Genetic analysis of an F2 intercross between two chicken lines divergently selected for body-weight

<p>Abstract</p> <p>Background</p> <p>We have performed Quantitative Trait Loci (QTL) analysis of an F₂intercross between two chicken lines divergently selected for juvenile body-weight. In a previous study 13 identified loci with effects on body-weight, only explained a small proportion of the large variation in the F₂population. Epistatic interaction analysis however, indicated that a network of interacting loci with large effect contributed to the difference in body-weight of the parental lines. This previous analysis was, however, based on a sparse microsatellite linkage map and the limited coverage could have affected the main conclusions. Here we present a revised QTL analysis based on a high-density linkage map that provided a more complete coverage of the chicken genome. Furthermore, we utilized genotype data from ~13,000 SNPs to search the genome for potential selective sweeps that have occurred in the selected lines.</p> <p>Results</p> <p>We constructed a linkage map comprising 434 genetic markers, covering 31 chromosomes but leaving seven microchromosomes uncovered. The analysis showed that seven regions harbor QTL that influence growth. The pair-wise interaction analysis identified 15 unique QTL pairs and notable is that nine of those involved interactions with a locus on chromosome 7, forming a network of interacting loci. The analysis of ~13,000 SNPs showed that a substantial proportion of the genetic variation present in the founder population has been lost in either of the two selected lines since ~60% of the SNPs polymorphic among lines showed fixation in one of the lines. With the current marker coverage and QTL map resolution we did not observe clear signs of selective sweeps within QTL intervals.</p> <p>Conclusion</p> <p>The results from the QTL analysis using the new improved linkage map are to a large extent in concordance with our previous analysis of this pedigree. The difference in body-weight between the parental chicken lines is caused by many QTL each with a small individual effect. Although the increased chromosomal marker coverage did not lead to the identification of additional QTL, we were able to refine the localization of QTL. The importance of epistatic interaction as a mechanism contributing significantly to the remarkable selection response was further strengthened because additional pairs of interacting loci were detected with the improved map.</p

A randomized multicenter study of the outcome of brachial-basilic arteriovenous fistula and prosthetic brachial-antecubital forearm loop as vascular access for hemodialysis

BackgroundVascular access is a necessity for patients with end-stage renal disease who need chronic intermittent hemodialysis. According to Kidney Disease Outcomes Quality Initiative (KDOQI) guidelines, radial-cephalic (RC) and brachial-cephalic (BC) arteriovenous fistulas (AVF) are the first and second choice for vascular access, respectively. If these options are not possible, an autogenous brachial-basilic fistula in the upper arm (BBAVF) or a prosthetic brachial-antecubital forearm loop (PTFE loop) may be considered. Until now, it was not clear which access type was preferable. We have performed a randomized study comparing BBAVF and prosthetic implantation in patients without the possibility for RCAVF or BCAVF.MethodsPatients with failed primary/secondary access or inadequate arterial and/or venous vessels were randomized for either BBAVF or PTFE loop creation. The numbers of complications and interventions were recorded. Kaplan-Meier method was used to calculate primary, assisted-primary and secondary patency rates. The patency rates were compared with the log-rank test. Complication and intervention rates were compared with the Mann-Whitney test.ResultsA total of 105 patients were randomized for a BBAVF or PTFE loop (52 vs 53, respectively). Primary and assisted-primary 1-year patency rates were significantly higher in the BBAVF group: 46% ± 7.4% vs 22% ± 6.1% (P = .005) and 87% ± 5.0% vs 71% ± 6.7% (P = .045) for the BBAVF and PTFE group, respectively. Secondary patencies were comparable for both groups; 89% ± 4.6% vs 85% ± 5.2% for the BBAVF and PTFE group, respectively. The incidence rate of complications was 1.6 per patient-year in the BBAVF group vs 2.7 per patient-year in the PTFE group. Patients in the BBAVF group needed a total of 1.7 interventions per patient-year vs 2.7 per patient-year for the PTFE group.ConclusionThese data show a significantly better primary and assisted-primary patency in the BBAVF group compared with the PTFE group. Furthermore, in the BBAVF group, fewer interventions were needed. Therefore, we conclude that BBAVF is the preferred choice for vascular access if RCAVF or BCAVF creation is impossible, or when these types of access have already failed

