Genetic pleiotropy between multiple sclerosis and schizophrenia but not bipolar disorder: differential involvement of immune-related gene loci

Converging evidence implicates immune abnormalities in schizophrenia (SCZ), and recent genome-wide association studies (GWAS) have identified immune-related single-nucleotide polymorphisms (SNPs) associated with SCZ. Using the conditional false discovery rate (FDR) approach, we evaluated pleiotropy in SNPs associated with SCZ (n=21 856) and multiple sclerosis (MS) (n=43 879), an inflammatory, demyelinating disease of the central nervous system. Because SCZ and bipolar disorder (BD) show substantial clinical and genetic overlap, we also investigated pleiotropy between BD (n=16 731) and MS. We found significant genetic overlap between SCZ and MS and identified 21 independent loci associated with SCZ, conditioned on association with MS. This enrichment was driven by the major histocompatibility complex (MHC). Importantly, we detected the involvement of the same human leukocyte antigen (HLA) alleles in both SCZ and MS, but with an opposite directionality of effect of associated HLA alleles (that is, MS risk alleles were associated with decreased SCZ risk). In contrast, we found no genetic overlap between BD and MS. Considered together, our findings demonstrate genetic pleiotropy between SCZ and MS and suggest that the MHC signals may differentiate SCZ from BD susceptibility.Molecular Psychiatry advance online publication, 28 January 2014; doi:10.1038/mp.2013.195.

The influence of providing perches and string on activity levels, fearfulness and leg health in commercial broiler chickens

The aim of this study was to assess the effect of providing environmental enrichment in the form of perches and string on the behaviour and welfare of commercial broiler chickens. Houses containing ~23 000 broiler chickens were assigned to one of four treatments in a 2×2 factorial design. Treatments involved two levels of access to perches (P) (present (24/house) ‘+P’ or absent ‘−P’) and two levels of access to string (S) (present (24/house) ‘+S’ or absent ‘−S’). All houses contained windows, and 30 straw bales were provided from day 10 of the rearing cycle. Treatments were applied in one of four houses on a single farm, and were replicated over four production cycles. Behaviour and leg health were observed in weeks 3 to 5 of the rearing cycle. Production performance and environmental parameters were also measured. There was an interaction between perches and age in the percentage of birds observed lying, with higher percentages of birds observed lying in the +P treatment than in the −P treatment during weeks 4 and 5. There was also a significant interaction between string and age in the percentage of birds observed in locomotion, with higher percentages observed in locomotion in the −S treatment than in the +S treatment during weeks 4 and 5. There was also an interaction between string and age in average gait scores, with lower gait scores in the +S treatment than in the −S treatment during weeks 3 and 5 but not within week 4. Daytime observations showed that perches and strings were used frequently, with one bout of perching occurring approximately every 80 s/perch, and one bout of pecking at string occurring every 78 s/string on average. There was a significant effect of age on use of perches (P<0.001) and string (P<0.001), with perching peaking during week 5 and string pecking peaking during week 3. We conclude that commercial broilers in windowed houses with access to straw bales display an interest in additional enrichment stimuli in the form of perches and string, and therefore that these stimuli have the potential to improve welfare. In addition, provision of string as a pecking device appeared to positively influence walking ability. However, this effect was numerically small, was only shown in certain weeks and was not reflected in the other leg health measure (latency to lie). The results also showed an apparent negative effect of string and perches on the activity levels of birds (recorded away from the immediate vicinity of these enrichments) towards the end of the production cycle. These results emphasise the need for further research into optimum design and layout of enrichment stimuli for modern broilers in windowed houses to ensure that their provision leads to clear welfare benefits.

