Domains of Brn-2 that mediate homodimerization and interaction with general and melanocytic transcription factors

The class III POU gene brn-2, encoding the Brn-2/N-Oct-3 transcription factor, is widely expressed in the developing mammalian central nervous system. Brn-2 has also been found to regulate the melanocytic phenotype with N-Oct-3 DNA binding activity elevated in malignant melanoma, however, its mode of action is yet to be defined. The functional role of the Brn-2 transcription factor has been investigated through the analysis of protein-protein interactions it forms with a number of basal and melanocytic transcriptional regulatory proteins. In vivo interactions were tested by gene-cotransfection using the mammalian GAL4-Herpes Simplex viral protein 16 (VP16) two hybrid formation and direct protein binding by in vitro glutathione S-transferase (GST)-pull down assay. The Brn-2 protein was found to homodimerize in vivo with high affinity, using Brn-2 deletion constructs dimer complex formation was found to be dependent on the presence of both the homeodomain and linker regions of the POU-domain. However, the POU-homoedomain was dispensable for the formation of the dimerization interface in one of the partner molecules but not both, when the POU-linker region was removed the ability to interact was lost irrespective of the presence of the homeodomain. Dimerization of Brn-2/N-Oct-3 was also found to occur in DNA binding assays using melanoma cell line nuclear extracts and a recently reported dimer target sequence probe, which may have significant consequences for gene regulation in melanocytic tumours. Low affinity Brn-2 protein contacts have also been found with the basal transcription complex, including TATA binding protein (TBP) and the transcriptional coactivator p300, and with the Sox-10 and Pax-3 transcription factors that are known to play an important role in melanocyte cell formation.

The human melanocortin-1 receptor locus: analysis of transcription unit, locus polymorphism and haplotype evolution

The complete sequence of the MC1R locus has been assembled, the coding region of the gene is intronless and placed within a 12 kb region flanked by the NULP1 and TUBB4 genes. The immediate promoter region has an E-box site with homology to the M-box consensus known to bind the microphthalmia transcription factor (MITF); however, promoter deletion analysis and transactivation studies have failed to show activation through this element by MITF. Polymorphism within the coding region, immediate 5' promoter region and a variable number tandem repeat (VNTR) minisatellite within the locus have been examined in a collection of Caucasian families and African individuals. Haplotype analysis shows linkage disequilibrium between the VNTR and MC1R coding region red hair variant alleles which can be used to estimate the age of these missense changes. Assuming a mean VNTR mutation rate of 1% and a star phylogeny, we estimate the Arg151Cys variant arose 7500 years before the present day, suggesting these variants may have arisen in the Caucasian population more recently than previously thought.

A polymorphism in the agouti signalling protein (ASIP) is associated with decreased levels of mRNA

To date, a role for agouti signalling protein (ASIP) in human pigmentation has not been well characterized. It is known that agouti plays a pivotal role in the pigment switch from the dark eumelanin to the light pheomelanin in the mouse. However, because humans do not have an agouti banded hair pattern, its role in human pigmentation has been questioned. We previously identified a single polymorphism in the 3'-untranslated region (UTR) of ASIP that was found at a higher frequency in African-Americans compared with other population groups. To compare allele frequencies between European-Australians and indigenous Australians, the g.8818A --> G polymorphism was genotyped. Significant differences were seen in allele frequencies between these groups (P < 0.0001) with carriage of the G allele highest in Australian Aborigines. In the Caucasian sample set a strong association was observed between the G allele and dark hair colour (P = 0.004) (odds ratio 4.6; 95% CI 1.4-15.27). The functional consequences of this polymorphism are not known but it was postulated that it might result in message instability and premature degradation of the transcript. To test this hypothesis, ASIP mRNA levels were quantified in melanocytes carrying the variant and non-variant alleles. Using quantitative real-time polymerase chain reaction the mean ASIP mRNA ratio of the AA genotype to the AG genotype was 12 (P < 0.05). This study suggests that the 3'-UTR polymorphism results in decreased levels of ASIP and therefore less pheomelanin production.

A 4.5-megabase YAC contig and physical map over the hemochromatosis gene region

We have constructed a yeast artificial chromosome (YAC) contig over the candidate hemochromatosis gene region. This contig comprises 16 YACs from the CEPH, Washington University, and ICI YAC libraries and covers 4.5 Mb at 6p21.3-6p22. The complete contig has been restriction mapped, enabling the precise relationship between the YACs to be determined and the mapping of a total of 12 STSs. Nine of these are highly polymorphic STSs that are closely linked to hemochromatosis; this series includes D6S265 and D6S1260, which comprise the most proximal and distal markers linked to HC. This is the first YAC contig that spans the hemochromatosis candidate region, and it provides valuable resource material for the cloning of this and other genes in the region distal to the MHC class I complex.

