No abstract

Alzheimer’s disease (AD) is a chronic neurodegenerative disorder characterized by progressive neuropathology and cognitive decline. We describe a cross-tissue analysis of methylomic variation in AD using samples from three independent human post-mortem brain cohorts. We identify a differentially methylated region in the ankyrin 1 (ANK1) gene that is associated with neuropathology in the entorhinal cortex, a primary site of AD manifestation. This region was confirmed as significantly hypermethylated in two other cortical regions (superior temporal gyrus and prefrontal cortex) but not in the cerebellum, a region largely protected from neurodegeneration in AD, nor whole blood obtained pre-mortem, from the same individuals. Neuropathology-associated ANK1 hypermethylation was subsequently confirmed in cortical samples from three independent brain cohorts. This study represents the first epigenome-wide association study (EWAS) of AD employing a sequential replication design across multiple tissues, and highlights the power of this approach for identifying methylomic variation associated with complex disease.

BackgroundSchizophrenia is a highly heritable, neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. Despite success in identifying genetic variants associated with schizophrenia, there remains uncertainty about the causal genes involved in disease pathogenesis and how their function is regulated.ResultsWe performed a multi-stage epigenome-wide association study, quantifying genome-wide patterns of DNA methylation in a total of 1714 individuals from three independent sample cohorts. We have identified multiple differentially methylated positions and regions consistently associated with schizophrenia across the three cohorts; these effects are independent of important confounders such as smoking. We also show that epigenetic variation at multiple loci across the genome contributes to the polygenic nature of schizophrenia. Finally, we show how DNA methylation quantitative trait loci in combination with Bayesian co-localization analyses can be used to annotate extended genomic regions nominated by studies of schizophrenia, and to identify potential regulatory variation causally involved in disease.ConclusionsThis study represents the first systematic integrated analysis of genetic and epigenetic variation in schizophrenia, introducing a methodological approach that can be used to inform epigenome-wide association study analyses of other complex traits and diseases. We demonstrate the utility of using a polygenic risk score to identify molecular variation associated with etiological variation, and of using DNA methylation quantitative trait loci to refine the functional and regulatory variation associated with schizophrenia risk variants. Finally, we present strong evidence for the co-localization of genetic associations for schizophrenia and differential DNA methylation.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1041-x) contains supplementary material, which is available to authorized users.

Spectrin is a vital component of the cytoskeleton, conferring flexibility on cells and providing a scaffold for a variety of proteins. It is composed of tandem, antiparallel coiled-coil repeats. We report four related crystal structures at 1.45 A, 2.0 A, 3.1 A, and 4.0 A resolution of two connected repeats of chicken brain alpha-spectrin. In all of the structures, the linker region between adjacent units is alpha-helical without breaks, kinks, or obvious boundaries. Two features observed in the structures are (1) conformational rearrangement in one repeat, resulting in movement of the position of a loop, and (2) varying degrees of bending at the linker region. These features form the basis of two different models of flexibility: a conformational rearrangement and a bending model. These models provide novel atomic details of spectrin flexibility.

We recently reported the detection of methanol emissions from leaves (R. MacDonald, R. Fall 119931 Atmos Environ 27A: 1709-171 3). This could represent a substantial flux of methanol to the atmosphere. Leaf methanol production and emission have not been investigated in detail, in part because of difficulties in sampling and analyzing methanol. In this study we used an enzymatic method to convert methanol to a fluorescent product and verified that leaves from severa1 species emit methanol. Methanol was emitted almost exclusively from the abaxial surfaces of hypostomatous leaves but from both surfaces of amphistomatous leaves, suggesting that methano1 exits leaves via stomates. The role of stomatal conductance was verified in experiments in which stomates were induced to close, resulting in reduced methanol. Free methanol was detected in bean leaf extracts, ranging from 26.8 pg g-' fresh weight in young leaves to 10.0 pg g-' fresh weight in older leaves. Methanol emission was related to leaf development, generally declining with increasing leaf age after leaf expansion; this is consistent with volatilization from a cellular pool that declines in older leaves. It is possible that leaf emission could be a major source of methanol found in the atmosphere of forests.

The interaction of DNA with a novel cationic phospholipid transfection reagent, 1,2-dioleoyl-sn-glycero-3-ethylphosphocholine (EDOPC), was investigated by monitoring thermal effects, particle size, vesicle rupture, and lipid mixing. By isothermal titration calorimetry, the heat of interaction between large unilamellar EDOPC vesicles and plasmid DNA was endothermic at both physiological and low ionic strength, although the heat absorbed was slightly larger at the higher ionic strength. The energetic driving force for DNA-EDOPC association is thus an increase in entropy, presumably due to release of counterions and water. The estimated minimum entropy gain per released counterion was 1.4 cal/mole- degrees K (about 0.7 kT), consistent with previous theoretical predictions. All experimental approaches revealed significant differences in the DNA-lipid particle, depending upon whether complexes were formed by the addition of DNA to lipid or vice versa. When EDOPC vesicles were titrated with DNA at physiological ionic strength, particle size increased, vesicles ruptured, and membrane lipids became mixed as the amount of DNA was added up to a 1.6:1 (+:-) charge ratio. This charge ratio also corresponded to the calorimetric end point. In contrast, when lipid was added to DNA, vesicles remained separate and intact until a charge ratio of 1:1 (+:-) was exceeded. Under such conditions, the calorimetric end point was 3:1 (+:-). Thus it is clear that fundamental differences in DNA-cationic lipid complexes exist, depending upon their mode of formation. A model is proposed to explain the major differences between these two situations. Significant effects of ionic strength were observed; these are rationalized in terms of the model. The implications of the analysis are that considerable control can be exerted over the structure of the complex by exploiting vectorial preparation methods and manipulating ionic strength.