Localized Flux Maxima of Arsenic, Lead, and Iron around Root Apices in Flooded Lowland Rice

In wetland-adapted plants, such as rice, it is typically root apexes, sites of rapid entry for water/nutrients, where radial oxygen losses (ROLs) are highest. Nutrient/toxic metal uptake therefore largely occurs through oxidized zones and pH microgradients. However, the processes controlling the acquisition of trace elements in rice have been difficult to explore experimentally because of a lack of techniques for simultaneously measuring labile trace elements and O2/pH. Here, we use new diffusive gradients in thin films (DGT)/planar optode sandwich sensors deployed in situ on rice roots to demonstrate a new geochemical niche of greatly enhanced As, Pb, and Fe(II) mobilization into solution immediately adjacent to the root tips characterized by O2 enrichment and low pH. Fe(II) mobilization was congruent to that of the peripheral edge of the aerobic root zone, demonstrating that the Fe(II) mobilization maximum only developed in a narrow O2 range as the oxidation front penetrates the reducing soil. The Fe flux to the DGT resin at the root apexes was 3-fold higher than the anaerobic bulk soil and 27 times greater than the aerobic rooting zone. These results provide new evidence for the importance of coupled diffusion and oxidation of Fe in modulating trace metal solubilization, dispersion, and plant uptake.

Stressor intensity determines antagonistic interactions between species invasion and multiple stressor effects on ecosystem functioning

Biological invasions, nutrient enrichment and ocean warming are known to threaten biodiversity and ecosystem functioning. The independent effects of these ecological stressors are well studied, however, we lack understanding of their cumulative effects, which may be additive, antagonistic or synergistic. For example, the impacts of biological invasions are often determined by environmental context, which suggests that the effects of invasive species may vary with other stressors such as pollution or climate change. This study examined the effects of an invasive seaweed (Sargassum muticum) on the structure and functioning of a benthic marine assemblage and tested explicitly whether these effects varied with nutrient enrichment and ocean warming. Overall, the presence of Sargassum muticum increased assemblage productivity rates and warming altered algal assemblage structure, which was characterised by a decrease in kelp and an increase in ephemeral green algae. The effects of Sargassum muticum on total algal biomass accumulation, however, varied with nutrient enrichment and warming producing antagonistic cumulative effects on total algal biomass accumulation. These findings show that the nature of stressor interactions may vary with stressor intensity and among response variables, which leads to less predictable consequences for the structure and functioning of communities.

A Microscopic Study of Iron and Manganese Oxide Distribution in Soils from East Tennessee (U.S.A.)

Soils and saprolites developed from interbedded shales and limestones of the Conasauga Group are widespread in the Valley and Ridge Province of East Tennessee. Thin sections from four soil profiles were examined by petrographic and scanning electron microscopy including backscatter electron and energy-dispersive X-ray analyses. Iron and manganese released by weathering had migrated differentially downward and precipitated as crystalline and noncrystalline oxides. Oxides were observed as nodules, granular particulates, pore fillings, and coatings on other minerals, packing voids, vesicles, channels, and chambers. Iron oxides formed predominantly as coatings on packing-void walls and on laminated clays in vesicles and channels. Manganese oxides occurred as an early replacement phase of packing voids and of fracture-filling carbonate minerals. Iron oxides were dominant in moderately well-drained and oxidized horizons of the soil solum, whereas manganese oxides were abundant in the oxidized and moderately leached saprolite zone where the water table fluctuates seasonally. Therefore, a manganese enrichment zone, on a bulk soil basis, occurred generally below the iron oxide zone in the soil profile. Such differential migration and accumulation of iron and manganese have been controlled by localized soil microenvironments. Micromorphologic features observed in this study are important in land-use evaluation for hazardous waste disposal. © 1990.

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

Regulatory and coding variants are known to be enriched with associations identified by genome-wide association studies (GWASs) of complex disease, but their contributions to trait heritability are currently unknown. We applied variance-component methods to imputed genotype data for 11 common diseases to partition the heritability explained by genotyped SNPs () across functional categories (while accounting for shared variance due to linkage disequilibrium). Extensive simulations showed that in contrast to current estimates from GWAS summary statistics, the variance-component approach partitions heritability accurately under a wide range of complex-disease architectures. Across the 11 diseases DNaseI hypersensitivity sites (DHSs) from 217 cell types spanned 16% of imputed SNPs (and 24% of genotyped SNPs) but explained an average of 79% (SE = 8%) of  from imputed SNPs (5.1× enrichment; p = 3.7 × 10⁻¹⁷) and 38% (SE = 4%) of  from genotyped SNPs (1.6× enrichment, p = 1.0 × 10⁻⁴). Further enrichment was observed at enhancer DHSs and cell-type-specific DHSs. In contrast, coding variants, which span 1% of the genome, explained <10% of  despite having the highest enrichment. We replicated these findings but found no significant contribution from rare coding variants in independent schizophrenia cohorts genotyped on GWAS and exome chips. Our results highlight the value of analyzing components of heritability to unravel the functional architecture of common disease.