Genetic Risk for Smoking: Disentangling Interplay Between Genes and Socioeconomic Status

This study aims to disentangle the contribution of genetic liability, educational attainment (EA), and their overlap and interaction in lifetime smoking. We conducted genome-wide association studies (GWASs) in UK Biobank (N = 394,718) to (i) capture variants for lifetime smoking, (ii) variants for EA, and (iii) variants that contribute to lifetime smoking independently from EA ('smoking-without-EA'). Based on the GWASs, three polygenic scores (PGSs) were created for individuals from the Netherlands Twin Register (NTR, N = 17,805) and the Netherlands Mental Health Survey and Incidence Study-2 (NEMESIS-2, N = 3090). We tested gene-environment (G × E) interactions between each PGS, neighborhood socioeconomic status (SES) and EA on lifetime smoking. To assess if the PGS effects were specific to smoking or had broader implications, we repeated the analyses with measures of mental health. After subtracting EA effects from the smoking GWAS, the SNP-based heritability decreased from 9.2 to 7.2%. The genetic correlation between smoking and SES characteristics was reduced, whereas overlap with smoking traits was less affected by subtracting EA. The PGSs for smoking, EA, and smoking-without-EA all predicted smoking. For mental health, only the PGS for EA was a reliable predictor. There were suggestions for G × E for some relationships, but there were no clear patterns per PGS type. This study showed that the genetic architecture of smoking has an EA component in addition to other, possibly more direct components. PGSs based on EA and smoking-without-EA had distinct predictive profiles. This study shows how disentangling different models of genetic liability and interplay can contribute to our understanding of the etiology of smoking.

Cross-Disorder Genetic Analysis of Tic Disorders, Obsessive-Compulsive, and Hoarding Symptoms

Hoarding, obsessive-compulsive disorder (OCD), and Tourette's disorder (TD) are psychiatric disorders that share symptom overlap, which might partly be the result of shared genetic variation. Population-based twin studies have found significant genetic correlations between hoarding and OCD symptoms, with genetic correlations varying between 0.1 and 0.45. For tic disorders, studies examining these correlations are lacking. Other lines of research, including clinical samples and GWAS or CNV data to explore genetic relationships between tic disorders and OCD, have only found very modest if any shared genetic variation. Our aim was to extend current knowledge on the genetic structure underlying hoarding, OC symptoms (OCS), and lifetime tic symptoms and, in a trivariate analysis, assess the degree of common and unique genetic factors contributing to the etiology of these disorders. Data have been gathered from participants in the Netherlands Twin Register comprising a total of 5293 individuals from a sample of adult monozygotic (n = 2460) and dizygotic (n = 2833) twin pairs (mean age 33.61 years). The data on Hoarding, OCS, and tic symptoms were simultaneously analyzed in Mplus. A liability threshold model was fitted to the twin data, analyzing heritability of phenotypes and of their comorbidity. Following the criteria for a probable clinical diagnosis in all phenotypes, 6.8% of participants had a diagnosis of probable hoarding disorder (HD), 6.3% of OCS, and 12.8% of any probable lifetime tic disorder. Genetic factors explained 50.4, 70.1, and 61.1% of the phenotypic covariance between hoarding-OCS, hoarding-tics, and OCS-tics, respectively. Substantial genetic correlations were observed between hoarding and OCS (0.41), hoarding and tics (0.35), and between OCS and tics (0.37). These results support the contribution of genetic factors in the development of these disorders and their comorbidity. Furthermore, tics were mostly influenced by specific environmental factors unshared with OCS and HD.

Binding of ractopamine HCl to ocular tissues of cattle and turkeys in vivo and to melanin in vitro

