Toll-like receptor 4 genetic diversity among pig populations

The transmembrane glycoprotein encoded by the Toll-like receptor 4 gene ( TLR4 ) acts as the transducing subunit of the lipopolysaccharide receptor complex of mammals, which is a major sensor of infections by Gram-negative bacteria. As variation in TLR4 may alter host immune response to lipopolysaccharide, the association between TLR4 polymorphisms and immune traits of the respiratory and gut systems has important implications for livestock. Here, a sequence dataset from 259 animals belonging to commercial and traditional European pig populations, consisting of 4305 bp of TLR4, including the full transcribed region, a portion of intron 2 and the putative promoter region, was used to explore genetic variation segregating at the TLR4 locus. We identified 34 single nucleotide polymorphisms, 17 in the coding sequence and 17 in the non-coding region. Five non-synonymous mutations clustered within, or in close proximity to, the hypervariable domain of exon 3. In agreement with studies in other mammals, a major exon 3 haplotype segregated at high frequency in the whole sample of 259 pigs, while variants carrying non-synonymous substitutions showed frequencies ranging between 0.6% and 8.7%. Although results on exon 3 provided suggestive evidence for purifying selection occurring at the porcine TLR4 gene, the analysis of both coding and non-coding regions highlighted the fact that demographic factors strongly influence the tests of departure from neutrality. The phylogenetic analysis of TLR4 identified three clusters of variation (ancestral, Asian, European), supporting the evidence of Asian introgression in European main breeds and the well documented history of pig breed domestication previously identified by mtDNA analysis.     

Nucleophosmin and its AML-associated mutant regulate c-Myc turnover through Fbw7 gamma

Mutations leading to aberrant cytoplasmic localization of nucleophosmin (NPM) are the most frequent genetic alteration in acute myelogenous leukemia (AML). NPM binds the Arf tumor suppressor and protects it from degradation. The AML-associated NPM mutant (NPMmut) also binds p19Arf but is unable to protect it from degradation, which suggests that inactivation of p19Arf contributes to leukemogenesis in AMLs. We report here that NPM regulates turnover of the c-Myc oncoprotein by acting on the F-box protein Fbw7gamma, a component of the E3 ligase complex involved in the ubiquitination and proteasome degradation of c-Myc. NPM was required for nucleolar localization and stabilization of Fbw7gamma. As a consequence, c-Myc was stabilized in cells lacking NPM. Expression of NPMmut also led to c-Myc stabilization because of its ability to interact with Fbw7gamma and delocalize it to the cytoplasm, where it is degraded. Because Fbw7 induces degradation of other growth-promoting proteins, the NPM-Fbw7 interaction emerges as a central tumor suppressor mechanism in human cancer.     

Laetiporic acids, a family of non-carotenoid polyene pigments from fruit-bodies and liquid cultures of Laetiporus sulphureus (Polyporales, Fungi)

The non-isoprenoid polyene laetiporic acid A, recently described from fruit-bodies of the wood-rotting fungus Laetiporus sulphureus, was found to be the major orange pigment also in mycelium grown in liquid culture. Its formation was variable, ranging from 0.1 to 6.7 mg/g dry weight in three strains, all of which were identified as L. sulphureus by ITS rDNA sequence analysis. A second pigment, 2-dehydro-3-deoxylaetiporic acid A, is also described and fully characterized by NMR spectroscopy. Two further minor pigments, laetiporic acids B and C, were produced in liquid culture. These resemble laetiporic acid A but are enlarged by two and four carbon atoms, respectively, resulting in chromophores with 11 or 12 instead of 10 conjugated double bonds as described for laetiporic acid A. Since fruit-bodies of L. sulphureus are edible, laetiporic acids might hold potential as food colourants.     

Mapping, identification of polymorphisms and analysis of allele frequencies in the porcine skeletal muscle myopalladin and titin genes

Genes coding for sarcomeric proteins may play a key role in muscle mass accretion and meat production. Screening a skeletal muscle cDNA library we isolated two partial sequences coding for the sarcomeric myopalladin and titin genes. In the present work we identified three SNPs in the 3' untranslated region, two at the myopalladin locus and one at the titin locus. Myopalladin was mapped on porcine chromosome (SSC) 14 using a somatic cell hybrid panel, a radiation hybrid panel and by linkage mapping. The linkage mapping of titin confirmed the position on SSC15. Then we analysed the allelic distribution of the alleles at both loci in six different porcine breeds. The analysis of the allele frequencies for these two loci in extremely divergent groups of pigs selected according to lean cuts (LC) and average daily gain (ADG) approached the significance level for myopalladin and LC trait. Further studies are needed to test the presence of a putative effect of myopalladin on lean meat content.     

