A genome-wide scan for signatures of directional selection in domesticated pigs

Background

Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication.

Results

Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an F_ST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness.

Conclusions

We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1330-x) contains supplementary material, which is available to authorized users.     

Heat stress in grapevine: the pros and cons of acclimation

Heat stress is a major limiting factor of grapevine production and quality. Acclimation and recovery are essential to ensure plant survival, and the recovery mechanisms can be independent of the heat response mechanisms. An experimental set up with and without acclimation to heat followed by recovery [stepwise acclimation and recovery (SAR) and stepwise recovery (SR), respectively] was applied to two grapevine varieties, Touriga Nacional (TN), and Trincadeira (TR), with different tolerance to abiotic stress. Major differences were found between leaves of SAR and SR, especially after recovery; in SAR, almost all parameters returned to basal levels while in SR they remained altered. Acclimation led to a swifter and short‐term antioxidative response, affecting the plant to a lesser extent than SR. Significant differences were found among varieties: upon stress, TN significantly increased ascorbate and glutathione reduction levels, boosting the cell's redox‐buffering capacity, while TR needed to synthesize both metabolites, its response being insufficient to keep the redox state at working levels. TR was affected by stress for a longer period and the up‐regulation pattern of antioxidative stress genes was more obvious. In TN, heat shock proteins were significantly induced, but the canonical heat‐stress gene signature was not evident probably because no shutdown of the housekeeping metabolism was needed.     

Blindness and Glaucoma: A Multicenter Data Review from 7 Academic Eye Clinics

PurposeTo evaluate frequency, conversion rate, and risk factors for blindness in glaucoma patients treated in European Universities.MethodsThis multicenter retrospective study included 2402 consecutive patients with glaucoma in at least one eye. Medical charts were inspected and patients were divided into those blind and the remainder (‘controls’). Blindness was defined as visual acuity≤0.05 and/or visual field loss to less than 10°.ResultsUnilateral and bilateral blindness were respectively 11.0% and 1.6% at the beginning, and 15.5% and 3.6% at the end of the observation period (7.5±5.5 years, range:1–25 years); conversion to blindness (at least unilateral) was 1.1%/year. 134 eyes (97 patients) developed blindness by POAG during the study. At the first access to study centre, they had mean deviation (MD) of -17.1±8.3 dB and treated intraocular pressure (IOP) of 17.1±6.6 mmHg. During follow-up the IOP decreased by 14% in these eyes but MD deteriorated by 1.1±3.5 dB/year, which was 5-fold higher than controls (0.2±1.6 dB/year). In a multivariate model, the best predictors for blindness by glaucoma were initial MD (p<0.001), initial IOP (p<0.001), older age at the beginning of follow-up (p<0.001), whereas final IOP was found to be protective (p<0.05).ConclusionsIn this series of patients, blindness occurred in about 20%. Blindness by glaucoma had 2 characteristics: late diagnosis and/or late referral, and progression of the disease despite in most cases IOP was within the range of normality and target IOP was achieved; it could be predicted by high initial MD, high initial IOP, and old age.     

Duodenal atresia in an infant with triple-X syndrome: a new associated malformation in 47,XXX

BACKGROUND: An association between the triple-X syndrome (47,XXX) and gastrointestinal malformations is extremely rare. Most 47,XXX patients present with a normal phenotype, but genitourinary malformations have been described. CASE: We report a case of a child with 47,XXX and duodenal atresia. Antenatal ultrasound scan showed a dilated fetal stomach and upper part of the duodenum (double bubble phenomenon) at 31 weeks of gestation in a 31-year-old woman with polyhydramnion. The amniotic fluid karyotype showed 47,XXX. After a scheduled delivery, duodenal atresia was confirmed and treated with duodeno-duodenostomy. CONCLUSIONS: The possible association of gastrointestinal and genitourinary tract anomalies requires a detailed postnatal clinical investigation and ultrasonographic examination of the abdomen, retroperitoneum, and pelvis on all triple-X syndrome patients.     

Competitively disrupting the neutrophil-specific receptor–autoantigen CD177:proteinase 3 membrane complex reduces anti-PR3 antibody-induced neutrophil activation

