Association Study of SNAP25 and Schizophrenia in Irish Family and Case-Control Samples

SNAP25 occurs on chromosome 20p12.2, which has been linked to schizophrenia in some samples, and recently linked to latent classes of psychotic illness in our sample. SNAP25 is crucial to synaptic functioning, may be involved in axonal growth and dendritic sprouting, and its expression may be decreased in schizophrenia. We genotyped 18 haplotype-tagging SNPs in SNAP25 in a sample of 270 Irish high-density families. Single marker and haplotype analyses were performed in FBAT and PDT. We adjusted for multiple testing by computing q values. Association was followed up in an independent sample of 657 cases and 411 controls. We tested for allelic effects on the clinical phenotype by using the method of sequential addition and 5 factor-derived scores of the OPCRIT. Nine of 18 SNPs had Pvalues

Variations in Apolipoprotein E Frequency With Age in a Pooled Analysis of a Large Group of Older People

Variation in the apolipoprotein E gene (APOE) has been reported to be associated with longevity in humans. The authors assessed the allelic distribution of APOE isoforms e2, e3, and e4 among 10,623 participants from 15 case-control and cohort studies of age-related macular degeneration (AMD) in populations of European ancestry (study dates ranged from 1990 to 2009). The authors included only the 10,623 control subjects from these studies who were classified as having no evidence of AMD, since variation within the APOE gene has previously been associated with AMD. In an analysis stratified by study center, gender, and smoking status, there was a decreasing frequency of the APOE e4 isoform with increasing age (?2 for trend = 14.9 (1 df); P = 0.0001), with a concomitant increase in the e3 isoform (?2 for trend = 11.3 (1 df); P = 0.001). The association with age was strongest in e4 homozygotes; the frequency of e4 homozygosity decreased from 2.7% for participants aged 60 years or less to 0.8% for those over age 85 years, while the proportion of participants with the e3/e4 genotype decreased from 26.8% to 17.5% across the same age range. Gender had no significant effect on the isoform frequencies. This study provides strong support for an association of the APOE gene with human longevity.

Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size ('size shifts'), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.

Unique genetic variation at a species' rear edge is under threat from global climate change

Global climate change is having a significant effect on the distributions of a wide variety of species, causing both range shifts and population extinctions. To date, however, no consensus has emerged on how these processes will affect the range-wide genetic diversity of impacted species. It has been suggested that species that recolonized from low-latitude refugia might harbour high levels of genetic variation in rear-edge populations, and that loss of these populations could cause a disproportionately large reduction in overall genetic diversity in such taxa. In the present study, we have examined the distribution of genetic diversity across the range of the seaweed Chondrus crispus, a species that has exhibited a northward shift in its southern limit in Europe over the last 40 years. Analysis of 19 populations from both sides of the North Atlantic using mitochondrial single nucleotide polymorphisms (SNPs), sequence data from two singlecopy nuclear regions and allelic variation at eight microsatellite loci revealed unique genetic variation for all marker classes in the rear-edge populations in Iberia, but not in the rear-edge populations in North America. Palaeodistribution modelling and statistical testing of alternative phylogeographic scenarios indicate that the unique genetic diversity in Iberian populations is a result not only of persistence in the region during the last glacial maximum, but also because this refugium did not contribute substantially to the recolonization of Europe after the retreat of the ice. Consequently, loss of these rear-edge populations as a result of ongoing climate change will have a major effect on the overall genetic diversity of the species, particularly in Europe, and this could compromise the adaptive potential of the species as a whole in the face of future global warming.

Microfaunal communities associated with epiphytic lichens in Belfast

The composition and richness of the microfauna on lime trees was surveyed in relation to the distribution and cover of lichens in Belfast. Parameters used to help interpret the results included distance from the city centre and available data on air quality. The percentage epiphyte cover on the trunks of lime trees was significantly correlated with distance from the city centre whereas that on tree bases as not. In contrast, the number of microfaunal species revealed strong positive correlations with distance for both the bases and the trunks of trees. Most of this increase in microfaunal species richness towards rural areas was due to protistans which are thus proposed as useful bioindicators of air pollution. The total species richness of fauna showed slight negative correlation with smoke but not SO2 levels.

