Erratum: Genomes reveal genetic diversity of Piscine orthoreovirus in farmed and free-ranging salmonids from Canada and USA.

[This corrects the article DOI: 10.1093/ve/veaa054.].

Genomes reveal genetic diversity of Piscine orthoreovirus in farmed and free-ranging salmonids from Canada and USA.

Piscine orthoreovirus (PRV-1) is a segmented RNA virus, which is commonly found in salmonids in the Atlantic and Pacific Oceans. PRV-1 causes the heart and skeletal muscle inflammation disease in Atlantic salmon and is associated with several other disease conditions. Previous phylogenetic studies of genome segment 1 (S1) identified four main genogroups of PRV-1 (S1 genogroups I-IV). The goal of the present study was to use Bayesian phylogenetic inference to expand our understanding of the spatial, temporal, and host patterns of PRV-1 from the waters of the northeast Pacific. To that end, we determined the coding genome sequences of fourteen PRV-1 samples that were selected to improve our knowledge of genetic diversity across a broader temporal, geographic, and host range, including the first reported genome sequences from the northwest Atlantic (Eastern Canada). Nucleotide and amino acid sequences of the concatenated genomes and their individual segments revealed that established sequences from the northeast Pacific were monophyletic in all analyses. Bayesian inference phylogenetic trees of S1 sequences using BEAST and MrBayes also found that sequences from the northeast Pacific grouped separately from sequences from other areas. One PRV-1 sample (WCAN_BC17_AS_2017) from an escaped Atlantic salmon, collected in British Columbia but derived from Icelandic broodstock, grouped with other S1 sequences from Iceland. Our concatenated genome and S1 analysis demonstrated that PRV-1 from the northeast Pacific is genetically distinct but descended from PRV-1 from the North Atlantic. However, the analyses were inconclusive as to the timing and exact source of introduction into the northeast Pacific, either from eastern North America or from European waters of the North Atlantic. There was no evidence that PRV-1 was evolving differently between free-ranging Pacific Salmon and farmed Atlantic Salmon. The northeast Pacific PRV-1 sequences fall within genogroup II based on the classification of Garseth, Ekrem, and Biering (Garseth, A. H., Ekrem, T., and Biering, E. (2013) 'Phylogenetic Evidence of Long Distance Dispersal and Transmission of Piscine Reovirus (PRV) between Farmed and Wild Atlantic Salmon', PLoS One, 8: e82202.), which also includes North Atlantic sequences from Eastern Canada, Iceland, and Norway. The additional full-genome sequences herein strengthen our understanding of phylogeographical patterns related to the northeast Pacific, but a more balanced representation of full PRV-1 genomes from across its range, as well additional sequencing of archived samples, is still needed to better understand global relationships including potential transmission links among regions.

Plasma lipidomics analysis finds long chain cholesteryl esters to be associated with Alzheimer's disease.

There is an urgent need for the identification of Alzheimer's disease (AD) biomarkers. Studies have now suggested the promising use of associations with blood metabolites as functional intermediate phenotypes in biomedical and pharmaceutical research. The aim of this study was to use lipidomics to identify a battery of plasma metabolite molecules that could predict AD patients from controls. We performed a comprehensive untargeted lipidomic analysis, using ultra-performance liquid chromatography/mass spectrometry on plasma samples from 35 AD patients, 40 elderly controls and 48 individuals with mild cognitive impairment (MCI) and used multivariate analysis methods to identify metabolites associated with AD status. A combination of 10 metabolites could discriminate AD patients from controls with 79.2% accuracy (81.8% sensitivity, 76.9% specificity and an area under curve of 0.792) in a novel test set. Six of the metabolites were identified as long chain cholesteryl esters (ChEs) and were reduced in AD (ChE 32:0, odds ratio (OR)=0.237, 95% confidence interval (CI)=0.10-0.48, P=4.19E-04; ChE 34:0, OR=0.152, 95% CI=0.05-0.37, P=2.90E-04; ChE 34:6, OR=0.126, 95% CI=0.03-0.35, P=5.40E-04; ChE 32:4, OR=0.056, 95% CI=0.01-0.24, P=6.56E-04 and ChE 33:6, OR=0.205, 95% CI=0.06-0.50, P=2.21E-03, per (log2) metabolite unit). The levels of these metabolites followed the trend control>MCI>AD. We, additionally, found no association between cholesterol, the precursor of ChE and AD. This study identified new ChE molecules, involved in cholesterol metabolism, implicated in AD, which may help identify new therapeutic targets; although, these findings need to be replicated in larger well-phenotyped cohorts.

