbreeding programs, genomic selection offers the opportunity to make efficient use of information on crossbred (CB) individuals in the selection of purebred (PB) candidates. In such programs, reference populations often contain genotyped PB animals, although the breeding objective is usually more focused on CB performance. The question is what would be the benefit of including a larger proportion of CB individuals in the reference population.

Methods

In a deterministic simulation study, we evaluated the benefit of including various proportions of CB animals in a reference population for genomic selection of PB animals in a crossbreeding program. We used a pig breeding scheme with selection for a moderately heritable trait and a size of 6000 for the reference population.

Results

Applying genomic selection to improve the performance of CB individuals, with a genetic correlation between PB and CB performance (r_PC) of 0.7, selection accuracy of PB candidates increased from 0.49 to 0.52 if the reference population consisted of PB individuals, it increased to 0.55 if the reference population consisted of the same number of CB individuals, and to 0.60 if the size of the CB reference population was twice that of the reference population for each PB line. The advantage of using CB rather than PB individuals increased linearly with the proportion of CB individuals in the reference population. This advantage disappeared quickly if r_PC was higher or if the breeding objective put some emphasis on PB performance. The benefit of adding CB individuals to an existing PB reference population was limited for high r_PC.

Conclusions

Using CB rather than PB individuals in a reference population for genomic selection can provide substantial advantages, but only when correlations between PB and CB performances are not high and PB performance is not part of the breeding objective.     

Bacteriocin-Related Siblicide in Clinical Isolates of Enterococci

Siblicide is a phenomenon defined in the present context as an Enterococcus strain that, while growing as a colony on solid media, exhibits an inhibitory effect on a lawn composed of the identical strain. It was shown to occur in seven clinical isolates of enterococci (one E. faecalis and six E. faecium). Four involve inhibitory anti-listerial activities consistent with class II bacteriocins, two of which appear to be up-regulated by extracellular autoinducers.     

p53 codon 271 CGT to CAT mutant fraction does not increase in nasal respiratory and olfactory epithelia of rats exposed to inhaled naphthalene

A 2-year rat tumor bioassay testing whole body exposure to naphthalene (NA) vapor found a significant increase in nasal respiratory epithelial adenomas in male rats and in olfactory epithelial neuroblastomas in female rats. To obtain mechanistic insight into NA-induced nasal carcinogenesis, NA dose-response was characterized in nasal epithelium using a tumor-relevant endpoint. Specifically, levels of p53 codon 271 CGT to CAT mutation were measured in nasal respiratory and olfactory epithelium of NA-exposed male and female rats by allele-specific competitive blocker-PCR (ACB-PCR). Male and female, 8-9 week-old F344 rats (5 rats/group) were exposed to 0, 0.1, 1.0, 10, and 30ppm NA vapor for 13 weeks (6h/day, 5 days/week). The geometric mean p53 mutant fraction (MF) levels in nasal epithelium of control treatment groups ranged between 2.05 × 10(-5) and 3.05 × 10(-5). No significant dose-related changes in p53 mutant fraction (MF) were observed in the olfactory or respiratory epithelia of female rats. However, statistically significant treatment-related differences were observed in male respiratory and olfactory epithelium, with the p53 MF in the respiratory epithelium of male rats exposed to 30ppm NA significantly lower than that in controls. Further, a significant trend of decreasing p53 MF with increasing dose was observed in the male respiratory epithelium. Of the tissue types analyzed, respiratory epithelium is the most sensitive to the cytotoxic effects of NA, suggesting cytotoxicity may be responsible for the loss of p53 mutation. Because ACB-PCR has been used successfully to detect the effects of known mutagenic carcinogens, the absence of any significant increases in p53 MF associated with NA exposure adds to the weight of evidence that NA does not operate through a directly mutagenic mode of action.     

