Sequence and Structure Based Protein Folding Studies With Implications

As the expression of the genetic blueprint, proteins are at the heart of all biological systems. The ever increasing set of available protein structures has taught us that diversity is the hallmark of their architecture, a fundamental characteristic that enables them to perform the vast array of functionality upon which all of life depends. This diversity, however, is central to one of the most challenging problems in molecular biology: how does a folding polypeptide chain navigate its way through all of the myriad of possible conformations to find its own particular biologically active form? With few overarching structural principles to draw upon that can be applied to all protein architecture, the search for a solution to the protein folding problem has yet to produce an algorithm that can explain and duplicate this fundamental biological process. In this thesis, we take a two-pronged approach for investigating the protein folding process. Our initial statistical studies of the distributions of hydrophobic and hydrophilic residues within α-helices and β-sheets suggest (i) that hydrophobicity plays a critical role in helix and sheet formation; and (ii) that the nucleation of these motifs may result in largely unidirectional growth. Most tellingly, from an examination of the amino acids found in the smallest β-sheets, we do not find any evidence of a β-nucleating code in the primary protein sequence. Complementing these statistical analyses, we have analyzed the structural environments of several ever-widening aspects of protein topology. Our examination of the gaps between strands in the smallest β-sheets reveals a common organizational principle underlying β-formation involving strands separated by large sequential gaps: with very few exceptions, these large gaps fold into single, compact structural modules, bringing the β-strands that are otherwise far apart in the sequence close together in space. We conclude, therefore, that β-nucleation in the smallest sheets results from the co-location of two strands that are either local in sequence, or local in space following prior folding events. A second study of larger β-sheets both corroborates and extends these findings: virtually all large sequential gaps between pairs of β-strands organize themselves into an hierarchical arrangement, creating a bread-crumb model of go-and-come-back structural organization that ultimately juxtaposes two strands of a parental β-structure that are far apart in the sequence in close spatial proximity. In a final study, we have formalized this go-and-come-back notion into the concept of anti-parallel double-strandedness (DS), and measure this property across protein architecture in general. With over 90% of all residues in a large, non-redundant set of protein structures classified as DS, we conclude that DS is a unifying structural principle that underpins all globular proteins. We postulate, moreover, that this one simple principle, anti-parallel double-strandedness, unites protein structure, protein folding and protein evolution.

Visual functioning and quality of life in the subfoveal radiotherapy study (SFRADS): SFRADS report 2

Aims: To determine whether or not self reported visual functioning and quality of life in patients with choroidal neovascularisation caused by age related macular degeneration (AMD) is better in those treated with 12 Gy external beam radiotherapy in comparison with untreated subjects. Methods: A multicentre single masked randomised controlled trial of 12 Gy of external beam radiation therapy (EBRT) delivered as 6x2 Gy fractions to the macula of an affected eye versus observation. Patients with AMD, aged 60 years or over, in three UK hospital units, who had subfoveal CNV and a visual acuity equal to or better than 6/60 (logMAR 1.0). Methods: Data from 199 eligible participants who were randomly assigned to 12 Gy teletherapy or observation were available for analysis. Visual function assessment, ophthalmic examination, and fundus fluorescein angiography were undertaken at baseline and at 3, 6, 12, and 24 months after study entry. To assess patient centred outcomes, subjects were asked to complete the Daily Living Tasks Dependent on Vision (DLTV) and the SF-36 questionnaires at baseline, 6, 12, and 24 months after enrolment to the study. Cross sectional and longitudinal analyses were conducted using arm of study as grouping variable. Regression analysis was employed to adjust for the effect of baseline co-variates on outcome at 12 months and 24 months. Results: Both control and treated subjects had significant losses in visual functioning as seen by a progressive decline in mean scores in the four dimensions of the DLTV. There were no statistically significant differences between treatment and control subjects in any of dimensions of the DLTV at 12 months or 24 months after study entry. Regression analysis confirmed that treatment status had no effect on the change in DLTV dimensional scores. Conclusions: The small benefits noted in clinical measures of vision in treated eyes did not translate into better self reported visual functioning in patients who received treatment when compared with the control arm. These findings have implications for the design of future clinical trials and studies.

