Deletion 17q12 is a recurrent copy number variant that confers high risk of autism and schizophrenia

Autism spectrum disorders (ASD) and schizophrenia are neurodevelopmental disorders for which recent evidence indicates an important etiologic role for rare copy number variants (CNVs) and suggests common genetic mechanisms. We performed cytogenomic array analysis in a discovery sample of patients with neurodevelopmental disorders referred for clinical testing. We detected a recurrent 1.4 Mb deletion at 17q12, which harbors HNF1B, the gene responsible for renal cysts and diabetes syndrome (RCAD), in 18/15,749 patients, including several with ASD, but 0/4,519 controls. We identified additional shared phenotypic features among nine patients available for clinical assessment, including macrocephaly, characteristic facial features, renal anomalies, and neurocognitive impairments. In a large follow-up sample, the same deletion was identified in 2/1,182 ASD/neurocognitive impairment and in 4/6,340 schizophrenia patients, but in 0/47,929 controls (corrected p = 7.37 × 10⁻⁵). These data demonstrate that deletion 17q12 is a recurrent, pathogenic CNV that confers a very high risk for ASD and schizophrenia and show that one or more of the 15 genes in the deleted interval is dosage sensitive and essential for normal brain development and function. In addition, the phenotypic features of patients with this CNV are consistent with a contiguous gene syndrome that extends beyond RCAD, which is caused by HNF1B mutations only.     

Evidence for Three Novel QTLs for Adiposity on Chromosome 2 With Epistatic Interactions: The NHLBI Family Heart Study

We sought to identify quantitative trait loci (QTLs) by genome‐wide linkage analysis for BMI and waist circumference (WC) exploring various strategies to address heterogeneity including covariate adjustments and complex models based on epistatic components of variance. Because cholesterol‐lowering drugs and diabetes medications may affect adiposity and risk of coronary heart disease, we excluded subjects medicated for hypercholesterolemia and hyperglycemia. The evidence of linkage increased on 2p25 (BMI: lod = 1.59 vs. 2.43, WC: lod = 1.32 vs. 2.26). Because environmental and/or genetic components could mask the effect of a specific locus, we investigated further whether a QTL could influence adiposity independently of lipid pathway and dietary habits. Strong evidence of linkage on 2p25 (BMI: lod = 4.31; WC: lod = 4.23) was found using Willet's dietary factors and lipid profile together with age and sex in adjustment. It suggests that lipid profile and dietary habits are confounding factors for detecting a 2p25 QTL for adiposity. Because evidence of linkage has been previously detected for BMI on 7q34 and 13q14 in National Heart, Lung, and Blood Institute Family Heart Study (NHLBI FHS), and for diabetes on 15q13, we investigated epistasis between chromosome 2 and these loci. Significant epistatic interactions were found between QTLs 2p25 and 7q34, 2q37 and 7q34, 2q31 and 13q14, and 2q31–q36 and 15q13. These results suggest multiple pathways and factors involving genetic and environmental effects influencing adiposity. By taking some of these known factors into account, we clarified our linkage evidence of a QTL on 2p25 influencing BMI and WC. The 2p25, 2q24–q31, and 2q36–q37 showed evidence of epistatic interaction with 7q34, 13q14, and 15q13.     

Blockade of the galactose-binding sites of ricin by its linkage to antibody. Specific cytotoxic effects of the conjugates