Exercise prevents leptin-induced increase in blood pressure in Sprague–Dawley rats

Although leptin has been shown to increase blood pressure (BP), it is however unclear if this increase can be prevented by exercise. This study therefore investigated the effect of leptin treatment with concurrent exercise on blood pressure (BP), sodium output, and endothelin-1 (ET-1) levels in normotensive rats. Male Sprague–Dawley rats weighing 250–270 g were divided into four groups consisting of a control group (n?=?6), leptin-treated (n?=?8), non-leptin-treated exercise group (n?=?8), and a leptin-treated exercise group (n?=?8). Leptin was given subcutaneously daily for 14 days (60 μg/kg/day). Animals were exercised on a treadmill for 30 min at a speed of 0.5 m/s and at 5° incline four times per week. Measurement of systolic blood pressure (SBP) and collection of urine samples for estimation of sodium and creatinine was done once a week. Serum samples were collected at the end of the experiment for determination of sodium, creatinine and ET-1. At day 14, mean SBP and serum ET-1 level in the leptin-treated group was significantly higher than that in the control group whereas mean SBP and serum ET-1 level was significantly lower in the leptin-treated exercise group than those in leptin-treated and control groups. Creatinine clearance, urinary sodium excretion, and urine output were not different between the four groups. Regular treadmill exercise prevents leptin-induced increases in SBP in rats, which might in part result from increased urinary sodium excretion and preventing the leptin-induced increases in serum ET-1 concentration.     

Time Space Translation: A Hox Mechanism for Vertebrate A-P Patterning

The vertebrate A-P axis is a time axis. The head is made first and more and more posterior levels are made at later and later stages. This is different to the situation in most other animals, for example, in Drosophila. Central to this timing is Hox temporal collinearity (see below). This occurs rarely in the animal kingdom but is characteristic of vertebrates and is used to generate the primary axial Hox pattern using time space translation and to integrate successive derived patterns (see below). This is thus a different situation than in Drosophila, where the primary pattern guiding Hox spatial collinearity is generated externally, by the gap and segmentation genes.     

A "retrocidal" plasmid in Enterococcus faecalis: passage and protection

Enterococcus faecalis MC4 harbors a 130 kb conjugative, pheromone (cCF10)-responding plasmid, pAMS1, conferring chloramphenicol, streptomycin and tetracycline resistances. A plasmid-borne class IIa bacteriocin (MC4-1) determinant and cognate immunity gene were present, but not expressed in MC4. However, pAMS1 transfer to E. faecalis JH2-2 (but not to the non-isogenic OG1SS) generated the surprising ability to express bacteriocin activity against the plasmid donor, MC4. The bacteriocin target spectrum includes E. faecalis, Enterococcus faecium, Enterococcus gallinarum, Enterococcus hirae, and Listeria monocytogenes. Those donors unable to express bacteriocin or immunity could protect themselves from the "retrocidal" behavior of transconjugants by a switch to bacteriocin resistance at a frequency of approximately 10(-3). Reversion to sensitivity occurred at a relatively high frequency, suggestive of involvement of a phase variation event. These observations concerning a conjugative plasmid with novel "retrocidal" properties, coupled with a defense mechanism independent of plasmid-borne immunity functions, may relate to phenomena exploiting regulatory features with broader ecological and evolutionary implications.     

Cubicle Refusal in Norwegian Dairy Herds

In order to survey the behaviour of choosing the alley area instead of a cubicle as a lying place (cubicle refusal), a questionnaire was sent to the 273 dairy farms in Norway known to keep cows in cubicle housing systems. Sixty-six percent of the farmers contacted were included in the study. The median herd size was 18 cows (range 7–118). More than 85% of the herds had sheds providing one or more cubicles per cow. The mean herd occurrence of cubicle refusal was 6%, but showed great variation (range 0–55%). Regression analysis showed a significant association between rearing heifers in slatted floor pens and an increased cubicle refusal occurrence (p = 0.02, R² = 0.05), while herd size, use of litter, or cubicle-to-animal ratio were not found to be associated with cubicle refusal. The practice of rearing heifers in slatted floor pens accounted for about one half of the observed cubicle refusal (etiologic fraction = 0.51).     

Autoantibody systems in rheumatoid arthritis: specificity, sensitivity and diagnostic value

The diagnosis of rheumatoid arthritis (RA) is primarily based on clinical symptoms, so it is often difficult to diagnose RA in very early stages of the disease. A disease-specific autoantibody that could be used as a serological marker would therefore be very useful. Most autoimmune diseases are characterized by a polyclonal B-cell response targeting multiple autoantigens. These immune responses are often not specific for a single disease. In this review, the most important autoantibody/autoantigen systems associated with RA are described and their utility as a diagnostic and prognostic tool, including their specificity, sensitivity and practical application, is discussed. We conclude that, at present, the antibody response directed to citrullinated antigens has the most valuable diagnostic and prognostic potential for RA.