Acoustically active liposomes (AAL), previously developed as ultrasound contrast agents, contain small amounts of air. These AAL have potential to carry pharmaceutics and their acoustic activity could enable them to respond to ultrasound stimulation by releasing their contents. Since liposomes can entrap many kinds of drugs, if such entrapment did not affect their echogenicity, then the release of contents could potentially be controlled by ultrasound stimulation. The aim of this research was to investigate the capacity of acoustically active liposomes for hydrophilic molecule encapsulation and to determine their sensitivity to ultrasound-triggered release. Liposomes, composed of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and cholesterol, were made acoustically active by hydrating a lipid film, sonication, freezing in the presence of mannitol, lyophilization, and rehydration. As a test molecule, calcein was added in the hydration step. The procedure for generating acoustically active liposomes was compatible with an encapsulation efficiency of 15% or more. The presence of mannitol during freeze-drying was essential not only for generation of acoustic activity but also for efficient encapsulation. Ultrasound-triggered release was achieved by applying 1 MHz ultrasound at 2 W/cm2 for 10 s. The inclusion of 4% diheptanolyphosphatidylcholine (DHPC) increased the sensitivity of liposomes to ultrasound stimulation and resulted in very efficient stimulated release of contents (1/3 released in 10 s, 2/3 released in six such applications). Release of contents was highly correlated with the loss of air induced either by ultrasound or rapid pressure reduction. These encapsulation and triggered release techniques are highly efficient, and hence may be applicable to drug delivery.

Two cationic phospholipid derivatives with asymmetric hydrocarbon chains were synthesized: ethyl esters of oleoyldecanoylethylphosphatidylcholine (C18:1͞C10-EPC) and stearoyldecanoylethylphosphatidylcholine (C18:0͞C10-EPC). The former was 50 times more effective as a DNA transfection agent (human umbilical artery endothelial cells) than the latter, despite their similar chemical structure and virtually identical lipoplex organization. A likely reason for the superior effectiveness of C18:1͞C10-EPC relative to C18:0͞C10-EPC (and to many other cationic lipoids) was suggested by the phases that evolved when these lipoids were mixed with negatively charged membrane lipid formulations. The saturated C18:0͞C10-EPC remained lamellar in mixtures with biomembranemimicking lipid formulations [e.g., dioleoyl-phosphatidylcholine͞ dioleoyl-phosphatidylethanolamine͞dioleoyl-phosphatidylserine͞ cholesterol at 45:20:20:15 (wt͞wt)]; in contrast, the unsaturated C18:1͞C10-EPC exhibited a lamellar-nonlamellar phase transition in such mixtures, which took place at physiological temperatures, Ϸ37°C. As is well known, lipid vehicles exhibit maximum leakiness and contents release in the vicinity of phase transitions, especially those involving nonlamellar phase formation. Moreover, nonlamellar phase-forming compositions are frequently highly fusogenic. Indeed, FRET experiments showed that C18:1͞C10-EPC exhibits lipid mixing with negatively charged membranes that is several times more extensive than that of C18:0͞C10-EPC. Thus, C18:1͞C10-EPC lipoplexes are likely to easily fuse with membranes, and, as a result of lipid mixing, the resultant aggregates should exhibit extensive phase coexistence and heterogeneity, thereby facilitating DNA release and leading to superior transfection efficiency. These results highlight the phase properties of the carrier lipid͞cellular lipid mixtures as a decisive factor for transfection success and suggest a strategy for the rational design of superior cationic lipid carriers.lipofection ͉ lipoplex ͉ mesophase I mportant therapeutic procedures, such as gene transfection and gene silencing, require efficient delivery of genetic material to cells. Synthetic cationic lipoids, which form complexes (lipoplexes) with polyanionic DNA, are promising gene carriers (1). Understanding the mechanism of lipid-mediated DNA delivery (lipofection) is essential for the successful application and rational design and synthesis of novel cationic lipoid compounds for enhanced gene delivery. Although considerable improvement in the transfection properties of cationic lipoids has come from the synthesis of new kinds of cationic amphiphiles or from the inclusion of noncationic helper lipids, an effective alternative strategy was recently described: The combination of two cationic lipid derivatives having the same headgroup but different hydrocarbon chains can synergistically enhance transfection (2). For example, the optimal combination of the long chain͞medium chain lipoids, dioleoyl-and dilauroyl-ethylphosphatidylcholines, de...