The ABC for Life Programme - Teaching Basic Life Support in Schools

Background Less than 1% of the general public know how to assess or manage someone who has collapsed. It has been estimated that if 15–20% of the population were capable of performing cardiopulmonary resuscitation (CPR), mortality of out of hospital cardiac arrest could be decreased significantly. Training basic life support (BLS) skills to school children would be the most cost effective way of achieving this goal and ensuring that a large proportion of the population acquire basic life saving skills. Aims To assess retention of knowledge of basic life support 6 months after a single course of instruction in cardiopulmonary resuscitation designed specifically for school children. Setting School pupils in a rural location in one region of the United Kingdom. Methods A course of instruction in cardiopulmonary resuscitation – the ‘ABC for life’ programme – specifically designed to teach 10–12-year-old school children basic life support skills. The training session was given to school pupils in a rural location in Northern Ireland. A 22 point questionnaire was used to assess acquisition and retention of basic life support knowledge. Results Children instructed in cardiopulmonary resuscitation showed a highly significant increase in level of knowledge following the training session. While their level of knowledge decreased over a period of 6 months it remained significantly higher than that of a comparable group of children who had never been trained. Conclusion A training programme designed and taught as part of the school curriculum would have a significant impact on public health.

Pupil participation in school life: an approach from the educational community

The Convention on the Rights of the Child (CRC, 1989) is currently the most ratified international treaty. Several authors have highlighted its potential for both a moral education and citizenship. However, paradoxically, different studies report its limited or occasional incorporation into school practices. This article explores experiences of participation in schools,the third P of the CRC, from the plurality of voices and actors of the educational community,by means of 14 discussion groups in 11 autonomous communities in Spain. Discourse analysis evidence low levels of student participation in school life. But, at the same time, a favorable educational environment for the development of projects that contribute to child participation is found, as well as for the incorporation of the CRC as a mover and a referential integrator of the different schools projects. However, it is also an educational background conductive to projects for its development, such as the incorporation of the CRC as a referential integrator of the schools projects.

A measure of satisfaction with food-related life

A measure of satisfaction with food-related life is developed and tested in three studies in eight European countries. Five items are retained from an original pool of seven; these items exhibit good reliability as measured by Cronbach's alpha, good temporal stability, convergent validity with two related measures, and construct validity as indicated by relationships with other indicators of quality of life, including the Satisfaction With Life and the SF-8 scales. It is concluded that this scale will be useful in studies trying to identify factors contributing to satisfaction with food-related life.

The nonformative elements of religious life: questioning the ‘sociology of spirituality’ paradigm

Sociological assertions of religious vitality in Euro-American societies have developed a paradigm of spirituality in which, following earlier studies of the New Age, a distinction is drawn between external authority and self-authority. Methodologically and theoretically problematic, this paradigm diverts attention from people’s social practices and interactions, especially in relation to multiple religious authorities. Drawing upon ethnographic fieldwork with an English religious network, and building upon the work of Pierre Bourdieu, this paper considers situations in which multiple authorities tend to relativize each other. Conceptualizing this in terms of nonformativeness - the lack of authorities’ abilities formatively to shape religious identity, habitus, and competition over religious capital - a new understanding of individual secularization emerges that questions assertions of vitality.