A method is described for preparing specific cytotoxic agents by linking intact ricin to antibodies in a manner that produces obstruction of the galactose-binding sites on the B chain of the toxin and so diminishes the capacity of the conjugate to bind non-specifically to cells. The conjugates were synthesised by reacting iodoacetylated ricin with thiolated immunoglobulin and the components of conjugate with reduced galactose-binding capacity were separated by affinity chromatography on Sepharose (a beta-galactosyl matrix) and asialofetuin-Sepharose. Fluorescence-activated cell sorter (FACS) analyses revealed that the fraction of a monoclonal anti-Thy1.1-ricin conjugate that passed through a Sepharose column had markedly diminished capacity to bind non-specifically to Thy1.2-expressing CBA thymocytes and EL4 lymphoma cells. The fraction of conjugate that passed through an asialofetuin-Sepharose column displayed no detectable non-specific binding. Both fractions of conjugate were potent cytotoxic agents for Thy1.1-expressing AKR-A lymphoma cells in tissue culture. They reduced the [3H]leucine incorporation of the cells by 50% at a concentration of 2-5 pM. Comparable inhibition of EL4 cells was only achieved with 3000-7500-fold greater concentrations of conjugate. By contrast, the fraction of anti-Thy1.1-ricin that retained Sepharose-binding capacity showed marked non-specific binding and toxicity to EL4 cells. A conjugate with diminished galactose-binding capacity was also prepared from the W3/25 monoclonal antibody which recognises an antigen upon helper T-lymphocytes in the rat. It elicited powerful and specific toxic effects upon W3/25 antigen-expressing rat T-leukaemia cells. This finding is of particular importance because isolated ricin A-chain disulphide-linked to W3/25 antibody is not cytotoxic. The property of the B-chain in intact ricin conjugates that facilitates delivery of the A-chain to the cytosol thus appears to be independent of galactose recognition. It is concluded that the 'blocked' ricin conjugates combine the advantages of high potency, which is often lacking in antibody-A-chain conjugates, with high specificity, which previously was lacking in intact ricin conjugates.     

Evaluation of Parkinson Disease Risk Variants as Expression-QTLs

The recent Parkinson Disease GWAS Consortium meta-analysis and replication study reports association at several previously confirmed risk loci SNCA, MAPT, GAK/DGKQ, and HLA and identified a novel risk locus at RIT2. To further explore functional consequences of these associations, we investigated modification of gene expression in prefrontal cortex brain samples of pathologically confirmed PD cases (N = 26) and controls (N = 24) by 67 associated SNPs in these 5 loci. Association between the eSNPs and expression was evaluated using a 2-degrees of freedom test of both association and difference in association between cases and controls, adjusted for relevant covariates. SNPs at each of the 5 loci were tested for cis-acting effects on all probes within 250 kb of each locus. Trans-effects of the SNPs on the 39,122 probes passing all QC on the microarray were also examined. From the analysis of cis-acting SNP effects, several SNPs in the MAPT region show significant association to multiple nearby probes, including two strongly correlated probes targeting the gene LOC644246 and the duplicated genes LRRC37A and LRRC37A2, and a third uncorrelated probe targeting the gene DCAKD. Significant cis-associations were also observed between SNPs and two probes targeting genes in the HLA region on chromosome 6. Expanding the association study to examine trans effects revealed an additional 23 SNP-probe associations reaching statistical significance (p<2.8×10⁻⁸) including SNPs from the SNCA, MAPT and RIT2 regions. These findings provide additional context for the interpretation of PD associated SNPs identified in recent GWAS as well as potential insight into the mechanisms underlying the observed SNP associations.     

The Nicotinic Receptor Alpha7 Impacts the Mouse Lung Response to LPS through Multiple Mechanisms

The nicotinic acetylcholine receptor alpha7 (α7) is expressed by neuronal and non-neuronal cells throughout the body. We examined the mechanisms of the lung inflammatory response to intranasal (i.n.) lipopolysaccharide (LPS) regulated by α7. This was done in mice using homologous recombination to introduce a point mutation in the α7 receptor that replaces the glutamate residue 260 that lines the pore with alanine (α7^E260A), which has been implicated in controlling the exceptional calcium ion conductance of this receptor. The α7^E260A mice exhibit normal inflammatory cell recruitment to the blood in response to i.n. LPS administration. This differs from the α7knock-out (α7^KO) in which upstream signaling to initiate the recruitment to the blood following i.n. LPS is significantly impaired. While hematopoietic cells are recruited to the bloodstream in the α7^E260A mouse, they fail to be recruited efficiently into both the interstitium and alveolar spaces of the lung. Bone marrow reconstitution experiments demonstrate that the responsiveness of both CD45⁺ and CD45^- cells of the α7^E260A mouse are impaired. The expression of several pro-inflammatory cytokine and chemokine RNAs including TNFα, IL-1α, Ccl2 and Cxcl10 are decreased in the α7^E260A mouse. However, there is a substantial increase in IL-13 expression by CD45^- lung interstitial cells in the α7^E260A mouse. Our results support the conclusion that α7 functional pleiotropy contributes to modulating the tissue response to an inflammatory insult through impacting upon a variety of mechanisms reflecting the individual cell composition of the lung.     

