Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations

Phospho- and sphingolipids are crucial cellular and intracellular compounds. These lipids are required for active transport, a number of enzymatic processes, membrane formation, and cell signalling. Disruption of their metabolism leads to several diseases, with diverse neurological, psychiatric, and metabolic consequences. A large number of phospholipid and sphingolipid species can be detected and measured in human plasma. We conducted a meta-analysis of five European family-based genome-wide association studies (N = 4034) on plasma levels of 24 sphingomyelins (SPM), 9 ceramides (CER), 57 phosphatidylcholines (PC), 20 lysophosphatidylcholines (LPC), 27 phosphatidylethanolamines (PE), and 16 PE-based plasmalogens (PLPE), as well as their proportions in each major class. This effort yielded 25 genome-wide significant loci for phospholipids (smallest P-value = 9.88×10⁻²⁰⁴) and 10 loci for sphingolipids (smallest P-value = 3.10×10⁻⁵⁷). After a correction for multiple comparisons (P-value<2.2×10⁻⁹), we observed four novel loci significantly associated with phospholipids (PAQR9, AGPAT1, PKD2L1, PDXDC1) and two with sphingolipids (PLD2 and APOE) explaining up to 3.1% of the variance. Further analysis of the top findings with respect to within class molar proportions uncovered three additional loci for phospholipids (PNLIPRP2, PCDH20, and ABDH3) suggesting their involvement in either fatty acid elongation/saturation processes or fatty acid specific turnover mechanisms. Among those, 14 loci (KCNH7, AGPAT1, PNLIPRP2, SYT9, FADS1-2-3, DLG2, APOA1, ELOVL2, CDK17, LIPC, PDXDC1, PLD2, LASS4, and APOE) mapped into the glycerophospholipid and 12 loci (ILKAP, ITGA9, AGPAT1, FADS1-2-3, APOA1, PCDH20, LIPC, PDXDC1, SGPP1, APOE, LASS4, and PLD2) to the sphingolipid pathways. In large meta-analyses, associations between FADS1-2-3 and carotid intima media thickness, AGPAT1 and type 2 diabetes, and APOA1 and coronary artery disease were observed. In conclusion, our study identified nine novel phospho- and sphingolipid loci, substantially increasing our knowledge of the genetic basis for these traits.     

Conserved movement of TMS11 between occluded conformations of LacY and XylE of the major facilitator superfamily suggests a similar hinge‐like mechanism

The Δ‐distance maps can detect local remodeling that is difficult to accurately determine using superimpositions. Transmembrane segments (TMSs) 11 in both LacY and XylE of the major facilitator superfamily uniquely contribute the greatest amount of mobile surface area in the outward‐occluded state and undergo analogous movements. The intracellular part of TMS11 moves away from the C‐terminal domain and into the substrate cavity during the conformational change from the outward‐occluded to the inward‐occluded state. A difference was noted between LacY and XylE when they assumed the inward open state after releasing a substrate to the inside in which TMS11 of LacY moved further into the substrate release space, whereas in XylE, TMS11 slightly retracted into the C‐terminal domain. Independent movement of the N‐terminal half of TMS11 suggests that it is flexible in the middle. Repeat‐swapped homology modeling was used to discover that a loop connecting TMSs 10 and 11 in LacY probably moves during the transition between the unavailable outward‐open state and the outward‐occluded state. TMSs 11 and the other elements displaying a notable domain‐independent movement colocalize with the interdomain linker, suggesting that these elements could drive the alternating access movement between the domain halves. Preliminary evidence indicates that analogous movements occur in other members of the major facilitator superfamily. Proteins 2015; 83:735–745. © 2015 Wiley Periodicals, Inc.     

Effects of aging and reproduction on protein quality control in soma and gametes of Drosophila melanogaster

In organisms with a soma-germ demarcation, the germline must be 'preserved' such that harmful damage is not transmitted to the offspring. Keeping the progeny free of damage may be achieved by gametes enjoying elevated, and/or more functional, homeostatic maintenance systems. This possibility was approached here by testing whether the soma and maturating oocytes (eggs) dissected from female Drosophila melanogaster in reproductive ages display differential capacities for protein quality control and whether these capacities change during aging and mating. Eggs exhibited a high capacity to prevent protein aggregation, strong capacity for 26S proteasome-dependent degradation and reduced levels of oxidatively damaged (carbonylated) proteins compared to the soma. The capacity to prevent protein aggregation was not affected in either soma or eggs by age and/or mating, while the 26S proteasome capacity declined in the soma but was maintained in the eggs of aged females. However, the levels of carbonylated proteins increased with age in both soma and eggs, and this increase was more pronounced in females allowed to mate continuously. Furthermore, the levels of carbonylated proteins in the eggs of mated flies correlated negatively with the propensity of the eggs to develop into an adult fly. In young flies, mating caused a decrease in 26S proteasome capacity and an increase in protein carbonylation in the soma, but not in the eggs. These results are in line with trade-off theories of aging where aging is considered a consequence of investment in reproduction over somatic maintenance.     