From stress to distress: Conceptualizing the British family farming patriarchal way of life

‘Rural stress’ and ‘farming stress’ are terms that have become commonly appropriated by British health-based academic disciplines, the medical profession and social support networks, especially since the agricultural ‘crises’ of B.S.E. and Foot and Mouth Disease. Looking beyond the media headlines, it is apparent that the terms in fact are colloquial catch-alls for visible psychological and physiological outcomes shown by individuals. Seldom have the underlying causes and origins of presentable medical outcomes been probed, particularly within the context of the patriarchal and traditionally patrilineal way of life which family forms of farming business activity in Britain encapsulate. Thus, this paper argues that insufficient attention has been paid to the conceptualization of the terms. They have become both over-used and ill-defined in their application to British family farm individuals and their life situations. A conceptual framework is outlined that attempts to shift the stress research agenda into the unilluminated spaces of the family farming ‘way of life’ and focus instead on ‘distress’. Drawing upon theorization from agricultural and feminist geography together with cultural approaches from rural geography, four distinct clusters of distress originate from the thoughts of individuals and the social practices now required to enact patriarchal family farming gender identities. These are explored using case study evidence from ethnographic repeated life history interviews with members of seven farming families in Powys, Mid Wales, an area dominated by family forms of farming business. Future research agendas need to be based firmly on the distressing reality of patriarchal family farming and also be inclusive of those who, having rejected the associated way of life, now lie beyond the farm gate.

Vis-á-Vis-á-Vis. The Three-dimensional and artistic view of a problem

ANPO (A Non-predefined Outcome) is an an art-making methodology that employs structuralist theory of language (Saussure, Lacan, Foucault) combined with Hegel’s dialectic and the theory of creation of space by Lefebvre to generate spaces of dialogue and conversation between community members and different stakeholders. These theories of language are used to find artistic ways of representing a topic that community members have previously chosen. The topic is approached in a way that allows a visual, aural, performative and gustative form. To achieve this, the methodology is split in four main steps: step 1 ‘This is not a chair’, Step 2 ‘The topic’, Step 3 ‘ Vis-á-vis-á-vis’ and step 4. ‘Dialectical representation’ where the defined topic is used to generate artistic representations.The step 1 is a warm up exercise informed by the Rene Magritte painting ‘This is not a Pipe’. This exercise aims to help the participants to see an object as something else than an object but as a consequence of social implications. Step 2, participants choose a random topic and vote for it. The artist/facilitator does not predetermine the topic, participants are the one who propose it and choose it. Step 3, will be analysed in this publication and finally step 4, the broken down topic is taken to be represented and analysed in different ways. 

Response shift in the assessment of quality of life among people attending cardiac rehabilitation

Objectives: To examine whether any response shift in quality of life assessment over the course of a cardiac rehabilitation programme could be explained by changes in individuals’ internal standards (recalibration), values (reprioritization) and/or conceptualization of quality of life and the extent to which any response shift could be explained by health locus of control, optimism and coping strategy. Design: Longitudinal survey design. Methods: The SEIQoL-DW was administered at the beginning and end of a cardiac rehabilitation programme. At the end of the programme, the SEIQoL-DW then-test was also administered to measure response shift. A total of 57 participants completed these measures and other measures to assess health locus of control, optimism and coping. Results: Response shift effects were observed in this population mainly due to recalibration. When response shift was incorporated into the analysis of QoL a larger treatment effect was observed. Active coping as a mechanism in the response shift model was found to have a significant positive correlation with response shift. Conclusion: This study showed that response shift occurs during cardiac rehabilitation. The occurrence of response shift in QoL ratings over time for this population could have implications for the estimation of the effectiveness of the intervention.

Limits of life in hostile environments: no barriers to biosphere function?

Environments that are hostile to life are characterized by reduced microbial activity which results in poor soil- and plant-health, low biomass and biodiversity, and feeble ecosystem development. Whereas the functional biosphere may primarily be constrained by water activity (a w) the mechanism(s) by which this occurs have not been fully elucidated. Remarkably we found that, for diverse species of xerophilic fungi at a w values of = 0.72, water activity per se did not limit cellular function. We provide evidence that chaotropic activity determined their biotic window, and obtained mycelial growth at water activities as low as 0.647 (below that recorded for any microbial species) by addition of compounds that reduced the net chaotropicity. Unexpectedly we found that some fungi grew optimally under chaotropic conditions, providing evidence for a previously uncharacterized class of extremophilic microbes. Further studies to elucidate the way in which solute activities interact to determine the limits of life may lead to enhanced biotechnological processes, and increased productivity of agricultural and natural ecosystems in arid and semiarid regions.

