Exploring gene-environment interactions in Parkinson’s disease

The objective of this study was to explore combined effects of four candidate susceptibility genes and two exposures on Parkinson’s disease (PD) risk; namely, α-synuclein (SNCA) promoter polymorphism REP1, microtubule-associated protein tau (MAPT) H1/H2 haplotypes, apolipoprotein E (APOE) ε2/ε3/ε4 polymorphism, ubiquitin carboxy-terminal esterase L1 (UCHL1) S18Y variant, cigarette smoking and caffeinated coffee consumption. 932 PD patients and 664 control subjects from the NeuroGenetics Research Consortium, with complete data on all six factors, were studied. Uniform protocols were used for diagnosis, recruitment, data collection and genotyping. A logistic regression model which included gene-exposure interactions was applied. Likelihood ratio tests (LRTs) were used for significance testing and Bayesian inference was used to estimate odds ratios (ORs). MAPT (P = 0.007), SNCA REP1 (P = 0.012), smoking (P = 0.001), and coffee (P = 0.011) were associated with PD risk. Two novel interactions were detected: APOE with coffee (P = 0.005), and REP1 with smoking (P = 0.021). While the individual main effects were modest, each yielding OR < 1.6, the effects were cumulative, with some combinations reaching OR = 12.6 (95% CI: 5.9–26.8). This study provides evidence for the long-held notion that PD risk is modulated by cumulative and interactive effects of genes and exposures. Furthermore, the study demonstrates that while interaction studies are useful for exploring risk relationships that might otherwise go undetected, results should be interpreted with caution because of the inherent loss of power due to multiple testing. The novel findings of this study that warrant replication are the evidence for interaction of coffee with APOE, and of smoking with REP1 on PD risk. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Development time and survival of Verrallina funerea (Theobald) (Diptera: Culicidae) immatures and other brackish water mosquito species in southeast Queensland, Australia

Abstract  Verrallina funerea (Theobald) is a brackish water mosquito that is recognised as an important pest and vector in southeast Queensland, Australia. Immature development time and survival of Ve. funerea was defined in the laboratory in response to a range of temperatures (17–34°C) and salinities (0–35 parts per thousand (p.p.t)). The expression of autogeny in this species was also assessed. Salinity only had a slight effect on mean development time from hatching to adult emergence (7.0–7.4 d at salinities of 0, 17.5 and 31.5 p.p.t) and survival was uniformly high (97.5–99.0%). Mean development times were shorter at 26, 29 and 32°C (7.0, 6.8 and 6.8 d, respectively) and longest at 17°C (12.2 d). The threshold temperature ( t ) was 5.8°C and the thermal constant ( K ) was 142.9 degree-days above t . Survival to adulthood decreased from >95% (at 17–29°C) to 78% (at 32°C) and 0% (at 34°C). No expression of autogeny was observed. Immature development times of Ve. funerea , Ochlerotatus vigilax (Skuse) and Oc. procax (Skuse) were then determined under field conditions at Maroochy Shire. Following tide and rain inundation, cohorts of newly hatched larvae were monitored daily by dipping, and time until pupation was noted. Tidal inundation triggered hatching of Ve. funerea and Oc. vigilax larvae whereas Oc. procax larvae were found only after rain inundation. Estimates of Ve. funerea and Oc. vigilax field development times were similar (8–9 d) while Oc. procax development time was slightly longer (9–10 d). Based on these survey results, control activities targeting Ve. funerea must be initiated 4 d (if using Bacillus thuringiensis var. israelensis de Barjac) or 5 d (if using s -methoprene) after inundation. However, Casuarina glauca Sieber canopy and branchlets covering breeding habitats may present a problem for the penetration of such treatments.     