Solvent Effects in the Spin Trapping Of Lipid Oxyl Radicals

Studies documenting spin trapping of lipid radicals in defined model systems have shown some surprising solvent effects with the spin trap DMPO. In aqueous reactions comparing the reduction of H₂O₂ and methyl linoleate hydroperoxide (MLOOH) by Fe^z+, hydroxyl (HO·) and lipid alkoxyl (LO·) radicals produce identical four-line spectra with line intensities 1:2:2:1. Both types of radicals react with commonly-used HO· scavengers, e.g. with ethanol to produce ·C(CH₃)HOH and with dirnethylsulfoxide (DMSO)togive ·CH₃. However, DMSO radicals (either ·CH₃or ·OOCH₃) react further with lipids, and when radicals are trapped in these MLOOH systems, multiple adducts are evident. When acetonitrile is added to the aqueous reaction systems in increasing concentrations, ·CH₂CN radicals resulting from HO· attack on acetonitrile are evident, even with trace quantities of that solvent. In contrast, little, if any, reaction of LO· with acetonitrile occurs, even in 100% acetonitrile. A single four-line signal persists in the lipid systems as long as any water is present, although the relative intensity of the two center lines decreases as solvent-induced changes gradually dissociate the nitrogen and β-hydrogen splitting constants. Extraction of the aqueous-phase adducts into ethyl acetate shows clearly that the identical four-line spectra in the H₂0₂ and MLOOH systems arise from different radical species in this study, but the lack of stability of the adducts to phase transfer may limit the use of this technique for routine adduct identification in more complex systems. These results indicate that the four-line 1:2:2:1. a_N = a_H = 14.9G spectrum from DMPO cannot automatically be assigned to the HO· adduct in reaction systems where lipid is present, even when the expected spin adducts from ethanol or DMSO appear confirmatory for HO-. Conclusive distinction between HO· and LO· ultimately will require use of ¹³C-labelled DMPO or HPLC-MS separation and specific identification of adducts when DMPO is used as the spin trap.     

High molecular and phenotypic diversity in the Merodon avidus complex (Diptera,Syrphidae): cryptic speciation in a diverse insect taxon

This paper examines molecular and phenotypic variability in the widely spread European hoverfly species complex Merodon avidus. Herein, based on the mitochondrial DNA (mtDNA) sequences of the cytochrome c oxidase subunit I (COI) and morphometric wing parameters, M. avidus is shown to comprise a complex of cryptic species, and one variety is redefined as a valid species: M. bicolor Gil Collado, 1930 (as var. of spinipes). The species M. bicolor, M. avidus A, and M. avidus B were clearly delimited based on their wing size. A total of 29 M. avidus and M. bicolor individuals presented 20 mtDNA haplotypes, four of which were shared by M. avidus A and M. avidus B, three were confined to M. bicolor, seven to M. avidus A, and six to M. avidus B. Sequence divergences between lineages occurring in the Balkan and in Spain ranged from 4.93 to 6.0 (uncorrected p in %) whereas divergences between M. avidus A and M. avidus B were 0.26 to 1.56. Divergence among morphologically identified individuals of M. avidus A and M. avidus B species ranged from 0.13 to 1.58, and from 0.13 to 0.52, respectively. The phenotypic substructuring and observed genetic uniqueness of populations in spatially and temporally fragmented M. avidus taxa were used to identify genetic units. The early split of two allopatric lineages, Spanish M. bicolor and Balkan M. avidus, was followed by diversification in each lineage. Present‐day morphological uniformity masks much of the genetic complexity of lineages within the M. avidus complex. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 819–833.     

Relationships Between Tree and Soil Properties in Picea abies and Pinus sylvestris Forests in Sweden

The exchange of elements between plants and the soil in which they are growing creates reciprocal control of their element composition. Within plants, the growth rate hypothesis from ecological stoichiometry implies a strong coupling between C, N, and P. No similar theory exists for predicting relationships between elements in the soil or relationships between plants and the soil. We used a data set of element concentrations in needles and humus of Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) forests in Sweden to investigate the extent to which relationships between elements (C, N, P, S, K, Ca, Mg, Fe, Mn, Al) can be observed within and between plants and soils. We found element composition to be more strongly controlled in needles than in humus. Elements that are covalently bound were also more strongly controlled, with no apparent differences between macro- and micronutrients. With the exception of N/C, there were surprisingly few relationships between elements in needles and humus. We found no major differences between the two tree species studied, but investigations of additional forest types are needed for firm conclusions. More control over element composition was exercised with respect to N than C, particularly in needles, so it might be advantageous to express nutrient concentrations relative to N rather than on a dry weight or carbon basis. Variations in many ecosystem variables appeared to lack ecological significance and thus an important task is to identify the meaningful predictors.     