A Multiple Indicators Multiple Causes (MIMIC) model of Behavioural and Psychological Symptoms in Dementia (BPSD).

INTRODUCTION: Although there is evidence for distinct behavioural sub-phenotypes in Alzheimer's disease (AD), their inter-relationships and the effect of clinical variables on their expression have been little investigated. METHODS: We have analysed a sample of 1850 probable AD patients from the UK and Greece with 10 item Neuropsychiatric Inventory (NPI) data. We applied a Multiple Indicators Multiple Causes (MIMIC) approach to investigate the effect of MMSE, disease duration, gender, age and age of onset on the structure of a four-factor model consisting of "psychosis", "moods", "agitation" and "behavioural dyscontrol". RESULTS: Specific clinical variables predicted the expression of individual factors. When the inter-relationship of factors is modelled, some previously significant associations are lost. For example, lower MMSE scores predict psychosis, agitation and behavioural dyscontrol factors, but psychosis and mood predict the agitation factor. Taking these associations into account MMSE scores did not predict agitation. CONCLUSIONS: The complexity of the inter-relations between symptoms, factors and clinical variables is efficiently captured by this MIMIC model.

The acute effects of synthetic intravenous Delta9-tetrahydrocannabinol on psychosis, mood and cognitive functioning.

BACKGROUND: Recent work suggests that heavy use of cannabis is associated with an increased risk of schizophrenia-like psychosis. However, there is a dearth of experimental studies of the effects of the constituents of cannabis, such as Delta9-tetrahydrocannabinol (THC). In a study of intravenous (i.v.) synthetic THC in healthy humans, we aimed to study the relationship of the psychotic symptoms induced by THC to the consequent anxiety and neuropsychological impairment. METHOD: Twenty-two healthy adult males aged 28+/-6 years (mean+/-s.d.) participated in experimental sessions in which i.v. THC (2.5 mg) was administered under double-blind, placebo-controlled conditions. Self-rated and investigator-rated measurements of mood and psychosis [the University of Wales Institute of Science and Technology Mood Adjective Checklist (UMACL), the Positive and Negative Syndrome Scale (PANSS) and the Community Assessment of Psychic Experiences (CAPE)] were made at baseline and at 30, 80 and 120 min post-injection. Participants also completed a series of neuropsychological tests [the Rey Auditory Verbal Learning Task (RAVLT), Digit Span, Verbal Fluency and the Baddeley Reasoning Task] within 45 min of injection. RESULTS: THC-induced positive psychotic symptoms, and participant- and investigator-rated measurements of these were highly correlated. Participants showed an increase in anxiety ratings but there was no relationship between either self- or investigator-rated positive psychotic symptoms and anxiety. THC also impaired neuropsychological performance but once again there was no relationship between THC-induced positive psychotic symptoms and deficits in working memory/executive function. CONCLUSIONS: These findings confirm that THC can induce a transient, acute psychotic reaction in psychiatrically well individuals. The extent of the psychotic reaction was not related to the degree of anxiety or cognitive impairment.

Vulnerability to depression: what is the role of stress genes in gene x environment interaction?

Vulnerability to depression has been linked to the interaction of genetic predisposition with stressful life events. This review considers the associations between serotonergic and hypothalamic-pituitary-adrenal (HPA) systems. We follow the standpoint of a previous Editorial Review (Bhagwagar & Cowen, Psychological Medicine 2008, 38, 307-313) and consider another possible mechanism of vulnerability to depressive disorder, that is we suggest that the gene x environment interaction involves complex participation of serotonergic genes modulating response to stress through the HPA system.

No association of the SOD1 locus and disease susceptibility or phenotype in sporadic ALS.

