Rare genetic variants underlie outlying levels of DNA methylation and gene-expression.

Testing the effect of rare variants on phenotypic variation is difficult due to the need for extremely large cohorts to identify associated variants given expected effect sizes. An alternative approach is to investigate the effect of rare genetic variants on DNA methylation (DNAm) as effect sizes are expected to be larger for molecular traits compared with complex traits. Here, we investigate DNAm in healthy ageing populations-the Lothian Birth Cohorts of 1921 and 1936-and identify both transient and stable outlying DNAm levels across the genome. We find an enrichment of rare genetic single nucleotide polymorphisms (SNPs) within 1 kb of DNAm sites in individuals with stable outlying DNAm, implying genetic control of this extreme variation. Using a family-based cohort, the Brisbane Systems Genetics Study, we observed increased sharing of DNAm outliers among more closely related individuals, consistent with these outliers being driven by rare genetic variation. We demonstrated that outlying DNAm levels have a functional consequence on gene expression levels, with extreme levels of DNAm being associated with gene expression levels toward the tails of the population distribution. This study demonstrates the role of rare SNPs in the phenotypic variation of DNAm and the effect of extreme levels of DNAm on gene expression.

The Coronary Artery Disease-associated Coding Variant in Zinc Finger C3HC-type Containing 1 (ZC3HC1) Affects Cell Cycle Regulation.

Genome-wide association studies have to date identified multiple coronary artery disease (CAD)-associated loci; however, for most of these loci the mechanism by which they affect CAD risk is unclear. The CAD-associated locus 7q32.2 is unusual in that the lead variant, rs11556924, is not in strong linkage disequilibrium with any other variant and introduces a coding change in ZC3HC1, which encodes NIPA. In this study, we show that rs11556924 polymorphism is associated with lower regulatory phosphorylation of NIPA in the risk variant, resulting in NIPA with higher activity. Using a genome-editing approach we show that this causes an effective decrease in cyclin-B1 stability in the nucleus, thereby slowing its nuclear accumulation. By perturbing the rate of nuclear cyclin-B1 accumulation, rs11556924 alters the regulation of mitotic progression resulting in an extended mitosis. This study shows that the CAD-associated coding polymorphism in ZC3HC1 alters the dynamics of cell-cycle regulation by NIPA.

The presentation of mental disturbance in modern Scottish literature.

The subject of madness features throughout world literature, but the literature of modern Scotland appears to be especially preoccupied with it. This paper gives a brief overview of the ways in which madness is represented in modern Scottish literature and the different artistic functions it performs. It will consider the subject on a thematic basis. First, there are accounts by writers who have experienced mental turmoil themselves. Second, there is the theme of the 'Narrative of personal crisis' which depicts in fictional form an individual's journey through madness. Third, there is the theme of the 'Gothic or divided selves'. The fourth theme is that of the 'Female voice' and the last is that of 'Outsiders and holy fools', whose existence is to unsettle the beliefs of a wider society.

'We are all a little mad in one or other particular'. The presentation of madness in the novels of Muriel Spark.

This paper examines the presentation of madness in the novels of the great Scottish writer, Muriel Spark (1918-2006). In her work, there is a large cast of mad characters as well as a succession of psychiatrists and psychoanalysts. Spark suggests several explanations as to the origins of madness. We see mental disturbance conceived in terms of the supernatural, the religious and the Gothic. She also depicts insanity as a form of personality defect, eccentricity or mental enfeeblement. She drew on Romantic notions of the madman as a seer and speaker of truth. In her portrayal of psychiatrists, both the pill-prescribers and the psychoanalysts, Spark is frequently sceptical of the two: medication can erase positive qualities in an individual, and analysts can spout meaningless gibberish.

The madness of Gerard de Nerval.

This paper examines the madness of Gerard de Nerval, the nineteenth-century French writer. It looks at his account of mental disturbance, how he responded to the psychiatric profession and how he reacted to being diagnosed as insane. It considers his autobiographical novella of madness, Aurelia, which he began at the suggestion of his alienist, Dr Emile Blanche, and while he was still an asylum inmate. Nerval's story raises important questions about the nature of madness. Is it, as he contended, a mystical experience revealing truths about spiritual worlds inaccessible to the 'sane'? Does psychiatry fail to understand it and inappropriately reduce it to the categories of scientific reason? Or are such notions of the spiritual value of madness guilty of the charge that they romanticise insanity? Do they make extravagant claims for an experience that is often disturbing and debilitating? What is the relationship between madness and recovery? Should an individual try to forget their experience of mental disturbance once they recover, or should they examine what the event reveals about themselves? Can the language of madness be decoded to unveil profound truths as Carl Jung and R.D. Laing have suggested, or is it, as the psychiatrist German Berrios maintains, merely a series of 'empty speech acts', signifying nothing? And finally, how does one avoid writing about madness, and instead write madness?

