Commercially Available Outbred Mice for Genome-Wide Association Studies

Genome-wide association studies using commercially available outbred mice can detect genes involved in phenotypes of biomedical interest. Useful populations need high-frequency alleles to ensure high power to detect quantitative trait loci (QTLs), low linkage disequilibrium between markers to obtain accurate mapping resolution, and an absence of population structure to prevent false positive associations. We surveyed 66 colonies for inbreeding, genetic diversity, and linkage disequilibrium, and we demonstrate that some have haplotype blocks of less than 100 Kb, enabling gene-level mapping resolution. The same alleles contribute to variation in different colonies, so that when mapping progress stalls in one, another can be used in its stead. Colonies are genetically diverse: 45% of the total genetic variation is attributable to differences between colonies. However, quantitative differences in allele frequencies, rather than the existence of private alleles, are responsible for these population differences. The colonies derive from a limited pool of ancestral haplotypes resembling those found in inbred strains: over 95% of sequence variants segregating in outbred populations are found in inbred strains. Consequently it is possible to impute the sequence of any mouse from a dense SNP map combined with inbred strain sequence data, which opens up the possibility of cataloguing and testing all variants for association, a situation that has so far eluded studies in completely outbred populations. We demonstrate the colonies' potential by identifying a deletion in the promoter of H2-Ea as the molecular change that strongly contributes to setting the ratio of CD4+ and CD8+ lymphocytes

The Functions of Myosin II and Myosin V Homologs in Tip Growth and Septation in Aspergillus nidulans

Because of the industrial and medical importance of members of the fungal genus Aspergillus, there is considerable interest in the functions of cytoskeletal components in growth and secretion in these organisms. We have analyzed the genome of Aspergillus nidulans and found that there are two previously unstudied myosin genes, a myosin II homolog, myoB (product = MyoB) and a myosin V homolog, myoE (product = MyoE). Deletions of either cause significant growth defects. MyoB localizes in strings that coalesce into contractile rings at forming septa. It is critical for septation and normal deposition of chitin but not for hyphal extension. MyoE localizes to the Spitzenkörper and to moving puncta in the cytoplasm. Time-lapse imaging of SynA, a v-SNARE, reveals that in myoE deletion strains vesicles no longer localize to the Spitzenkörper. Tip morphology is slightly abnormal and branching occurs more frequently than in controls. Tip extension is slower than in controls, but because hyphal diameter is greater, growth (increase in volume/time) is only slightly reduced. Concentration of vesicles into the Spitzenkörper before incorporation into the plasma membrane is, thus, not required for hyphal growth but facilitates faster tip extension and a more normal hyphal shape

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges

Particle development and characterisation in Pt(acac)(2) and Pt(acac)(2)/GeBu4 derived catalysts supported upon porous and mesoporous SiO2: effect of reductive environment, and support structure

In situ, time resolved energy dispersive EXAFS (EDE) has been used in conjunction with temperature programmed reduction/decomposition (TPR/TPD), transmission electron microscopy (TEM), powder X-ray diffraction (PXRD), and diffuse reflectance infrared spectroscopy (DRIFTS) to probe the evolution and character of Pt and PtGe alloy particles, derived from Pt(acac)(2) and GeBu4 precursors, supported upon amorphous and mesoporous silicas. The reduction kinetics and final particle size distributions obtained are found to be functions of the reductive environment, the support architecture, and the presence of GeBu4. Reduction of the Pt-only systems in H-2 is found to have an autocatalytic character resulting in the rapid formation of large (N1Pt–Pt>8) particles at ca. 390 K. Reduction in the absence of hydrogen and/or in the presence of co-adsorbed GeBu4, results in a considerable retardation of particle growth and shows a dependence upon the support architecture. Both EDE and DRIFTS show that, in the case of PtGe alloy system elemental Pt particles form first (in the region of 400-500 K) and it is only at temperatures in excess of 500 K that significant alloy (Pt3Ge) formation is observed along with a concomitant reduction in average particle size. This same pattern of behaviour is also observed when Pt particles are pre-formed prior to the introduction of GeBu4 and subsequent reduction. These results are discussed in terms of the reductive processes at work in these systems, the support architecture, and the effects of retained carbonaceous materials on developing particles

Simultaneous determination of structural and kinetic parameters characterizing the interconversion of highly dispersed species: the interaction of NO with Rh-I(CO)(2)/gamma-Al2O3

Energy-dispersive EXAFS (EDE), combined with mass spectrometry and a flow microreactor system, has been used to investigate the reaction of an Al2O3-supported Rh-I(CO)(2) species with NO. This combined in situ approach uniquely permits a priori analysis of the structures of the species involved (on a time scale of ca. 2 s) and simultaneous determination of reaction mechanism and kinetic parameters. In the current case, it is found that the Al(O)Rh-I(CO)(2)Cl species reacts to form an intermediate Al(O)Rh(NO)(2)Cl Cl species (v approximate to 0.357 +/- 0.125 s(-1), E-act approximate to 11 +/- 1.25 kJ mol(-1)), which subsequently forms an (AlO)(2)Rh(NO)Cl- species and N2O(g) (v approximate to 2 +/- 0.5 x 10(4) s(-1), E-act approximate to 40 +/- 3.5 kJ mol(-1)) showing a bent (134 degrees) RhNO bond. This combination of rapid and complementary techniques should be applicable to a wide range of disciplines where quantitative structural and kinetic determinations are of importance