Mutations in the copper zinc superoxide dismutase gene (SOD1) are found in 20% of familial and 3% of sporadic ALS patients. SOD1 protein aggregation can be detected in motor neurons of mutation-negative sporadic cases but a pathogenic role for wild-type SOD1 in ALS has not been demonstrated. In this study of 233 ALS cases and 248 controls the authors found no significant association between four individual single nucleotide polymorphisms and a deletion spanning the SOD1 locus (or their combined haplotypes), and disease susceptibility, or phenotype.

Cognitive and psychological correlates of smoking abstinence, and predictors of successful cessation.

The neural circuitry implicated in addictive drug use, which appears to be down-regulated in early abstinence, corresponds closely with brain reward pathways. A literature review suggests that responses to incentive stimuli and the ability to inhibit reflexive responses, both of which have been associated with normal functioning in these pathways, might be weakened during acute abstinence from chronic drug use. In an ongoing study, 82 smokers, abstinent overnight before two separate testing occasions, have been assessed after administration of nicotine and placebo lozenges (order of sessions counterbalanced). Nicotine administration is associated with a significant reduction in anhedonia, a near-significant increase in response to financial incentive, enhanced ability to inhibit reflexive eye movements, and increased attentional bias to words with appetitive significance. Fifty-nine participants then initiated a quit attempt and 19 reported relapsing within 7 days. Comparing their performance in the two prequit lozenge assessment sessions, relapsers showed a stronger effect of nicotine on enhancing their ability to inhibit reflexive eye movements and a near-significant trend towards greater nicotine-induced increases in attentional bias toward appetitive words.

beta-1,3-Glucuronyltransferase-1 gene implicated as a candidate for a schizophrenia-like psychosis through molecular analysis of a balanced translocation.

We have mapped and sequenced both chromosome breakpoints of a balanced t(6;11)(q14.2;q25) chromosome translocation that segregates with a schizophrenia-like psychosis. Bioinformatics analysis of the regions revealed a number of confirmed and predicted transcripts. No confirmed transcripts are disrupted by either breakpoint. The chromosome 6 breakpoint region is gene poor, the closest transcript being the serotonin receptor 1E (HTR1E) at 625 kb telomeric to the breakpoint. The chromosome 11 breakpoint is situated close to the telomere. The closest gene, beta-1,3-glucuronyltransferase (B3GAT1 or GlcAT-P), is 299 kb centromeric to the breakpoint. B3GAT1 is the key enzyme during the biosynthesis of the carbohydrate epitope HNK-1, which is present on a number of cell adhesion molecules important in neurodevelopment. Mice deleted for the B3GAT1 gene show defects in hippocampal long-term potentiation and in spatial memory formation. We propose that the translocation causes a positional effect on B3GAT1, affecting expression levels and making it a plausible candidate for the psychosis found in this family. More generally, regions close to telomeres are highly polymorphic in both sequence and length in the general population and several studies have implicated subtelomeric deletions as a common cause of idiopathic mental retardation. This leads us to the hypothesis that polymorphic or other variation of the 11q telomere may affect the activity of B3GAT1 and be a risk factor for schizophrenia and related psychoses in the general population.

Diagnostic strategies in CADASIL.

BACKGROUND: Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an inherited autosomal dominant condition characterized by migraine, recurrent stroke, and dementia. It results from mutations in the notch3 gene but mutations may occur at multiple sites making molecular diagnosis time consuming. It has been suggested that the presence of granular osmiophilic material (GOM) on skin biopsy and involvement of the anterior temporal lobe and external capsule on MRI may help in diagnosis. METHODS: The authors identified 83 potential index cases from the British population and screened exons 2 to 23 of notch3. MRI scans were scored using a modified Scheltens scale. Skin biopsy was performed in a subgroup. RESULTS: Fifteen different point mutations were identified in 48 families, 73% of which were in exon 4, 8% in exon 3, and 6% in each of exons 5 and 6. Moderate or severe involvement of the anterior temporal pole on MRI had a sensitivity of 89% and specificity of 86% for diagnosis of CADASIL, whereas external capsule involvement had a high sensitivity of 93% but a low specificity of 45%. Skin biopsy, performed in 18 cases, had a sensitivity of 45% and specificity of 100%. CONCLUSIONS: The spectrum of mutations in this study can be used to plan appropriate screening protocols; a suggested protocol is to screen exon 4, and proceed to exons 3, 5, and 6 where indicated. GOM on skin biopsy is diagnostic but can be negative. Anterior temporal pole involvement on MRI is a useful diagnostic marker.