Karl Jaspers' phenomenology in the light of histological and X-ray metaphors.

The study considers the origins of Karl Jaspers' phenomenology. What did phenomenology mean to Jaspers and what was his personal perspective? What metaphors did he associate with it? This paper describes his phenomenological method by using the metaphors of histology and the X-ray. This perspective enables a better understanding, not only of the origins and essence of his phenomenology but also of its value for Jaspers himself. In Jaspers' daily life, he would have been familiar with microscopes and X-ray machines.

'Groaning under the miseries of a diseased nervous System': Robert Burns and Melancholy.

Many currents in eighteenth-century Scotland--philosoph- ical, literary, medical and religious--served to influence how the poet, Robert Burns, understood his disturbed moods and how he described them in his poetry and letters. By tracking the chronology of his illness and the particular medical language he and his biographers drew upon in relation to the nervous theories current in Scotland and the cult of Romantic sensibility, this chapter examines how Burns' melancholy reflected and was related to the culture and historical period in which he lived.

A molecular dynamics study of C1r and C1s dimers: implications for the structure of the C1 complex.

Complement is an important part of the immune system. It is initiated through three different pathways known as the classical, lectin, and alternative pathway. The multimolecular C1 complex of the classical pathway consists of a subcomponent, C1q, which binds to a tetramer comprising two C1r and two C1s proteases. A detailed description of the structure of the C1 complex is essential to fully understand how the complex acts on pathogens. A variety of different models have been proposed, which differ mainly in the way the proteases interact with C1q. In this study, we have used a combination of homology-based structure prediction and molecular dynamics to predict a partial structure of the C1s/C1r/C1r/C1s tetramer. For computational expediency the study was restricted to the CUB(1) -EGF-CUB(2) domains which are directly involved in the formation of the tetramer and its interaction with C1q; the catalytic fragments (CCP(1) -CCP(2) -SP), which mediate C1 activation and subsequent cleavage of substrates, were omitted. A systematic molecular dynamics (MD) study of several possible dimeric combinations suggest that the tetramer is formed when a pair of C1r/C1s dimers form a "doughnut" via a C1s/C1s head-to-tail interaction, which is stabilized by several putative salt bridges at the dimer interface. This result is consistent with biochemical data which have shown that self assembly requires the formation of C1r-C1s contacts and that electrostatic interactions play a key role. Furthermore, it identifies a number of putative binding residues that can be tested using site-directed mutagenesis.

Optimization of Low-Biomass Sample Collection and Quantitative PCR-Based Titration Impact 16S rRNA Microbiome Resolution.

The major aquatic interface between host and environment in teleost finfish species is the gill. The diversity of this infraclass, high complexity of the organ, and its direct exposure to the surrounding environment make it an ideal candidate for furthering our understanding of the intertwined relationships between host and microbiome. Capturing the structure and diversity of bacterial communities from this low-biomass, inhibitor-rich tissue can, however, prove challenging. Lessons learned in doing so are directly applicable to similar sample types in other areas of microbiology. Through the development of a quantitative PCR assay for both host material and 16S rRNA genes, we tested and developed a robust method for low-biomass sample collection which minimized host DNA contamination. Quantification of 16S rRNA facilitated not only the screening of samples prior to costly library construction and sequencing but also the production of equicopy libraries based on 16S rRNA gene copies. A significant increase in diversity of bacteria captured was achieved, providing greater information on the true structure of the microbial community. Such findings offer important information for determining functional processes. Results were confirmed across fresh, brackish, and marine environs with four different fish species, with results showing broad homology between samples, demonstrating the robustness of the approach. Evidence presented is widely applicable to samples similar in composition, such as sputum or mucus, or those that are challenging due to the inherent inclusion of inhibitors. IMPORTANCE The interaction between the fish gill and surrounding bacteria-rich water provides an intriguing model for examining the interaction between the fish, free-floating bacteria, and the bacterial microbiome on the gill surface. Samples that are inherently low in bacteria, or that have components that inhibit the ability to produce libraries that identify the components of microbial communities, present significant challenges. Gill samples present both of these types of challenges. We developed methods for quantifying both the bacterial and host DNA material and established a sampling method which both reduced inhibitor content and maximized bacterial diversity. By quantifying and normalizing bacteria prior to library construction, we showed significant improvements with regards to the fidelity of the final data. Our results support wide-ranging applications for analyzing samples of similar composition, such as mucus and sputum, in other microbiological spheres.

"A bruised reed shall he not break": John Miles's portraits of patients at the Royal Edinburgh Asylum. Part 1.