Automated tumour annotation and analysis for molecular pathology using TissueMark (R)

Objective: Molecular pathology relies on identifying anomalies using PCR or analysis of DNA/RNA. This is important in solid tumours where molecular stratification of patients define targeted treatment. These molecular biomarkers rely on examination of tumour, annotation for possible macro dissection/tumour cell enrichment and the estimation of % tumour. Manually marking up tumour is error prone. Method: We have developed a method for automated tumour mark-up and % cell calculations using image analysis called TissueMark® based on texture analysis for lung, colorectal and breast (cases=245, 100, 100 respectively). Pathologists marked slides for tumour and reviewed the automated analysis. A subset of slides was manually counted for tumour cells to provide a benchmark for automated image analysis. Results: There was a strong concordance between pathological and automated mark-up (100 % acceptance rate for macro-dissection). We also showed a strong concordance between manually/automatic drawn boundaries (median exclusion/inclusion error of 91.70 %/89 %). EGFR mutation analysis was precisely the same for manual and automated annotation-based macrodissection. The annotation accuracy rates in breast and colorectal cancer were 83 and 80 % respectively. Finally, region-based estimations of tumour percentage using image analysis showed significant correlation with actual cell counts. Conclusion: Image analysis can be used for macro-dissection to (i) annotate tissue for tumour and (ii) estimate the % tumour cells and represents an approach to standardising/improving molecular diagnostics.

Hydrogeochemistry and Arsenic Contamination of Groundwater in the Haor Basins of Bangladesh

Hydrogeochemical relationships and the level of arsenic (As) contamination of groundwater in the Haor Basin, a low-lying, semi-natural, region of remnant wetland environs to the northeast of Bangladesh, were studied to assess the As biogeochemical cycling. Most of the shallow and deep tubewells in the study area are contaminated with As (2-331 mu g/l). The relatively higher proportions of Na+ (8-156 mg/l) in groundwater suggest a mixing of connate marine water with freshwater aquifer. Non-significant association between As and PO43- has been found. Highly significant (P <0.001) relationship of As with DOC in groundwater indicates biodegradation of organic matter, creating an overall reducing environment in the aquifer sediments, which facilitates the release of As in the groundwater. The inverse As-Fe, As-Mn, As-Ca and As-Mg relationships in groundwater could be related to the precipitation of Fe-, Mn-, Ca-and Mg-minerals.

“A quiet still voice that just touches”: music’s relevance for adults living with life-threatening cancer diagnoses.

Purpose
Music has historically aided health and loss-adaptation, however, cancer patients’ experience of music for self-care is not well understood. This study examines adult cancer patients’ views about music’s role before and after diagnosis.
Methods
Constructivist approach, with grounded theory informed design using convenience, snowball and theoretical sampling. Patients from Australian metropolitan cancer and hospice settings completed demographic questionnaires and participated in semi-structured interviews. Qualitative inter-rater reliability was applied.
Results
Fifty-two patients reported comparable time spent experiencing music pre-post diagnosis. Music may remain incidental; however, many patients adapt music usage to ameliorate cancer’s aversive effects. Patients often draw from their musical lives and explore unfamiliar music to: remain connected with pre-illness identities; strengthen capacity for enduring treatment, ongoing survival (even when knowing “you’re going to die”), or facing death; reframe upended worlds; and live enriched lives. Patients can ascribe human or physical properties to music when describing its transformative effects. Familiar lyrics maybe reinterpreted, and patients’ intensified emotional reactions to music can reflect their threatened mortality. Sometimes music becomes inaccessible, elusive, and/or intensifies distress and is avoided. Families’, friends’ and professionals’ recognition of patients’ altered musical lives and music-based suggestions can extend patients’ use of music for self-care.
Conclusion
Health professionals can support patients by inquiring about their music behaviours and recognising that altered music usage may signify vulnerability. Although commonly recommended, hospital concerts and music broadcasts need sensitive delivery. Patients’ preferred music should be available in diagnostic, treatment and palliative settings because it can promote endurance and life enrichment.