Equilibrium charge-state distributions of sodium ions in carbon foil

The equilibrium charge-state distributions have been measured for sodium ions at the exit of a carbon foil for energies ranging from 0.43 to 1.66 Me V. A comparison of our results with available models is performed and an empirical formula for calculating the charge-state fractions of sodium ions is deduced

Compiling polymorphic miRNA-target interactions: the Patrocles database.

Using positional cloning, we have recently identified the mutation responsible for muscular phenotype of the Texel sheep. It is located in the 3’UTR of the GDF8 gene - a known developmental repressor of muscle growth - and creates an illegitimate target site for miRNA expressed in the same tissue. This causes miRNA-mediated translation inhibition of mutant GDF8 transcripts which leads to muscle hypertrophy. We followed up on this finding by searching for common polymorphisms and mutations that affect either (i) RNAi silencing machinery components, (ii) miRNA precursors or (iii) target sites. These might likewise alter miRNA-target interaction and could be responsible for substantial differences in gene expression level. They have been compiled in a public database (“Patrocles”: www.patrocles.org), where they are classified in (i) DNA sequence polymorphisms (DSP) affecting the silencing machinery, (ii) DSP affecting miRNA structure or expression and (iii) DSP affecting miRNA target sites. DSP from the last category were organized in four classes: destroying a target site conserved between mammals (DC), destroying a non-conserved target site (DNC), creating a non-conserved target site (CNC), or shifting a target site (S). To aid in the identification of the most relevant DSP (such as those were a target site is created in an antitarget gene), we have quantified the level of coexpression for all miRNA-gene pairs. Analysis of the numbers of Patrocles-DSP as well as their allelic frequency distribution indicates that a substantial proportion of them undergo purifying selection. The signature of selection was most pronounced for the DC class but was significant for the DNC and CNC class as well, suggesting that a significant proportion of non-conserved targets is truly functional. The Patrocles database allowed for the selection of DSP that are likely to affect gene function and possibly disease susceptibility. The effect of these DSP is being studied both in vitro and in vivo. In conclusion, Patrocles-DSP could be widespread and underlie an appreciable amount of phenotypic variation, including common disease susceptibility

Lifetime measurements in Yb II with time-resolved laser spectroscopy

Natural radiative lifetimes of 10 levels of singly ionized ytterbium have been measured with time-resolved laser spectroscopy. Free Yb+ ions were produced in a laser-induced plasma. A stimulated Brillouin scattering technique has been used to produce laser pulses as short as 1 ns for the excitation of short-lived Yb+ states. Pseudo-relativistic Hartree-Fock calculations, taking into account the core-polarization effects, have also been performed. A good agreement of the measured and the calculated lifetime values has been achieved

Atomic Lifetimes and Transition Probabilities in Boron-like (Na VII) and Beryllium-like (Na VIII) Sodium Ions

Spectra and decay curves of boron-like (Na VII) and beryllium-like (Na VIII) sodium ions produced by beam-foil excitation have been recorded in the 30–60 nm spectral range and the radiative lifetimes of seven n=2 levels have been measured. The experimental results are compared with the available theoretical values and with new results obtained in the framework of two theoretical approaches: the Relativistic Hartree-Fock approximation and the Multiconfiguration Dirac-Fock method. Corroborated by the fair agreement of the new theory data with experiment, a new set of accurate transition probabilities for the $2s^22p$-$2s2p^2$ and $2s2p^2$-$2p^3$ transitions of Na VII is presented