This is the first of two papers which examine a series of portraits of patients at the Royal Edinburgh Asylum (REA) which were undertaken in the 1880s by John Miles, who, as well as being a professional painter, was also an inmate of the Morningside institution. The portraits by John Miles are of interest for several reasons. They are an example of patient art, only a small portion of which has survived from nineteenth century asylums. They are also in the tradition of patient portraiture. Miles's work is of interest because he was both a professional artist and a patient. His portraits also provide some insight into the patients' world: their appearance, demeanour, posture, clothing and their surroundings in the asylum. The patients in the portraits have been identified and their case notes examined. This information complements Miles's portraits and helps to build up a fuller picture of individual patients and their life in the Morningside Asylum. The case notes also reveal the symptomatology and behaviour of the patients. Alongside the portraits by Miles, we discuss a second series of portraits of the same patients and contained in a collection entitled 'Bruised Reeds'. We discuss if these portraits were also by Miles.

"A bruised reed shall he not break": John Miles's portraits of patients at the Royal Edinburgh Asylum. Part 2.

This is the second of two papers which examine a series of portraits of patients at the Royal Edinburgh Asylum (REA) which were undertaken in the 1880s by John Miles, who, as well as being a professional painter, was also an inmate of the Morningside institution. Alongside the portraits by Miles, we began, in Paper 1, to discuss a second series of portraits of the same patients, contained in a collection, entitled Bruised Reeds. In this paper we focus on the remaining portraits in this collection, before discussing the wider implications of the two series of portraits. These two series are of interest for several reasons. They are an example of patient art, only a small portion of which has survived from nineteenth century asylums. They are also in the tradition of patient portraiture. The patients in the portraits have been identified and their case notes examined. This information complements the portraits and helps to build a fuller picture of individual patients and their life in the Morningside Asylum. The case notes also reveal the symptomatology and behaviour of the patients. We discuss if the Bruised Reeds portraits were also by Miles, and suggest they were not.

Characterization of External Mucosal Microbiomes of Nile Tilapia and Grey Mullet Co-cultured in Semi-Intensive Pond Systems.

The external mucosal surfaces of the fish harbor complex microbial communities, which may play pivotal roles in the physiological, metabolic, and immunological status of the host. Currently, little is known about the composition and role of these communities, whether they are species and/or tissue specific and whether they reflect their surrounding environment. Co-culture of fish, a common practice in semi-intensive aquaculture, where different fish species cohabit in the same contained environment, is an easily accessible and informative model toward understanding such interactions. This study provides the first in-depth characterization of gill and skin microbiomes in co-cultured Nile tilapia (Oreochromis niloticus) and grey mullet (Mugil capito) in semi-intensive pond systems in Egypt using 16S rRNA gene-based amplicon sequencing. Results showed that the microbiome composition of the external surfaces of both species and pond water was dominated by the following bacterial phyla: Proteobacteria, Fusobacteriota, Firmicutes, Planctomycetota, Verrucomicrobiota, Bacteroidota, and Actinobacteriota. However, water microbial communities had the highest abundance and richness and significantly diverged from the external microbiome of both species; thus, the external autochthonous communities are not a passive reflection of their allochthonous communities. The autochthonous bacterial communities of the skin were distinct from those of the gill in both species, indicating that the external microbiome is likely organ specific. However, gill autochthonous communities were clearly species specific, whereas skin communities showed higher commonalities between both species. Core microbiome analysis identified the presence of shared core taxa between both species and pond water in addition to organ-specific taxa within and between the core community of each species. These core taxa included possibly beneficial genera such as Uncultured Pirellulaceae, Exiguobacterium, and Cetobacterium and opportunistic potential pathogens such as Aeromonas, Plesiomonas, and Vibrio. This study provides the first in-depth mapping of bacterial communities in this semi-intensive system that in turn provides a foundation for further studies toward enhancing the health and welfare of these cultured fish and ensuring sustainability.

The madness of King George III: a psychiatric re-assessment.

This research, based on a study of King George III's medical records and of contemporary diaries of his courtiers and equerries, further confirms the considerable doubt on the claim of Richard Hunter and Ida Macalpine that the King suffered from recurrent attacks of acute porphyria.The present study examines the above records from a psychiatric viewpoint, together with some additional reports, to re-assess the nature of the King's maladies. It concludes that he suffered from recurrent mania (four episodes), with chronic mania and possibly a degree of fatuity during the last decade of his life.This is in agreement with previous reports that he suffered from manic-depressive psychosis.

Rapid characterization of binding specificity and cross-reactivity of antibodies using recombinant human protein arrays.