Yield‐biodiversity trade‐off in patchy fields of Miscanthus × giganteus

Increasing crop productivity to meet rising demands for food and energy, but doing so in an environmentally sustainable manner, is one of the greatest challenges for agriculture to date. In Ireland, Miscanthus × giganteus has the potential to become a major feedstock for bioenergy production, but the economic feasibility of its cultivation depends on high yields. Miscanthus fields can have a large number of gaps in crop cover, adversely impacting yield and hence economic viability. Predominantly positive effects of Miscanthus on biodiversity reported from previous research might be attributable to high crop patchiness, particularly during the establishment phase. The aim of this research was to assess crop patchiness on a field scale and to analyse the relationship between Miscanthus yield and species richness and abundance of selected taxa of farmland wildlife. For 14 Miscanthus fields at the end of their establishment phase (4–5 years after planting), which had been planted either on improved grassland (MG) or tilled arable land (MT), we determined patchiness of the crop cover, percentage light penetration (LP) to the lower canopy, Miscanthus shoot density and height, vascular plants and epigeic arthropods. Plant species richness and noncrop vegetation cover in Miscanthus fields increased with increasing patchiness, due to higher levels of LP to the lower canopy. The species richness of ground beetles and the activity density of spiders followed the increase in vegetation cover. Plant species richness and activity density of spiders on both MT and MG fields, as well as vegetation cover and activity density of ground beetles on MG fields, were negatively associated with Miscanthus yield. In conclusion, positive effects of Miscanthus on biodiversity can diminish with increasing productivity. This matter needs to be considered when assessing the relative ecological impacts of developing biomass crops in comparison with other land use.     

Latitudinal variation in resistance and tolerance to herbivory in the perennial herb Lythrum salicaria is related to intensity of herbivory and plant phenology

Both the length of the growing season and the intensity of herbivory often vary along climatic gradients, which may result in divergent selection on plant phenology, and on resistance and tolerance to herbivory. In Sweden, the length of the growing season and the number of insect herbivore species feeding on the perennial herb Lythrum salicaria decrease from south to north. Previous common‐garden experiments have shown that northern L. salicaria populations develop aboveground shoots earlier in the summer and finish growth before southern populations do. We tested the hypotheses that resistance and tolerance to damage vary with latitude in L. salicaria and are positively related to the intensity of herbivory in natural populations. We quantified resistance and tolerance of populations sampled along a latitudinal gradient by scoring damage from natural herbivores and fitness in a common‐garden experiment in the field and by documenting oviposition and feeding preference by specialist leaf beetles in a glasshouse experiment. Plant resistance decreased with latitude of origin, whereas plant tolerance increased. Oviposition and feeding preference in the glasshouse and leaf damage in the common‐garden experiment were negatively related to damage in the source populations. The latitudinal variation in resistance was thus consistent with reduced selection from herbivores towards the northern range margin of L. salicaria. Variation in tolerance may be related to differences in the timing of damage in relation to the seasonal pattern of plant growth, as northern genotypes have developed further than southern have when herbivores emerge in early summer.     

The NOD2-RICK complex signals from the plasma membrane

NOD2 plays an important role in the innate immunity of the intestinal tract. By sensing the muramyl dipeptide (MDP), a bacterial wall component, NOD2 triggers the NF-kappaB signaling pathway and promotes the release of proinflammatory cytokines such as interleukin-8. Mutations in Nod2 (1007FS, R702W, G908R) impinge on NOD2 functions and are associated with the pathogenesis of Crohn disease, a chronic inflammatory bowel disease. Although NOD2 is usually described as a cytosolic receptor for MDP, the protein is also localized at the plasma membrane, and the 1007FS mutation delocalizes NOD2 to the cytoplasm (Barnich, N., Aguirre, J. E., Reinecker, H. C., Xavier, R., and Podolsky, D. K. (2005) J. Cell Biol. 170, 21-26; McDonald, C., Chen, F. F., Ollendorff, V., Ogura, Y., Marchetto, S., Lecine, P., Borg, J. P., and Nunez, G. (2005) J. Biol. Chem. 280, 40301-40309). In this study, we demonstrate that membrane-bound versions of NOD2 and Crohn disease-associated mutants R702W and G908R are capable of responding to MDP and activating the NF-kappaB pathway from this location. In contrast, the 1007FS mutant remains unable to respond to MDP from the plasma membrane. We also show that NOD2 promotes the membrane recruitment of RICK, a serine-threonine kinase involved in NF-kappaB activation downstream of NOD2. Furthermore, the artificial attachment of RICK at the plasma membrane provokes a constitutive and strong activation of the NF-kappaB pathway and secretion of interleukin-8 showing that optimal RICK activity depends upon its subcellular localization. Finally, we show that endogenous RICK localizes at the plasma membrane in the THP1 cell line. Thus, our data suggest that NOD2 is responsible for the membrane recruitment of RICK to induce a regulated NF-kappaB signaling and production of proinflammatory cytokines.