Hair snaring and molecular genetic identification for reconstructing the spatial structure of Eurasian lynx populations

Non-invasive genetic sampling (NGS) is being increasingly applied in wildlife monitoring and population genetic research. This study was designed to evaluate the use of NGS for reconstructing the spatial structure of populations of large felids. We developed a procedure for reliably genotyping individuals of Eurasian lynx (Lynx lynx) from samples obtained through a hair-trapping scheme based on a network of lynx scent-marking sites. The spatial locations of the identified genotypes were matched with the home ranges distribution of radio-tracked individuals, thus cross-checking the accuracy of the two methods. We analyzed DNA extracted from 170 hair samples and 11 blood samples from live-trapped lynx collected in 2004–2009 in the Bia?owie?a Primeval Forest, Poland. We obtained PCR products in 96 (67%) hair samples; 82 (85%) of them were reliably genotyped at 12 autosomal microsatellite loci following a multiple-tubes protocol and stringent quality-controls of the data set. The sample included 29 distinct genotypes; 18 were found only in hair samples, five were determined only in live-trapped animals, and six in both hair and blood samples. Based on linkage disequilibrium we estimated an effective population size N_e = 20.3 (90% CI = 15–28). The total population size estimated with Capwire was N_c = 32 (95% CI = 25–37) in close agreement with the observed number of genotypes. The genotypes obtained from hair samples were re-sampled on average 3.9 times and 50% of them were recorded for more than one year. The spatial distribution of six hair-genotypes was consistent with their home ranges obtained by radio-tracking in the same period. The distribution ranges of hair-trapped genotypes overlapped on average in 86.4% (mode 100%) with home ranges of the corresponding individuals. Hair-trapping and molecular identification is a reliable method for reconstructing the spatial organization of lynx population. It is likely to be also efficiently used in other rare and endangered species of felids in combination with data from other monitoring techniques, such as radio- and snow-tracking and photo-trapping.     

Differentiation of Human Embryonic Stem Cells into Cells with Corneal Keratocyte Phenotype

Corneal transparency depends on a unique extracellular matrix secreted by stromal keratocytes, mesenchymal cells of neural crest lineage. Derivation of keratocytes from human embryonic stem (hES) cells could elucidate the keratocyte developmental pathway and open a potential for cell-based therapy for corneal blindness. This study seeks to identify conditions inducing differentiation of pluripotent hES cells to the keratocyte lineage. Neural differentiation of hES cell line WA01(H1) was induced by co-culture with mouse PA6 fibroblasts. After 6 days of co-culture, hES cells expressing cell-surface NGFR protein (CD271, p75NTR) were isolated by immunoaffinity adsorption, and cultured as a monolayer for one week. Keratocyte phenotype was induced by substratum-independent pellet culture in serum-free medium containing ascorbate. Gene expression, examined by quantitative RT-PCR, found hES cells co-cultured with PA6 cells for 6 days to upregulate expression of neural crest genes including NGFR, SNAI1, NTRK3, SOX9, and MSX1. Isolated NGFR-expressing cells were free of PA6 feeder cells. After expansion as a monolayer, mRNAs typifying adult stromal stem cells were detected, including BMI1, KIT, NES, NOTCH1, and SIX2. When these cells were cultured as substratum-free pellets keratocyte markers AQP1, B3GNT7, PTDGS, and ALDH3A1 were upregulated. mRNA for keratocan (KERA), a cornea-specific proteoglycan, was upregulated more than 10,000 fold. Culture medium from pellets contained high molecular weight keratocan modified with keratan sulfate, a unique molecular component of corneal stroma. These results show hES cells can be induced to differentiate into keratocytes in vitro. Pluripotent stem cells, therefore, may provide a renewable source of material for development of treatment of corneal stromal opacities.     

Associations of functional candidate genes derived from gene-expression profiles of prenatal porcine muscle tissue with meat quality and muscle deposition

Ten genes (ANK1, bR10D1, CA3, EPOR, HMGA2, MYPN, NME1, PDGFRA, ERC1, TTN), whose candidacy for meat-quality and carcass traits arises from their differential expression in prenatal muscle development, were examined for association in 1700 performance-tested fattening pigs of commercial purebred and crossbred herds of Duroc, Pietrain, Pietrain x (Landrace x Large White), Duroc x (Landrace x Large White) as well as in an experimental F(2) population based on a reciprocal cross of Duroc and Pietrain. Comparative sequencing revealed polymorphic sites segregating across commercial breeds. Genetic mapping results corresponded to pre-existing assignments to porcine chromosomes or current human-porcine comparative maps. Nine of these genes showed association with meat-quality and carcass traits at a nominal P-value of < or = 0.05; PDGFRA revealed no association reaching the P < or = 0.05 threshold. In particular, HMGA2, CA3, EPOR, NME1 and TTN were associated with meat colour, pH and conductivity of loin 24 h postmortem; CA3 and MYPN exhibited association with ham weight and lean content (FOM) respectively at P-values of < 0.003 that correspond to false discovery rates of < 0.05. However, none of the genes showed significant associations for a particular trait across all populations. The study revealed statistical-genetic evidence for association of the functional candidate genes with traits related to meat quality and muscle deposition. The polymorphisms detected are not likely causal, but markers were identified that are in linkage disequilibrium with causal genetic variation within particular populations.