Nitrogen dynamics in the hyporheic zone of a forested stream during a small storm, Hokkaido, Japan

Water and dissolved nitrogen flows through the hyporheic zone of a 3rd-order mountain stream in Hokkaido, northern Japan were measured during a small storm in August 1997. A network of wells was established to measure water table elevations and to collect water samples to analyze dissolved nitrogen concentrations. Hydraulic conductivity and the depth to bedrock were surveyed. We parameterized the groundwater flow model, MODFLOW, to quantify subsurface flows of both stream water and soil water through the hyporheic zone. MODFLOW simulations suggest that soil water inflow from the adjacent hill slope increased by 1.7-fold during a small storm. Dissolved organic nitrogen (DON) and ammonium (NH ₄ ⁺ ) in soil water from the hill slope were the dominant nitrogen inputs to the riparian zone. DON was consumed via mineralization to NH ₄ ⁺ in the hyporheic zone. NH ₄ ⁺ was the dominant nitrogen species in the subsurface, and showed a net release during both base and storm flow. Nitrate appeared to be lost to denitrification or immobilized by microorganisms and/or vegetation in the riparian zone. Our results indicated that the riparian and hyporheic system was a net source of NH ₄ ⁺ to the stream.     

Increased sensitivity of the ryanodine receptor to halothane-induced oligomerization in malignant hyperthermia-susceptible human skeletal muscle.

Mutations in the skeletal muscle RyR1 isoform of the ryanodine receptor (RyR) Ca2+-release channel confer susceptibility to malignant hyperthermia, which may be triggered by inhalational anesthetics such as halothane. Using immunoblotting, we show here that the ryanodine receptor, calmodulin, junctin, calsequestrin, sarcalumenin, calreticulin, annexin-VI, sarco(endo)plasmic reticulum Ca2+-ATPase, and the dihydropyridine receptor exhibit no major changes in their expression level between normal human skeletal muscle and biopsies from individuals susceptible to malignant hyperthermia. In contrast, protein gel-shift studies with halothane-treated sarcoplasmic reticulum vesicles from normal and susceptible specimens showed a clear difference. Although the alpha2-dihydropyridine receptor and calsequestrin were not affected, clustering of the Ca2+-ATPase was induced at comparable halothane concentrations. In the concentration range of 0.014-0.35 mM halothane, anesthetic-induced oligomerization of the RyR1 complex was observed at a lower threshold concentration in the sarcoplasmic reticulum from patients with malignant hyperthermia. Thus the previously described decreased Ca2+-loading ability of the sarcoplasmic reticulum from susceptible muscle fibers is probably not due to a modified expression of Ca2+-handling elements, but more likely a feature of altered quaternary receptor structure or modified functional dynamics within the Ca2+-regulatory apparatus. Possibly increased RyR1 complex formation, in conjunction with decreased Ca2+ uptake, is of central importance to the development of a metabolic crisis in malignant hyperthermia.     

Crustacean Species Richness in Temporary Pools: Relationships with Habitat Traits

We examined species richness separately for cladocerans and ostracods in 52 temporary pools in a small geographical area, relating species richness with habitat traits using multiple regressions. Habitat traits considered included surface area, water depth, permanence and sediment depth. Permanence was an important predictor of species richness of both cladocerans and ostracods. Additionally, variation in ostracod species richness was significantly explained by water depth (negative relationship) and sediment depth (positive relationship). Surface area was not a statistically significant factor in any of our analyses. The importance of permanence supports the hypothesis that extinction due to pool drying is a major driving force behind the structuring of microcrustacean communities in temporary pools.     

The relative availabilities of complementary resources affect the feeding preferences of ant colonies

Theory predicts that consumers selecting among complementaryresources will show stronger preferences for items that becomerelatively less available. I tested this hypothesis in a fieldstudy that compared the preferences of ant colonies given simultaneousaccess to experimental foods differing in carbohydrate and proteincontent. In the first part of the study, I examined the effectof nutrient supplementation on colony-level preference in theant Dorymyrmex smithi. Colonies that had received a proteinsolution for 24 h consumed proportionally more carbohydratesthan control colonies that had been given access to water, suggestingthat colonies preferred nutrients when they became relativelyrare. In the second part of the study, I compared colony-levelpreference among eight species of ants that differ in theirrelative access to carbohydrates and protein in the field. Ifound that species with relatively easy access to carbohydratespreferred protein, whereas species with greater access to proteinpreferred carbohydrates. These results suggest that the benefitsof a nutritionally mixed diet coupled with differences in therelative availability of nutrients may explain variation infeeding decisions both within and among ant species.     