Experiments were conducted to determine the total residues remaining in ocular tissues of cattle and turkeys after oral administration of [14C]ractopamine HCl. Twelve cattle were intraruminally dosed with 0.9 mg x kg(-1) x d(-1) of [14C]ractopamine HCl for 7 d. Four cattle each were slaughtered with withdrawal periods of 48,96, and 144 h. Radioactive residues were not detectable in whole-eye homogenates from the cattle. Eight male and eight female turkeys per treatment received either 7.5, 22.5, or 30 ppm dietary [14C]ractopamine HCl (0.33, 1.02, and 1.36 mg x kg(-1) x d(-1); treatment groups 1, 2, and 3, respectively) for 7 d, and the birds were slaughtered with a 0-d withdrawal period. Eyes were dissected into retina/choroid/schlera (RCS), cornea/iris (CI), and aqueous humor (AH) fractions. Residues in RCS, CI, and AH of treatment 1 turkeys were not detectable. Residues in AH were < 0.02 ppm in treatment groups 2 and 3. Mean residues in RCS ranged from 0.15 to 0.26 ppm, and mean CI residues ranged from <0.09 to 0.17 ppm for treatment groups 2 and 3, respectively. The propensities of ractopamine and synthetic ractopamine metabolites to bind to melanin were studied in vitro using radiolabeled ligands with centrifugal filtration to separate melanin from unbound ligand. In vitro studies showed that [14C]ractopamine HCl binds to melanin rapidly and was displaced from melanin by other beta-agonists. Glucuronidation of ractopamine, which produced the major biotransformation product of ractopamine in all species studied to date, prevented binding to melanin. These studies demonstrate that the propensity for the in vivo binding of ractopamine HCl to pigmented ocular tissues is less than that reported for clenbuterol.

Exploring the role of low-frequency and rare exonic variants in alcohol and tobacco use

BACKGROUND

Alcohol and tobacco use are heritable phenotypes. However, only a small number of common genetic variants have been identified, and common variants account for a modest proportion of the heritability. Therefore, this study aims to investigate the role of low-frequency and rare variants in alcohol and tobacco use.

METHODS

We meta-analyzed ExomeChip association results from eight discovery cohorts and included 12,466 subjects and 7432 smokers in the analysis of alcohol consumption and tobacco use, respectively. The ExomeChip interrogates low-frequency and rare exonic variants, and in addition a small pool of common variants. We investigated top variants in an independent sample in which ICD-9 diagnoses of "alcoholism" (N = 25,508) and "tobacco use disorder" (N = 27,068) had been assessed. In addition to the single variant analysis, we performed gene-based, polygenic risk score (PRS), and pathway analyses.

RESULTS

The meta-analysis did not yield exome-wide significant results. When we jointly analyzed our top results with the independent sample, no low-frequency or rare variants reached significance for alcohol consumption or tobacco use. However, two common variants that were present on the ExomeChip, rs16969968 (p = 2.39 × 10^-7) and rs8034191 (p = 6.31 × 10^-7) located in CHRNA5 and AGPHD1 at 15q25.1, showed evidence for association with tobacco use.

DISCUSSION

Low-frequency and rare exonic variants with large effects do not play a major role in alcohol and tobacco use, nor does the aggregate effect of ExomeChip variants. However, our results confirmed the role of the CHRNA5-CHRNA3-CHRNB4 cluster of nicotinic acetylcholine receptor subunit genes in tobacco use.

The spinal muscular atrophy gene region at 5q13.1 has a paralogous chromosomal region at 6p21.3

Paralogous regions are duplicated segments of chromosomal DNA that have been acquired during the evolution of the genome. Subsequent divergent evolution of the genes within paralogous regions can lead to the formation of gene families. Here, we report the identification of a region on Chromosome (Chr) 6 at 6p21.3 that is paralogous with the Spinal Muscular Atrophy (SMA) gene region on Chr 5 at 5q13.1. Partial characterization of this region identified nine sequences all of which are highly homologous to DNA sequences of the SMA gene region at 5q13.1. These sequences include four beta-glucuronidase sequences, two retrotransposon sequences, a novel cDNA, a Sequence Tagged Site (STS), and one that is homologous to exon 9 of the Neuronal Apoptosis Inhibitor Protein (NAIP) gene. The 6p21.3 paralogous SMA region may contain genes that are related to those in the SMA region at 5q13.1; however, a direct association of this region with SMA is unlikely given that no linkage of SMA with Chr 6 has been reported.

Suicide Risk in Schizophrenia, a 20 Year Cohort Study, Part 1: Outcome and associated social factors