Devotional Culture in Late Medieval England and Europe: Diverse Imaginations of Christ’s Life

Christ’s life, as related through the Gospel narratives and early Apocrypha, was subject to a riot of literary-devotional adaptation in the medieval period. This collection provides a series of groundbreaking studies centring on the devotional and cultural significance of Christianity’s pivotal story during the Middle Ages.

The collection represents an important milestone in terms of mapping the meditative modes of piety that characterize a number of Christological traditions, including the Meditationes vitae Christi and the numerous versions it spawned in both Latin and the vernacular. A number of chapters in the volume track how and why meditative piety grew in popularity to become a mode of spiritual activity advised not only to recluses and cenobites as in the writings of Aelred of Rievaulx, but also reached out to diverse lay audiences through the pastoral regimens prescribed by devotional authors such as the Carthusian prior Nicholas Love in England and the Parisian theologian and chancellor of the University of Paris, Jean Gerson.

Through exploring these texts from a variety of perspectives — theoretical, codicological, theological — and through tracing their complex lines of dissemination in ideological and material terms, this collection promises to be invaluable to students and scholars of medieval religious and literary culture.

The Creative Life of Law: Improvisation, Between Tradition and Suspicion

Originally applying solely to chefs, waiters, dishwashers and the like, New York City (NYC) regulations governing cabaret employees were altered in 1943 to include musicians and entertainers, who until the late 1960’s would be required to hold a NYC Cabaret Employee’s Identification Card. The introduction of these notorious “police cards” occurred roughly contemporaneously to the emergence in after-hours night clubs in Harlem of a new and supposedly “wild”, improvisatory brand of jazz: bebop. This article adds to the many rather practical theories on why these cards were introduced a more abstract discussion coined in terms of the relationship between suspicion and tradition and focusing on differing essences of law and improvisatory jazz. While law breathes tradition and is suspicious of improvisation and unpredictability, the converse is true of jazz. Allusion to tradition in jazz improvisation is often viewed as a betrayal of its creative and spontaneous nature. And yet it is only through its departure from the stable transmission of past meaning that improvisation gains meaning. Law, in contrast, while appearing to be entirely composed of tradition, to transmit some sort of determinate and fixed meaning, is constantly betraying itself. As no two legal actions can be exactly the same, judges must improvise on tradition and past precedent every time they are asked to decide a case. Law can thus neither dispense with nor be completely determined by tradition. The legal decision instead lies on the border between what it “is” and what it otherwise could be and every judicial act is, in some sense, a species of improvisation. This article uses the cabaret cards to explore this uncertain terrain between law and improvisation, between tradition and suspicion.

Reading the Irishwoman: Studies in Cultural Encounter and Exchange, 1714-1960

In 1700 few Irishwomen were literate. Most lived in a rural environment, rarely encountered a book or a play or ventured much beyond their own domestic space. By 1960 literacy was universal, all Irishwomen attended primary school, had access to a variety of books, magazines, newspapers and other forms of popular media and the wider world was now part of their every-day life. This study seeks to examine the cultural encounters and exchanges inherent in this transformation. It analyses reading and popular and consumer culture as sites of negotiation of gender roles. This is not an exhaustive treatment of the theme but focusses on three key points of cultural encounter: the Enlightenment, emigration and modernism. The writings and intellectual discourse generated by the Enlightenment was one of the most influential forces shaping western society. It set the agenda for scientific, political and social thought for the eighteenth and nineteenth centuries. The migration of peoples to north America was another key historical marker in the development of the modern world. Emigration altered and shaped American society as well as the lives of those who remained behind. By the twentieth century, aesthetic modernism suspicious of enlightenment rationalism and determined to produce new cultural forms developed in a complex relationship with the forces of industrialisation, urbanisation and social change. This study analyses the impact of these three key forces in Western culture on changing roles and perceptions of Irish women from 1700 to 1960.