Inactivation of mitochondrial respiratory chain complex I leads mitochondrial nitric oxide synthase to become pro-oxidative

We recently demonstrated that mitochondrial nitric oxide synthase (mtNOS) functionally couples with mitochondrial respiratory chain complex I to produce nitric oxide [M.S. Parihar, R.R. Nazarewicz, E. Kincaid, U. Bringold, P. Ghafourifar, Association of mitochondrial nitric oxide synthase activity with respiratory chain complex I, Biochem. Biophys. Res. Commun. 366 (2008) 23-28] [1]. The present report shows that inactivation of complex I leads mtNOS to become pro-oxidative. Our findings suggest a crucial role for mtNOS in oxidative stress caused by mitochondrial complex I inactivation.     

TROSY-based NMR evidence for a novel class of 20S proteasome inhibitors

The proteasome plays a central role in maintaining cellular homeostasis, in controlling the cell cycle, in removing misfolded proteins that can be toxic, and in regulating the immune system. It is also an important target for novel anticancer drugs, such as bortezomib, a potent inhibitor that has been used successfully in the treatment of multiple myeloma. Here, we show that the antimalaria drug chloroquine inhibits proteasome function in eukaryotic cell extracts and in preparations of purified 20S archaeal proteasome from Thermoplasma acidophilium. Methyl-TROSY-based NMR spectroscopy experiments conducted with the 670 kDa 20S proteasome localize chloroquine binding to regions between the alpha and beta subunits of the alpha-beta-beta-alpha barrel-like structure, approximately 20 A from the proteolytic active sites in this 7-fold symmetric molecule. Complementary amide TROSY experiments that provide further probes of proteasome-inhibitor interactions were performed on a novel 180 kDa single-ring construct containing only alpha subunits, the proper assembly of which was confirmed by electron microscopy. In contrast to the chloroquine-proteasome interaction described here, all previously reported inhibitors of the proteasome, including MG132, bind the catalytic region directly. Consistent with the NMR chemical shift perturbation data reported here that place chloroquine binding distal from sites of proteolysis, we show that MG132 and chloroquine can bind the proteasome simultaneously, further establishing that they exploit two completely separate binding pockets. Our data thus establish a novel class of proteasome inhibitor that functions via a mechanism distinct from binding to active sites.     

Properties of group I allergens from grass pollen and their relation to cathepsin B, a member of the C1 family of cysteine proteinases.

Expansins are a family of proteins that catalyze pH-dependent long-term extension of isolated plant cell walls. They are divided into two groups, alpha and beta, the latter consisting of the grass group I pollen allergens and their vegetative homologs. Expansins are suggested to mediate plant cell growth by interfering with either structural proteins or the polysaccharide network in the cell wall. Our group reported papain-like properties of beta-expansin of Timothy grass (Phleum pratense) pollen, Phl p 1, and suggested that cleavage of cell wall structural proteins may be the underlying mechanism of expansin-mediated wall extension. Here, we report additional data showing that beta-expansins resemble ancient and modern cathepsin B, which is a member of the papain (C1) family of cysteine proteinases. Using the Pichia pastoris expression system, we show that cleavage of inhibitory prosequences from the recombinant allergen is facilitated by its N-glycosylation and that the truncated, activated allergen shows proteolytic activity, resulting in very low stability of the protein. We also show that deglycosylated, full-length allergen is not activated efficiently and therefore is relatively stable. Motif and homology search tools detected significant similarity between beta-expansins and cathepsins of modern animals as well as the archezoa Giardia lamblia, confirming the presence of inhibitory prosequences, active site and other functional amino-acid residues, as well as a conserved location of these features within these molecules. Lastly, we demonstrate by site-directed mutagenesis that the conserved His104 residue is involved in the catalytic activity of beta-expansins. These results indicate a common origin of cathepsin B and beta-expansins, especially if taken together with their previously known biochemical properties.