<p><strong>Objective:</strong> This study prospectively followed up, after a period of 20 years, a group of patients with schizophrenia who were considered to be at high risk for suicide. In Part 1, we reported on outcome and associated social factors, and in this paper we discuss re-evaluated suicide risk in these patients and investigated symptomology and pharmacotherapy over the last 2 decades.</p><p><strong> Method:</strong> The subjects were interviewed, and a questionnaire evaluating suicide risk was completed. The Beck Hopelessness Scale (BHS) was administered and ratings were compared to those from the original study. The Calgary Depression Scale for Schizophrenia (CDSS) was also administered. Cross tabulations were then performed to identify factors associated with increased suicide risk. For those subjects who committed suicide since the original study, a psychological autopsy was performed.</p><p><strong>Results:</strong> Fourteen of the original 33 high suicide risk schizophrenia patients were found. Three subjects committed suicide during the 20 year period. Among the living subjects, risks for suicide were found to be lower than 20 years ago. Hopelessness and depressive symptoms correlated with independently evaluated suicide risk. Social withdrawal, blunting of affect and delusions were also associated with elevated risk. Good insight into illness and a history of previous suicide attempts correlate with high suicide risk. Cannabis abuse, poor or periodic adherence to treatment, as well as weight gain, akathisia and parkinsonian adverse effects were also associated with an increase in risk for suicide. Formal thought disorder, avolition and cognitive impairment were associated with lower risk of suicide.</p><p><strong>Conclusion:</strong> Hopelessness, depression, certain positive symptoms and adverse effects of medication, found in this study to be congruent with suicide risk in patients with schizophrenia, coincide with those mentioned in the literature. Despite current knowledge about this subject, suicide remains notoriously and ominously unpredictable in patients with schizophrenia.</p>

Role of International Oil Companies in the Net-Zero Emission Energy Transition

Scientific and engineering capabilities in hydrocarbon supply chains developed over decades in international oil and gas companies (IOCs) uniquely position these companies to drive rapid scale-up and transition to a net-zero emission economy. Flexible large-scale production of energy carriers such as hydrogen, ammonia, methanol, and other synthetic fuels produced with low- or zero-emission renewable power, nuclear energy, or hydrogen derived from natural gas with carbon capture and storage will enable long-distance transport and permanent storage options for clean energy. Use of energy carriers can overcome the inherent constraints of a fully electrified energy system by providing the energy and power densities, as well as transport and storage capacity, required to achieve energy supply and security in a net-zero emission economy, and over time allow optimization to the lowest cost for a consumer anywhere on the globe.

Genome-wide association study identifies 30 obsessive-compulsive disorder associated loci

Obsessive-compulsive disorder (OCD) affects ~1% of the population and exhibits a high SNP-heritability, yet previous genome-wide association studies (GWAS) have provided limited information on the genetic etiology and underlying biological mechanisms of the disorder. We conducted a GWAS meta-analysis combining 53,660 OCD cases and 2,044,417 controls from 28 European-ancestry cohorts revealing 30 independent genome-wide significant SNPs and a SNP-based heritability of 6.7%. Separate GWAS for clinical, biobank, comorbid, and self-report sub-groups found no evidence of sample ascertainment impacting our results. Functional and positional QTL gene-based approaches identified 249 significant candidate risk genes for OCD, of which 25 were identified as putatively causal, highlighting WDR6, DALRD3, CTNND1 and genes in the MHC region. Tissue and single-cell enrichment analyses highlighted hippocampal and cortical excitatory neurons, along with D1- and D2-type dopamine receptor-containing medium spiny neurons, as playing a role in OCD risk. OCD displayed significant genetic correlations with 65 out of 112 examined phenotypes. Notably, it showed positive genetic correlations with all included psychiatric phenotypes, in particular anxiety, depression, anorexia nervosa, and Tourette syndrome, and negative correlations with a subset of the included autoimmune disorders, educational attainment, and body mass index.. This study marks a significant step toward unraveling its genetic landscape and advances understanding of OCD genetics, providing a foundation for future interventions to address this debilitating disorder.

Suicide Risk in Schizophrenia - a follow-up study after 20 years. Part 2: Symptomatology and pharmacotherapy

<p><strong>Objective: </strong> This study prospectively re-evaluated, after a period of 20 years, a cohort of patients with schizophrenia who had been considered to be at high risk for suicide. The outcome and social factors associated with their suicide risk were investigated over the 2 decades. Method Subjects were contacted and interviewed face-to-face by following a questionnaire devised for this purpose. The Beck Hopelessness Scale (BHS) was administered and ratings were compared to those from the original study. The Calgary Depression Scale for Schizophrenia (CDSS) was administered. Cross tabulations were performed to identify factors associated with increased suicide risk. A psychological autopsy was performed, for those subjects who had committed suicide since the original study.</p><p><strong>Results:</strong>Fourteen of the original 33 high suicide risk schizophrenia patients were found. Three subjects committed suicide during the 20 year period. Among the living subjects, risks for suicide were found to be lower than 20 years ago. Male gender, poor social support, early age of illness onset, current admission to or recent discharge from hospital and a higher level of education were all factors associated with increased suicide risk. <strong></strong></p><p><strong>Conclusion:</strong> Demographic factors and those related to illness course, found in this study to be associated with suicide risk in patients with schizophrenia, are congruous with those mentioned in the literature.</p>