CD177 is a neutrophil-specific receptor presenting the proteinase 3 (PR3) autoantigen on the neutrophil surface. CD177 expression is restricted to a neutrophil subset, resulting in CD177^pos/mPR3^high and CD177^neg/mPR3^low populations. The CD177^pos/mPR3^high subset has implications for antineutrophil cytoplasmic autoantibody (ANCA)–associated autoimmune vasculitis, wherein patients harbor PR3-specific ANCAs that activate neutrophils for degranulation. Here, we generated high-affinity anti-CD177 monoclonal antibodies, some of which interfered with PR3 binding to CD177 (PR3 “blockers”) as determined by surface plasmon resonance spectroscopy and used them to test the effect of competing PR3 from the surface of CD177^pos neutrophils. Because intact anti-CD177 antibodies also caused neutrophil activation, we prepared nonactivating Fab fragments of a PR3 blocker and nonblocker that bound specifically to CD177^pos neutrophils. We observed that Fab blocker clone 40, but not nonblocker clone 80, dose-dependently reduced anti-PR3 antibody binding to CD177^pos neutrophils. Importantly, preincubation with clone 40 significantly reduced respiratory burst in primed neutrophils challenged with either monoclonal antibodies to PR3 or PR3–ANCA immunoglobulin G from ANCA-associated autoimmune vasculitis patients. After separating the two CD177/mPR3 neutrophil subsets from individual donors by magnetic sorting, we found that PR3–ANCAs provoked significantly more superoxide production in CD177^pos/mPR3^high than in CD177^neg/mPR3^low neutrophils, and that anti-CD177 Fab clone 40 reduced the superoxide production of CD177^pos cells to the level of the CD177^neg cells. Our data demonstrate the importance of the CD177:PR3 membrane complex in maintaining a high ANCA epitope density and thereby underscore the contribution of CD177 to the severity of PR3–ANCA diseases.     

Aflatoxin contamination of rice in the United Arab Emirates

Many people in the United Arab Emirates store rice in large quantities for long periods of time before use. Five hundred samples of rice were collected from households in Al-Ain city during the summers of 1992-1994. Aflatoxin B₁ was detected in 160 samples (64%) of long grain rice and 81 Samples (32%) of short grain rice at levels ranging from 1.2 to 16.5 μg/kg. The moisture content of samples varied between 5.7% and 15.3%. Species ofAspergillus andPenicillium (includingA. flavus andA. parasiticus) were isolated from discoloured, broken and insect damaged grain and it was confirmed that at least two of the isolates ofA. flavus were aflatoxigenic. These findings demonstrate that rice may contribute to dietary exposure to aflatoxins which are known to be carcinogenic and immunosuppressive.     

Glutamine synthetase in the phloem plays a major role in controlling proline production

To inhibit expression specifically in the phloem, a 274-bp fragment of a cDNA (Gln1-5) encoding cytosolic glutamine synthetase (GS1) from tobacco was placed in the antisense orientation downstream of the cytosolic Cu/Zn superoxide dismutase promoter of Nicotiana plumbaginifolia. After Agrobacterium-mediated transformation, two transgenic N. tabacum lines exhibiting reduced levels of GS1 mRNA and GS activity in midribs, stems, and roots were obtained. Immunogold labeling experiments allowed us to verify that the GS protein content was markedly decreased in the phloem companion cells of transformed plants. Moreover, a general decrease in proline content in the transgenic plants in comparison with wild-type tobacco was observed when plants were forced to assimilate large amounts of ammonium. In contrast, no major changes in the concentration of amino acids used for nitrogen transport were apparent. A (15)NH(4)(+)-labeling kinetic over a 48-hr period confirmed that in leaves of transgenic plants, the decrease in proline production was directly related to glutamine availability. After 2 weeks of salt treatment, the transgenic plants had a pronounced stress phenotype, consisting of wilting and bleaching in the older leaves. We conclude that GS in the phloem plays a major role in regulating proline production consistent with the function of proline as a nitrogen source and as a key metabolite synthesized in response to water stress.     

Situation of mycotoxins in milk, dairy products and human milk in Egypt

Abstact  Milk and dairy products purchased at Egyptian markets and breast milk from lactating mothers in Cairo and Giza governorates were analyzed for some mycotoxins. Three of 15 cows’ milk samples were found positive for Afl. M₁ with mean value 6.3 ppb. Only one sample of dried milk was positive (5 ppb). Two of 10 hard cheese samples contained detectable levels of Afl. M₁ (3and 6 ppb), whereas one sample containing Afl. B₁ and G₁ (10 and 4 ppb resp.). For soft cheese one sample of 10 was positive for Afl. M₁ (0.5 ppb). Blue veined cheeses were free of Afl. M₁ and PR-toxins. For breast milk two of 10 samples were positive for Afl. M₁ (20%) with mean value 2.75 ppb, while 3 of 10 samples were positive for Ochratoxin A (30 %).     

The Gram Staining Mechanism of Cat Tongue Keratin. II. The Role of Potassium Iodide-Iodine Solution

The aniline-xylene decolorizer of the Gram-Weigert staining procedure failed to remove crystal violet dye from stained sections of cat tongue without prior treatment of the sections with potassium iodide-iodine solution. The potassium iodide of the iodide-iodine solution was found to release the major part of the crystal violet dye bound by the tongue sections. Iodine appeared also to play a role in dye release, but only to a slight degree. The amount of Gram-positive staining was increased both by alkaline treatment of the tissue prior to staining, and by increasing the pH of the iodide-iodine solution.