Identification of genomic organisation, sequence variants and analysis of the role of the human dishevelled 1 gene in late onset Alzheimer's disease.

Alzheimer's disease (AD) is a disorder characterised by a progressive deterioration in memory and other cognitive functions. Neurofibrillary tangles (NFT) are a major pathological hallmark of AD, these are aggregations of paired helical filaments (PHF) comprised of the hyperphosphorylated microtubule associated protein tau. Several kinases, such as glycogen synthase kinase 3 beta (GSK3beta) and c-Jun N-terminal kinase (JNK), phosphorylate tau at sites that are phosphorylated in PHF. Dishevelled 1 (DVL1) is thought to act as a positive regulator of the wnt signalling pathway, and inhibits GSK3beta activity preventing beta-catenin degradation and thus allowing wnt target gene expression. JNK activation is also regulated by DVL1, however it is unclear if this is via the wnt signalling pathway. These observations suggest a central role for DVL1 in tau phosphorylation and AD and led us to investigate DVL1 as a candidate gene for this disorder. We determined the genomic structure of the DVL1 gene by sequencing and data mining and searched for sequence variations in the coding sequences and flanking introns. The DVL1 gene spans a region of approximately 13.8 kb (not including the 5' untranslated region) and is encoded by 15 exons. Analysis of over 4.3 kb of sequence, including 98% of exonic sequences and introns 2, 3, 6, 7, 9, 10, 11 and 12, revealed there to be six rare (< or =6%) sequence variations. None of these had any association with late onset AD. This would suggest that polymorphic variations in the coding sequences of DVL1 are not important in AD. However further analysis of regulatory regions may lead to the identification of other sequence variations which may be implicated in AD.

The microtubule associated protein Tau gene and Alzheimer's disease--an association study and meta-analysis.

Several studies have suggested an association between polymorphisms and an extended haplotype of the microtubule associated protein tau gene and Alzheimer's disease (AD) in synergy with apolipoprotein E (APOE) epsilon 4 status. However these findings have not been consistently replicated. We investigated the role of the tau haplotype in AD by conducting an association study as well as a meta-analysis of all the studies conducted to date. We examined six polymorphisms known to be in the extended tau haplotypes, one in exon 7 and five in and around exon 9 in 200 late onset AD and 189 control samples. All the polymorphisms examined fell into the recognised tau haplotypes. There was no statistical significant association with any of the polymorphisms and late onset AD. Stratification of data by APOE epsilon 4 status also produced no strongly significant association. The meta-analysis showed no significant differences between AD cases and controls, however stratification of data by APOE epsilon 4 status showed a small significant decrease in the H1 haplotype in AD before correction for multiple testing.

Mutations in the lysyl oxidase gene are not associated with amyotrophic lateral sclerosis.

BACKGROUND: There is an urgent need to identify genes involved in familial ALS (FALS), as mutations in the CuZn superoxide dismutase (SOD1) gene can account for 20% of FALS cases. The mechanisms by which the many mutations in the SOD1 gene lead to motoneuron degeneration are unknown, although current experimental evidence supports a toxic gain of function, possibly through copper-induced cytotoxicity. Copper is an integral component of a number of enzymes as well as SOD1. Since abnormalities in connective tissue cross-linking have been reported in ALS patients, an enzyme of possible relevance is lysyl oxidase (LOX), a copper-containing enzyme which catalyses the crosslinking of collagens and elastin. The aim of this study was to investigate the hypothesis that allelic variants or mutants of LOX gene result in altered function of LOX in ALS patients. METHODS: The coding regions of the LOX gene were screened for polymorphism and mutations in a cohort of sporadic and familial ALS patients. RESULTS: A novel polymorphism, Pro159Gln, was identified in eight individuals with sporadic ALS (5.0%) and five controls (3.6%). The previously identified Arg158Gln polymorphism was also detected in ALS patients and controls. These polymorphisms were genotyped in 192 ALS patients, including 31 unrelated familial cases and 138 controls, and no association was found between any of these polymorphisms and amyotrophic lateral sclerosis or its phenotype. CONCLUSION: Mutations in the LOX gene are unlikely to be directly causative of ALS.