Functional effect of the C242T polymorphism in the NAD(P)H oxidase p22phox gene on vascular superoxide production in atherosclerosis.

BACKGROUND:

Increased superoxide anion production increases oxidative stress and reduces nitric oxide bioactivity in vascular disease states. NAD(P)H oxidase is an important source of superoxide in human blood vessels, and some studies suggest a possible association between polymorphisms in the NAD(P)H oxidase CYBA gene and atherosclerosis; however, no functional data address this hypothesis. We examined the relationships between the CYBA C242T polymorphism and direct measurements of superoxide production in human blood vessels.

METHODS AND RESULTS:

Vascular NAD(P)H oxidase activity was determined in human saphenous veins obtained from 110 patients with coronary artery disease and identified risk factors. Immunoblotting, reverse-transcription polymerase chain reaction, and DNA sequencing showed that p22phox protein, mRNA, and 242C/T allelic variants are expressed in human blood vessels. Vascular superoxide production, both basal and NADH-stimulated, was highly variable between patients, but the presence of the CYBA 242T allele was associated with significantly reduced vascular NAD(P)H oxidase activity, independent of other clinical risk factors for atherosclerosis.

CONCLUSIONS:

Association of the CYBA 242T allele with reduced NAD(P)H oxidase activity in human blood vessels suggests that genetic variation in NAD(P)H oxidase components may play a significant role in modulating superoxide production in human atherosclerosis.

Agricultural intensification and biodiversity partitioning in European landscapes comparing plants, carabids, and birds

Effects of agricultural intensification (AI) on biodiversity are often assessed on the plot scale, although processes determining diversity also operate on larger spatial scales. Here, we analyzed the diversity of vascular plants, carabid beetles, and birds in agricultural landscapes in cereal crop fields at the field (n = 1350), farm (n = 270), and European-region (n = 9) scale. We partitioned diversity into its additive components alpha, beta, and gamma, and assessed the relative contribution of beta diversity to total species richness at each spatial scale. AI was determined using pesticide and fertilizer inputs, as well as tillage operations and categorized into low, medium, and high levels. As AI was not significantly related to landscape complexity, we could disentangle potential AI effects on local vs. landscape community homogenization. AI negatively affected the species richness of plants and birds, but not carabid beetles, at all spatial scales. Hence, local AI was closely correlated to beta diversity on larger scales up to the farm and region level, and thereby was an indicator of farm-and region-wide biodiversity losses. At the scale of farms (12.83-20.52%) and regions (68.34-80.18%), beta diversity accounted for the major part of the total species richness for all three taxa, indicating great dissimilarity in environmental conditions on larger spatial scales. For plants, relative importance of alpha diversity decreased with AI, while relative importance of beta diversity on the farm scale increased with AI for carabids and birds. Hence, and in contrast to our expectations, AI does not necessarily homogenize local communities, presumably due to the heterogeneity of farming practices. In conclusion, a more detailed understanding of AI effects on diversity patterns of various taxa and at multiple spatial scales would contribute to more efficient agri-environmental schemes in agroecosystems.

Predicting community responses to perturbations in the face of imperfect knowledge and network complexity

How best to predict the effects of perturbations to ecological communities has been a long-standing goal for both applied and basic ecology. This quest has recently been revived by new empirical data, new analysis methods, and increased computing speed, with the promise that ecologically important insights may be obtainable from a limited knowledge of community interactions. We use empirically based and simulated networks of varying size and connectance to assess two limitations to predicting perturbation responses in multispecies communities: (1) the inaccuracy by which species interaction strengths are empirically quantified and (2) the indeterminacy of species responses due to indirect effects associated with network size and structure. We find that even modest levels of species richness and connectance (similar to 25 pairwise interactions) impose high requirements for interaction strength estimates because system indeterminacy rapidly overwhelms predictive insights. Nevertheless, even poorly estimated interaction strengths provide greater average predictive certainty than an approach that uses only the sign of each interaction. Our simulations provide guidance in dealing with the trade-offs involved in maximizing the utility of network approaches for predicting dynamics in multispecies communities.