Antibodies are routinely used as research tools, in diagnostic assays and increasingly as therapeutics. Ideally, these applications require antibodies with high sensitivity and specificity; however, many commercially available antibodies are limited in their use as they cross-react with non-related proteins. Here we describe a novel method to characterize antibody specificity. Six commercially available monoclonal and polyclonal antibodies were screened on high-density protein arrays comprising of ~10,000 recombinant human proteins (Imagenes). Two of the six antibodies examined; anti-pICln and anti-GAPDH, bound exclusively to their target antigen and showed no cross-reactivity with non-related proteins. However, four of the antibodies, anti-HSP90, anti-HSA, anti-bFGF and anti-Ro52, showed strong cross-reactivity with other proteins on the array. Antibody-antigen interactions were readily confirmed using Western immunoblotting. In addition, the redundant nature of the protein array used, enabled us to define the epitopic region within HSP90 of the anti-HSP90 antibody, and identify possible shared epitopes in cross-reacting proteins. In conclusion, high-density protein array technology is a fast and effective means for determining the specificity of antibodies and can be used to further improve the accuracy of antibody applications.

A novel approach to the history of medicine: a look at the relationship between fiction and medical history.

This paper examines the recent upsurge in novels concerned with the history of medicine. It selects a range of different novels and asks how they relate to the work of the professional medical historian. Do these novels stimulate interest in the history of medicine or do they distort historical events? It is concluded that although writers often take liberties with the historical record, on balance, their work helps us to engage with the past and is likely to inspire readers to find out more about the history of medicine.

Linked Mutations at Adjacent Nucleotides Have Shaped Human Population Differentiation and Protein Evolution.

Despite the fundamental importance of single nucleotide polymorphisms (SNPs) to human evolution, there are still large gaps in our understanding of the forces that shape their distribution across the genome. SNPs have been shown to not be distributed evenly, with directly adjacent SNPs found unusually frequently. Why this is the case is unclear. We illustrate how neighboring SNPs that cannot be explained by a single mutation event (that we term here sequential dinucleotide mutations [SDMs]) are driven by distinct processes to SNPs and multinucleotide polymorphisms (MNPs). By studying variation across populations, including a novel cohort of 1,358 Scottish genomes, we show that, SDMs are over twice as common as MNPs and like SNPs display distinct mutational spectra across populations. These biases are not only different to those observed among SNPs and MNPs but are also more divergent between human population groups. We show that the changes that make up SDMs are not independent and identify a distinct mutational profile, CA → CG → TG, that is observed an order of magnitude more often than expected from background SNP rates and the numbers of other SDMs involving the gain and deamination of CpG sites. Intriguingly particular pathways through the amino acid code appear to have been favored relative to that expected from intergenic SDM rates and the occurrences of coding SNPs, and in particular those that lead to the creation of single codon amino acids. We finally present evidence that epistatic selection has potentially disfavored sequential nonsynonymous changes in the human genome.

Examining the Impact of Imputation Errors on Fine-Mapping Using DNA Methylation QTL as a Model Trait.

Genetic variants disrupting DNA methylation at CpG dinucleotides (CpG-SNP) provide a set of known causal variants to serve as models to test fine-mapping methodology. We use 1716 CpG-SNPs to test three fine-mapping approaches (Bayesian imputation-based association mapping, Bayesian sparse linear mixed model, and the J-test), assessing the impact of imputation errors and the choice of reference panel by using both whole-genome sequence (WGS), and genotype array data on the same individuals (n = 1166). The choice of imputation reference panel had a strong effect on imputation accuracy, with the 1000 Genomes Project Phase 3 (1000G) reference panel (n = 2504 from 26 populations) giving a mean nonreference discordance rate between imputed and sequenced genotypes of 3.2% compared to 1.6% when using the Haplotype Reference Consortium (HRC) reference panel (n = 32,470 Europeans). These imputation errors had an impact on whether the CpG-SNP was included in the 95% credible set, with a difference of ∼23% and ∼7% between the WGS and the 1000G and HRC imputed datasets, respectively. All of the fine-mapping methods failed to reach the expected 95% coverage of the CpG-SNP. This is attributed to secondary cis genetic effects that are unable to be statistically separated from the CpG-SNP, and through a masking mechanism where the effect of the methylation disrupting allele at the CpG-SNP is hidden by the effect of a nearby SNP that has strong linkage disequilibrium with the CpG-SNP. The reduced accuracy in fine-mapping a known causal variant in a low-level biological trait with imputed genetic data has implications for the study of higher-order complex traits and disease.

An object-oriented programming system for the integration of internet-based bioinformatics resources.

The Internet consists of a vast inhomogeneous reservoir of data. Developing software that can integrate a wide variety of different data sources is a major challenge that must be addressed for the realisation of the full potential of the Internet as a scientific research tool. This article presents a semi-automated object-oriented programming system for integrating web-based resources. We demonstrate that the current Internet standards (HTML, CGI [common gateway interface], Java, etc.) can be exploited to develop a data retrieval system that scans existing web interfaces and then uses a set of rules to generate new Java code that can automatically retrieve data from the Web. The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data.