Intron 7 retention and exon 9 skipping EAAT2 mRNA variants are not associated with amyotrophic lateral sclerosis.

Glutamate-mediated excitotoxicity is implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS). The astroglial glutamate transporter EAAT2 plays a major role in maintaining low levels of extracellular glutamate in the central nervous system. Multiple EAAT2 mRNA transcripts have been described, but those retaining intron 7 or skipping exon 9 are reported to be specific to the motor cortex, spinal cord, and cerebrospinal fluid of ALS patients. We sought to verify these findings using a TaqMan (Elmer Biosystems, Warrington, UK) real-time reverse transcriptase polymerase chain reaction assay, which provides a sensitive and reliable quantitative measure of EAAT2 transcript copy ratios. We analyzed RNA extracted from frozen postmortem tissue from affected and unaffected central nervous system regions dissected from 17 sporadic ALS patients, 7 Alzheimer's disease patients, and 19 control subjects. We have demonstrated unequivocally that intron 7 retaining and exon 9 skipping variants can be detected in all individuals and in all central nervous system regions studied. The mean ratio of "variant" to "normal" transcripts did not differ significantly between patient and control groups. Although our assay could detect transcript concentrations in cerebrospinal fluid as low as 10 pg/ml, none were detected in 17 ALS and 8 control samples. We conclude that ALS is not associated with elevated levels of EAAT2 transcripts retaining intron 7 and skipping exon 9. An alternative explanation must be sought for the disturbance of glutamate homeostasis reported in ALS.

Association study of the 5-HT(2A) receptor gene polymorphism, T102C and essential hypertension.

BACKGROUND: Serotonin dysfunction has been implicated in hypertension due to its ability to induce vasoconstriction via stimulation of 5-HT(2) receptors and due to the antihypertensive effect of ketanserin, an antagonist at the 5-HT(2A) receptor subtype, expressed both on arteries and the brain. The silent T102C polymorphism in the 5-HT(2A) gene is in absolute linkage disequilibrium with a polymorphism in the promoter and may contribute to genetic predisposition possibly by modifying the transcription of the gene. OBJECTIVE: To examine the genetic contribution of the T102C 5-HT(2A)polymorphism in essential hypertension in a case-control sample of UK residents. DESIGN: The hypertensive group consisted of 342 subjects over 75 years and the community-based control group consisted of 319 subjects. Subjects were genotyped for the T102C polymorphism by Mspl restriction enzyme digestion following PCR amplification. RESULTS: Sex-specific association analysis revealed significant differences between hypertensive and normotensive subjects in the genotypes distribution (P = 0.016) and allelic frequencies (P = 0.007) in the female group. The direction of significance was increased frequency of the 102-C allele in the hypertensive subjects. There were no association between haplotype and age or body mass index, which suggest that the effect of the T102C variant is not influenced by these variables. CONCLUSION: This data indicates that the T102C polymorphism in the 5-HT(2A) gene might be an independent risk factor for increased blood pressure in female individuals with essential hypertension.

Identification of sequence variants and analysis of the role of the glycogen synthase kinase 3 beta gene and promoter in late onset Alzheimer's disease.

Alzheimer's disease (AD) is a disorder characterised by a progressive deterioration in memory and other cognitive functions. Glycogen synthase kinase 3 beta (GSK3 beta) phosphorylates the microtubule associated protein tau at sites that are aberrantly phosphorylated in AD. GSK3 beta binds to presenilin 1 and plays a role in wnt and insulin signalling cascades, both of which have been proposed to be linked to AD. Moreover GSK3 beta activity may be altered in AD brain. These observations suggest a central role for GSK3 beta in AD and led us to investigate GSK3 beta as a candidate gene for AD. We sought to identify sequence variations in the gene and its promoter, as these could have an effect on activity and expression leading to abnormal function. Sequencing over 3000 bp of the GSK3 beta putative promoter revealed there to be five sequence variations, two of which were common (>10%). However on further examination none of these, either alone or in synergy, had any association with late onset AD. Stratification of the data by APOE epsilon 4 status also produced no significant association. Sequencing of the GSK3 beta coding region revealed no variations. This would suggest that the aberrant phosphorylation of tau by GSK3 beta in AD is not due to sequence variations in the gene or its promoter.