Scaling of Food-Web Properties with Diversity and Complexity Across Ecosystems

Trophic scaling models describe how topological food-web properties such as the number of predator prey links scale with species richness of the community. Early models predicted that either the link density (i.e. the number of links per species) or the connectance (i.e. the linkage probability between any pair of species) is constant across communities. More recent analyses, however, suggest that both these scaling models have to be rejected, and we discuss several hypotheses that aim to explain the scale dependence of these complexity parameters. Based on a recent, highly resolved food-web compilation, we analysed the scaling behaviour of 16 topological parameters and found significant power law scaling relationships with diversity (i.e. species richness) and complexity (i.e. connectance) for most of them. These results illustrate the lack of universal constants in food-web ecology as a function of diversity or complexity. Nonetheless, our power law scaling relationships suggest that fundamental processes determine food-web topology, and subsequent analyses demonstrated that ecosystem-specific differences in these relationships were of minor importance. As such, these newly described scaling relationships provide robust and testable cornerstones for future structural food-web models.

THE INTERSTELLAR-MEDIUM

The interstellar medium is the tenuous gas that fills the space between the stars of our Galaxy. Though insignificant optically, its variety and richness are revealed in observations at other wavelengths. From relatively dense clouds of gas new stars are formed. The deme clouds show, through infrared and millimetre wave measurements, a complex chemistry. We describe in particular how an understanding of the chemistry brings with it information about the nature of the clouds and how they are evolving. We show how the techniques that have been developed for interstellar clouds may also be applied to circumstellar environments and to ejecta from transient dramatic events such as novae and supernovae.

The long-term impacts of fisheries on epifaunal assemblage function and structure, in a special area of conservation

Fisheries can have profound effects on epifaunal community function and structure. We analysed the results from five dive surveys (1975–1976, 1980, 1983, 2003 and 2007), taken in a Special Area of Conservation, Strangford Lough, Northern Ireland before and after a ten year period of increased trawling activity between 1985 and 1995. There were no detectable differences in the species richness or taxonomic distinctiveness before (1975–1983) and after (2003–2007) this period. However, there was a shift in the epifaunal assemblage between the surveys in 1975–1983 and 2003–2007. In general, the slow-moving, or sessile, erect, filterfeeders were replaced by highly mobile, swimming, scavengers and predators. There were declines in the frequency of the fished bivalve Aequipecten opercularis and the non-fished bivalves Modiolus modiolus and Chlamys varia and some erect sessile invertebrates between the surveys in 1975–1983 and 2003–2007. In contrast, there were increases in the frequency of the fished and reseeded bivalves Pecten maximus and Ostrea edulis, the fished crabs Cancer pagurus and Necora puber and the non-fished sea stars Asterias rubens, Crossaster papposus and Henricia oculata between the surveys in 1975–1983 and 2003–2007. We suggest that these shifts could be directly and indirectly attributed to the long-termimpacts of trawl fishing gear, although increases in the supply of discarded bait and influxes of sediment may also have contributed to changes in the frequency of some taxa. These results suggest that despite their limitations, historical surveys and repeat sampling over long periods can help to elucidate the inferred patterns in the epifaunal community. The use of commercial fishing gear was banned from two areas in Strangford Lough in 2011, making it a model ecosystem for assessing the long-term recovery of the epifaunal community from the impacts of mobile and pot fishing gear.

Ecological coherence in marine reserve network design: an empirical evaluation of sequential site selection using genetic structure