Untargeted Metabolomic Analysis of Human Plasma Indicates Differentially Affected Polyamine and L-Arginine Metabolism in Mild Cognitive Impairment Subjects Converting to Alzheimer’s Disease

This study combined high resolution mass spectrometry (HRMS), advanced chemometrics and pathway enrichment analysis to analyse the blood metabolome of patients attending the memory clinic: cases of mild cognitive impairment (MCI; n = 16), cases of MCI who upon subsequent follow-up developed Alzheimer's disease (MCI_AD; n = 19), and healthy age-matched controls (Ctrl; n = 37). Plasma was extracted in acetonitrile and applied to an Acquity UPLC HILIC (1.7μm x 2.1 x 100 mm) column coupled to a Xevo G2 QTof mass spectrometer using a previously optimised method. Data comprising 6751 spectral features were used to build an OPLS-DA statistical model capable of accurately distinguishing Ctrl, MCI and MCI_AD. The model accurately distinguished (R2 = 99.1%; Q2 = 97%) those MCI patients who later went on to develop AD. S-plots were used to shortlist ions of interest which were responsible for explaining the maximum amount of variation between patient groups. Metabolite database searching and pathway enrichment analysis indicated disturbances in 22 biochemical pathways, and excitingly it discovered two interlinked areas of metabolism (polyamine metabolism and L-Arginine metabolism) were differentially disrupted in this well-defined clinical cohort. The optimised untargeted HRMS methods described herein not only demonstrate that it is possible to distinguish these pathologies in human blood but also that MCI patients 'at risk' from AD could be predicted up to 2 years earlier than conventional clinical diagnosis. Blood-based metabolite profiling of plasma from memory clinic patients is a novel and feasible approach in improving MCI and AD diagnosis and, refining clinical trials through better patient stratification.

Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria

BACKGROUND: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.

RESULTS: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.

CONCLUSIONS: The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.

Genome-wide gene pathway analysis of psychotic illness symptom dimensions based on a new schizophrenia-specific model of the OPCRIT

Empirically derived phenotypic measurements have the potential to enhance gene-finding efforts in schizophrenia. Previous research based on factor analyses of symptoms has typically included schizoaffective cases. Deriving factor loadings from analysis of only narrowly defined schizophrenia cases could yield more sensitive factor scores for gene pathway and gene ontology analyses. Using an Irish family sample, this study 1) factor analyzed clinician-rated Operational Criteria Checklist items in cases with schizophrenia only, 2) scored the full sample based on these factor loadings, and 3) implemented genome-wide association, gene-based, and gene-pathway analysis of these SCZ-based symptom factors (final N= 507). Three factors emerged from the analysis of the schizophrenia cases: a manic, a depressive, and a positive symptom factor. In gene-based analyses of these factors, multiple genes had q<. 0.01. Of particular interest are findings for PTPRG and WBP1L, both of which were previously implicated by the Psychiatric Genomics Consortium study of SCZ; results from this study suggest that variants in these genes might also act as modifiers of SCZ symptoms. Gene pathway analyses of the first factor indicated over-representation of glutamatergic transmission, GABA-A receptor, and cyclic GMP pathways. Results suggest that these pathways may have differential influence on affective symptom presentation in schizophrenia.

Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data

BACKGROUND: Urothelial pathogenesis is a complex process driven by an underlying network of interconnected genes. The identification of novel genomic target regions and gene targets that drive urothelial carcinogenesis is crucial in order to improve our current limited understanding of urothelial cancer (UC) on the molecular level. The inference of genome-wide gene regulatory networks (GRN) from large-scale gene expression data provides a promising approach for a detailed investigation of the underlying network structure associated to urothelial carcinogenesis.