χ Recombination Activity in Phage λ Decays as a Function of Genetic Distance

In Escherichia coli, χ is a recombination hotspot that stimulates RecBCD-dependent exchange at and to one side of itself. χ activity is highest at χ and decreases with distance from χ. The decrease in χ activity may be a simple property of the physical distance over which χ can stimulate recombination. Alternatively, the decay in χ activity with distance may reflect the high likelihood that χ-stimulated recombination occurs in a single χ-proximal act, to the exclusion of additional χ-stimulated exchanges more distal to χ. To test the models, we determined if χ activity decreases as a function of physical distance (i.e., DNA base pairs) or genetic distance (homologous DNA base pairs). Our results indicate that χ activity decays as a function of genetic distance. In addition, we found that the sbcB gene product (exonuclease I, a 3' -> 5' ssDNA exonuclease) modulates the distance over which χ can act. In contrast, the recJ gene product (a 5' -> 3' ssDNA exonuclease) does not alter the decay of χ activity.     

Morphology of the granular secretory glands in skin of poison-dart frogs (Dendrobatidae)

The granular glands of nine species of dendrobatid frogs were examined using light and electron microscopy. The glands are surrounded by a discontinuous layer of smooth muscle cells. Within the glands proper the secretory cells form a true syncytium. Multiple flattened nuclei lie at the periphery of the gland. The peripheral cytoplasm also contains mitochondria, rough surfaced endoplasmic reticulum, the Golgi apparatus, and an abundance of smooth endoplasmic reticulum. Centrally, most of the gland is filled with membrane-bound granules surrounded by amorphous cytoplasm. Few other organelles are found in this region. Early in the secretory cycle, the central part of the gland is filled with flocculent material which appears to be progressively partitioned off by membranes to form the droplet anlage. As granules form, the structure of the contents becomes progressively more vesicular. Dense vesicles, which bud off from the Golgi apparatus, fuse with the granular membrane during the development of granules, and might contain enzymes involved in toxin synthesis. The granules at this point resemble multivesicular bodies. Their structure is similar in all species of dendrobatid frogs even though the different frogs secrete substances of different chemical structure and toxicity.     

Flow field-flow fractionation as a methodology for protein separation and characterization

Flow field-flow fractionation is introduced as a new tool applicable to protein studies. Specific advantages of this method are discussed, including the capability for measuring diffusivities and Stokes radii directly, even for trace components. The theoretical equations of flow FFF are summarized and expanded to include an explicit dependence on the Stokes radius. Several native proteins are retained. The retention is shown to be systematically controllable by changes in cross flow and the results are in quantitative agreement with theory. Fractograms of different rat plasmas are then shown to produce coincident peaks, while human plasma exhibits several systematic peak shifts with respect to the fractogram of the rat plasma. Finally, changes in the Stokes radii of ferritin peaks are shown after various forms of treatment with SDS. Flow FFF in this study demonstrates a capability of working with a mass range of ∼ 10⁵ in a single run.     

A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase

We have combined equilibrium and steered molecular dynamics (SMD) simulations with principal component and correlation analyses to probe the mechanism of allosteric regulation in imidazole glycerol phosphate (IGP) synthase. An evolutionary analysis of IGP synthase revealed a conserved network of interactions leading from the effector binding site to the glutaminase active site, forming conserved communication pathways between the remote active sites. SMD simulations of the undocking of the ribonucleotide effector N1-[(5'-phosphoribulosyl)-formino]-5'-aminoimidazole carboxamide ribonucleotide (PRFAR) resulted in a large scale hinge-opening motion at the interface. Principal component analysis and a correlation analysis of the equilibration protein motion indicate that the dynamics involved in the allosteric transition are mediated by coupled motion between sites that are more than 25 A apart. Furthermore, conserved residues at the substrate-binding site, within the barrel, and at the interface were found to exhibit highly correlated motion during the allosteric transition. The coupled motion between PRFAR unbinding and the directed opening of the interface is interpreted in combination with kinetic assays for the wild-type and mutant systems to develop a model of allosteric regulation in IGP synthase that is monitored and investigated with atomic resolution.