Ecological coherence is a multifaceted conservation objective that includes some potentially conflicting concepts. These concepts include the extent to which the network maximises diversity (including genetic diversity) and the extent to which protected areas interact with non-reserve locations. To examine the consequences of different selection criteria, the preferred location to complement protected sites was examined using samples taken from four locations around each of two marine protected areas: Strangford Lough and Lough Hyne, Ireland. Three different measures of genetic distance were used: FST, Dest and a measure of allelic dissimilarity, along with a direct assessment of the total number of alleles in different candidate networks. Standardized site scores were used for comparisons across methods and selection criteria. The average score for Castlehaven, a site relatively close to Lough Hyne, was highest, implying that this site would capture the most genetic diversity while ensuring highest degree of interaction between protected and unprotected sites. Patterns around Strangford Lough were more ambiguous, potentially reflecting the weaker genetic structure around this protected area in comparison to Lough Hyne. Similar patterns were found across species with different dispersal capacities, indicating that methods based on genetic distance could be used to help maximise ecological coherence in reserve networks. ⺠Ecological coherence is a key component of marine protected area network design. ⺠Coherence contains a number of competing concepts. ⺠Genetic information from field populations can help guide assessments of coherence. ⺠Average choice across different concepts of coherence was consistent among species. ⺠Measures can be combined to compare the coherence of different network designs.

Biodiversity and ecosystem processes in shallow coastal waters: an experimental approach

The relationship between biodiversity and ecological processes is currently the focus of considerable research effort, made all the more urgent by the rate of biodiversity loss world-wide. Rigorous experimental approaches to this question have been dominated by terrestrial ecologists, but shallow-water marine systems offer great opportunities by virtue of their relative ease of manipulation, fast response times and well-understood effects of macrofauna on sediment processes. In this paper, we describe a series of experiments whereby species richness has been manipulated in a controlled way and the concentrations of nutrients (ammonium, nitrate and phosphate) in the overlying water measured under these different treatments. The results indicate variable effects of species and location on ecosystem processes, and are discussed in the context of emerging mainstream ecological theory on biodiversity and ecosystem relations. Extensions of the application of the experimental approach to species-rich, large-scale benthic systems are discussed and the potential for novel analyses of existing data sets is highlighted. (C) 2002 Elsevier Science B.V. All rights reserved.

Detecting the effects of diversity on measures of ecosystem function: experimental design, null models and empirical observations

Here we present a novel experimental approach to examine the relationship between diversity and ecosystem Function. We develop four null predictive models, with which to differentiate between the 'sampling effect' - the chance inclusion of a highly productive species, and 'species complementarity' - the complementary use of resources by species that differ in their niche or resource use. We investigate the effects of manipulating species and functional richness on ecosystem function in marine benthic system and using empirical data from our own experiments we illustrate the application of these models.

The Adult Cystic Fibrosis Airway Microbiota Is Stable over Time and Infection Type, and Highly Resilient to Antibiotic Treatment of Exacerbations

Cystic fibrosis (CF) is characterized by defective mucociliary clearance and chronic airway infection by a complex microbiota. Infection, persistent inflammation and periodic episodes of acute pulmonary exacerbation contribute to an irreversible decline in CF lung function. While the factors leading to acute exacerbations are poorly understood, antibiotic treatment can temporarily resolve pulmonary symptoms and partially restore lung function. Previous studies indicated that exacerbations may be associated with changes in microbial densities and the acquisition of new microbial species. Given the complexity of the CF microbiota, we applied massively parallel pyrosequencing to identify changes in airway microbial community structure in 23 adult CF patients during acute pulmonary exacerbation, after antibiotic treatment and during periods of stable disease. Over 350,000 sequences were generated, representing nearly 170 distinct microbial taxa. Approximately 60% of sequences obtained were from the recognized CF pathogens Pseudomonas and Burkholderia, which were detected in largely non-overlapping patient subsets. In contrast, other taxa including Prevotella, Streptococcus, Rothia and Veillonella were abundant in nearly all patient samples. Although antibiotic treatment was associated with a small decrease in species richness, there was minimal change in overall microbial community structure. Furthermore, microbial community composition was highly similar in patients during an exacerbation and when clinically stable, suggesting that exacerbations may represent intrapulmonary spread of infection rather than a change in microbial community composition. Mouthwash samples, obtained from a subset of patients, showed a nearly identical distribution of taxa as expectorated sputum, indicating that aspiration may contribute to colonization of the lower airways. Finally, we observed a strong correlation between low species richness and poor lung function. Taken together, these results indicate that the adult CF lung microbiome is largely stable through periods of exacerbation and antibiotic treatment and that short-term compositional changes in the airway microbiota do not account for CF pulmonary exacerbations.