Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans

The identification of quantitative trait loci (QTLs) of small effect size that underlie complex traits poses a particular challenge for geneticists due to the large sample sizes and large numbers of genetic markers required for genomewide association scans. An efficient solution for screening purposes is to combine single nucleotide polymorphism (SNP) microarrays and DNA pooling (SNP-MaP), an approach that has been shown to be valid, reliable and accurate in deriving relative allele frequency estimates from pooled DNA for groups such as cases and controls for 10K SNP microarrays. However, in order to conduct a genomewide association study many more SNP markers are needed. To this end, we assessed the validity and reliability of the SNP-MaP method using Affymetrix GeneChip(®) Mapping 100K Array set. Interpretable results emerged for 95% of the SNPs (nearly 110 000 SNPs). We found that SNP-MaP allele frequency estimates correlated 0.939 with allele frequencies for 97 605 SNPs that were genotyped individually in an independent population; the correlation was 0.971 for 26 SNPs that were genotyped individually for the 1028 individuals used to construct the DNA pools. We conclude that extending the SNP-MaP method to the Affymetrix GeneChip(®) Mapping 100K Array set provides a useful screen of >100 000 SNP markers for QTL association scans

Generation and transcriptional programming of intestinal dendritic cells: essential role of retinoic acid

The vitamin A metabolite retinoic acid (RA) regulates adaptive immunity in the intestines, with well-characterized effects on IgA responses, Treg induction and gut trafficking of T and B effector cells. It also controls the generation of cDC precursors in the bone marrow and regulates cDC subset representation, but its roles in the specialization of intestinal cDC subsets is understudied. Here we show that RA acts cell-intrinsically in developing gut-tropic pre-mucosal DC (pre-μDC) to effect the differentiation and drive the specialization of intestinal CD103+CD11b− (cDC1) and of CD103+CD11b+ (cDC2). Systemic deficiency or DC-restricted antagonism of RA signaling resulted in altered phenotypes of intestinal cDC1 and cDC2, and reduced numbers of cDC2. Effects of dietary deficiency were most apparent in the proximal small intestine, and were rapidly reversed by reintroducing vitamin A. In cultures of pre-μDC with Flt3L and GM-CSF, RA induced cDC with characteristic phenotypes of intestinal cDC1 and cDC2 by controlling subset-defining cell surface receptors, regulating subset-specific transcriptional programs, and suppressing proinflammatory NF-κB-dependent gene expression. Thus RA is required for transcriptional programming and maturation of intestinal cDC, and with GM-CSF and Flt3L provides a minimal environment for in vitro generation of intestinal cDC1- and cDC2-like cDC from specialized precursors

Dibromido(4,7-diazadecane-1,10-di­amine)­copper(II)

In the title compound, [CuBr2(C8H22N4)], the CuII atom is six-coordinate forming a distorted octa­hedral complex and is bonded to two axial bromide anions and four equatorial nitro­gen donors. The equatorial Cu—N bond distances range from 2.005 (8) to 2.046 (8) Å while the axial Cu—Br distances are 2.8616 (17) and 2.9402 (17) Å, thus the six-coordinate Cu complex shows the usual Jahn–Teller distortion. All amine hydrogen atoms participate in either inter- or intra­molecular hydrogen bonding to the Br anions

A second polymorph of (2E)-1-(4-fluoro­phen­yl)-3-(3,4,5-trimethoxy­phen­yl)prop-2-en-1-one

The crystal structure of the title compound, C18H17FO4, reported here is a polymorph of the structure first reported by Patil et al. [Mol. Cryst. Liq. Cryst. Sci. Technol. Sect. A (2007), 461, 123–130]. It is a chalcone analog and consists of substituted phenyl rings bonded at the opposite ends of a propenone group, the biologically active region. The dihedral angle between the mean planes of the aromatic rings within the 4-fluoro­phenyl and trimethoxy­phenyl groups is 28.7 (1)° compared to 20.8 (6)° in the published structure. The angles between the mean plane of the prop-2-ene-1-one group and the mean plane of aromatic rings within the 4-fluoro­phenyl and trimethoxy­phenyl groups are 30.3 (4) and 7.4 (7)°, respectively, in contast to 10.7 (3) and 12.36° for the polymorph. While the two 3-meth­oxy groups are in the plane of the trimeth­oxy-substituted ring, the 4-meth­oxy group is in a synclinical [−sc = −78.1 (2)°] or anti­clinical [+ac = 104.0 (4)°] position, compared to a +sc [53.0 (4)°] or −ac [−132.4 (7)°] position. While no classical hydrogen bonds are present, weak inter­molecular C—H⋯π-ring inter­actions are observed which contribute to the stability of the crystal packing. The two polymorphs crystallize in the same space group, P21/c, but have different cell parameters for the a, b and c axes and the β angle. A comparison of the mol­ecular geometries of both polymorphs to a geometry optimized density functional theory (DFT) calculation at the B3-LYP/6–311+G(d,p) level for each structure provides additional support to these observations

Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies

<p>Abstract</p> <p>Background</p> <p>Genetic influences underpinning complex traits are thought to involve multiple quantitative trait loci (QTLs) of small effect size. Detection of such QTL associations requires systematic screening of large numbers of DNA markers within large sample populations. Using pooled DNA on SNP microarrays to screen for allelic frequency differences between groups such as cases and controls (called SNP Microarray and Pooling, or SNP-MaP) has been validated as an efficient solution on both 10 k and 100 k platforms. We demonstrate that this approach can be effectively applied to the truly genomewide Affymetrix GeneChip^®Mapping 500 K Array.</p> <p>Results</p> <p>In comparisons between five independent DNA pools (<it>N </it>~200 per pool) on separate Affymetrix GeneChip^®Mapping 500 K Array sets, we show that, for SNPs with minor allele frequencies > 0.05, the reliability of the rank order of estimated allele frequencies, assessed as the average correlation between allele frequency estimates across the DNA pools, was 0.948 (average mean difference across the five pools = 0.069). Similarly, validity of the SNP-MaP approach was demonstrated by a rank-order correlation of 0.937 (average mean difference = 0.095) between the average DNA pool allele frequency estimates and the allele frequencies of an independent (CEPH) sample of 60 unrelated individually genotyped subjects.</p> <p>Conclusion</p> <p>We conclude that SNP-MaP can be extended for use on the Affymetrix GeneChip^®Mapping 500 K Array, providing a cost-effective, reliable and valid initial screen of 500 K SNP microarrays in genomewide association scans.</p

A Constructivist Study of Graduate Assistants\u27 Healthcare Experiences in a Research University

This constructivist study explores 16 graduate assistants’ (GAs) healthcare experiences and uses grounded theory to create a model of graduate assistants’ experiences with university-provided healthcare in a large research university. The model is composed of four broad components: (a) systems; (b) access, care and coverage; (c) knowledge, quality and cost; and (d) self. Graduate assistants’ needs and expectations constantly negotiate various systems in the model. Expanding upon the limited research regarding graduate student healthcare, this study provides implications for higher education administrators and policy makers. Based on our study findings we argue that it is not sufficient for university administrations to simply provide paid health insurance “options” without robust support systems on campus. Because students are often stressed out, lack time and energy, and find it hard to navigate the complicated systems of profit-driven health care industry, the lack of direct support in graduate students’ day-to-day healthcare needs can cause tremendous loss on their success and productivity. Hence, universities have tremendous opportunities to better understand and address their graduate students’ real needs so as to add value to institutional success and productivity

Oceanographic conditions associated with white shark (Carcharodon carcharias) habitat use along eastern Australia

Management of species with wide-ranging migrations is a complex issue, made more challenging when the species is both protected and poses a risk to humans. Understanding the oceanic conditions associated with shark habitat use can help develop mitigation strategies or warning systems that meet both conservation and human safety objectives. Using satellite tracks from 77 juvenile and sub-adult white sharks tagged over 10 yr, we modelled individual movement patterns using hidden Markov models and applied generalised additive (mixed) models to explore correlations between movement patterns (presence−absence, habitat selection and behavioural state) and oceanographic and bathymetric variables. White sharks used the whole of the continental shelf, down to depths of 350 m on the continental slope. Sharks were present over a wide range of sea surface temperatures (SSTs; 10−27°C), with the highest probability of occurring at ~20°C. However, the number of average daily tag positions was greatest when SST was between 14 and 18°C, and sharks were more likely to exhibit area-restricted movement when SST was between ~19 and 23°C. Sharks were more likely to be present and selected habitats in productive areas with moderate to high surface chl a concentrations as well as thermal and productivity fronts. Although mesoscale eddies did not influence the likelihood of individuals being present in an area, there was a higher density of sharks in cold-core eddies compared to warm-core eddies. This study indicates that white shark presence and dispersal may be linked, perhaps via prey distribution, to oceanic conditions, potentially assisting development of suitable shark bite mitigation strategies