Examination of variation in sternal rib end morphology relevant to age assessment.

The morphology of the sternal end of the right fourth rib has been proffered as an accurate age assessor in skeletonized individuals of both sexes. This technique was tested for its applicability on left and right II, III, V-IX. Tests were performed between phase scores obtained from right and left ribs; right rib IV phase scores and scores obtained from the others in the right rib series; and between right rib IV scores and a composite score composed of the average of an individual's phase scores (omitting rib IV). Left ribs IV-IX were found not to vary significantly from their right counterparts. Although only right rib II was found to vary significantly from rib IV, use of the other ribs in the series should be undertaken with caution due to questions concerning their statistical significance. A composite score is therefore recommended for use instead.

MRI hyperintensities of the temporal lobe and external capsule in patients with CADASIL.

BACKGROUND: Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an inherited, autosomal dominant condition caused by mutations of the Notch3 gene. Affected individuals have migraine, mood disturbance, and recurrent strokes, often progressing to subcortical dementia and premature death. MRI findings include focal lacunar infarcts and diffuse T2-weighted hyperintensity, or leukoaraiosis. However, such findings are seen much more commonly in patients with cardiovascular risk factors, particularly hypertension, where they are believed to represent cerebral small vessel disease. No previous study has sought to identify specific radiologic markers of CADASIL. METHODS: MRI scans from 20 consecutive patients with CADASIL and 20 patients with sporadic leukoaraiosis due to presumed small-vessel disease were compared using the previously validated semiquantitative MRI rating scale devised by Scheltens et al. Analysis was blinded to clinical category. RESULTS: Scores for hyperintensities of the temporal white matter and external capsule-insula region were significantly higher in patients with CADASIL. Hyperintensity confined to the pole of the temporal lobe was a characteristic finding in CADASIL, occurring in 19 patients with CADASIL but no patients with ischemic leukoaraiosis. Involvement of the external capsule, though less specific, was seen early in the disease course. In a few patients with CADASIL, involvement of the corpus callosum was observed. CONCLUSIONS: Temporal pole hyperintensity is a radiologic marker of CADASIL. Involvement of the external capsule and corpus callosum are also characteristic findings that may help to distinguish the disease.

The extended haplotype of the microtubule associated protein tau gene is not associated with Pick's disease.

Pick's disease (PiD) is a rare neurodegenerative condition and is a member of a heterogeneous group of disorders known as tauopathies, so-called because of the predominantly neuronal aberrant tau accumulations found in these diseases. The tauopathy, familial frontotemporal dementia (FTD), is caused by mutations in the tau gene. Moreover, progressive supranuclear palsy (PSP) is associated with the tau H1 haplotype. In certain familial forms of FTD and in PSP the microtubule-binding four repeat tau isoform principally accumulates in neuropathological lesions. However, in PiD three repeat tau accumulations are found. We therefore investigated whether either the tau H1 or H2 haplotype was associated with PiD. Our results indicate a slight increase in H2H2 frequency in Pick's cases which is not statistically significant.

Vegetative Compatibility and Seasonal Variation Among Isolates of Sclerotinia homoeocarpa.

Dollar spot of amenity turf, caused by Sclerotinia homoeocarpa, occurs in two seasonal epidemics in the northern United States, one from May to late July and a second from mid-August through October. It is not known whether these seasonal epidemics are the result of multiple species or due to seasonal variation within a single species. Isolates of S. homoeocarpa were collected from dollar spot lesions obtained from golf courses in Michigan, Illinois, and Wisconsin. Vegetative compatibility reactions between isolates identified six vegetative compatibility groups (VCGs) among more than 1,300 isolates collected from the eight locations. Most VCGs were present throughout the season, but one was generally recovered only in the late epidemic. Sequences of the nuclear ribosomal internal transcribed spacer 1 (ITS1) were identical among VCGs, indicating that the VCGs represent a single species. The results of this study suggest that the seasonal dollar spot epidemics observed in the northern United States are caused by a single species.