METHODS: In our study we inferred and compared three GRNs by the application of the BC3Net inference algorithm to large-scale transitional cell carcinoma gene expression data sets from Illumina RNAseq (179 samples), Illumina Bead arrays (165 samples) and Affymetrix Oligo microarrays (188 samples). We investigated the structural and functional properties of GRNs for the identification of molecular targets associated to urothelial cancer.

RESULTS: We found that the urothelial cancer (UC) GRNs show a significant enrichment of subnetworks that are associated with known cancer hallmarks including cell cycle, immune response, signaling, differentiation and translation. Interestingly, the most prominent subnetworks of co-located genes were found on chromosome regions 5q31.3 (RNAseq), 8q24.3 (Oligo) and 1q23.3 (Bead), which all represent known genomic regions frequently deregulated or aberated in urothelial cancer and other cancer types. Furthermore, the identified hub genes of the individual GRNs, e.g., HID1/DMC1 (tumor development), RNF17/TDRD4 (cancer antigen) and CYP4A11 (angiogenesis/ metastasis) are known cancer associated markers. The GRNs were highly dataset specific on the interaction level between individual genes, but showed large similarities on the biological function level represented by subnetworks. Remarkably, the RNAseq UC GRN showed twice the proportion of significant functional subnetworks. Based on our analysis of inferential and experimental networks the Bead UC GRN showed the lowest performance compared to the RNAseq and Oligo UC GRNs.

CONCLUSION: To our knowledge, this is the first study investigating genome-scale UC GRNs. RNAseq based gene expression data is the data platform of choice for a GRN inference. Our study offers new avenues for the identification of novel putative diagnostic targets for subsequent studies in bladder tumors.

The Evaluation and Quantitation of Dihydrogen Metabolism Using Deuterium Isotope in Rats

Purpose: Despite the significant interest in molecular hydrogen as an antioxidant in the last eight years, its quantitative metabolic parameters in vivo are still lacking, as is an appropriate method for determination of hydrogen effectivity in the mammalian organism under various conditions.

Basic Procedures: Intraperitoneally-applied deuterium gas was used as a metabolic tracer and deuterium enrichment was determined in the body water pool. Also, in vitro experiments were performed using bovine heart submitochondrial particles to evaluate superoxide formation in Complex I of the respiratory chain.

Main Findings: A significant oxidation of about 10% of the applied dose was found under physiological conditions in rats, proving its antioxidant properties. Hypoxia or endotoxin application did not exert any effect, whilst pure oxygen inhalation reduced deuterium oxidation. During in vitro experiments, a significant reduction of superoxide formation by Complex I of the respiratory chain was found under the influence of hydrogen. The possible molecular mechanisms of the beneficial effects of hydrogen are discussed, with an emphasis on the role of iron sulphur clusters in reactive oxygen species generation and on iron species-dihydrogen interaction.

Principal Conclusions: According to our findings, hydrogen may be an efficient, non-toxic, highly bioavailable and low-cost antioxidant supplement for patients with pathological conditions involving ROS-induced oxidative stress.

Convergent genetic and expression data implicate immunity in Alzheimer's disease

Background: Late-onset Alzheimer's disease (AD) is heritable with 20 genes showing genome-wide association in the International Genomics of Alzheimer's Project (IGAP). To identify the biology underlying the disease, we extended these genetic data in a pathway analysis.

Methods: The ALIGATOR and GSEA algorithms were used in the IGAP data to identify associated functional pathways and correlated gene expression networks in human brain.

Results: ALIGATOR identified an excess of curated biological pathways showing enrichment of association. Enriched areas of biology included the immune response (P = 3.27 X 10(-12) after multiple testing correction for pathways), regulation of endocytosis (P = 1.31 X 10(-11)), cholesterol transport (P = 2.96 X 10(-9)), and proteasome-ubiquitin activity (P = 1.34 X 10(-6)). Correlated gene expression analysis identified four significant network modules, all related to the immune response (corrected P = .002-.05).

Conclusions: The immime response, regulation of endocytosis, cholesterol transport, and protein ubiquitination represent prime targets for AD therapeutics. (C) 2015 Published by Elsevier Inc. on behalf of The Alzheimer's Association.