Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

New suburbia: designing in urban resilience by closing resource cycles

By utilising a research by design methodology, the paper develops a process-based and phased design to develop a new emergent form to these neighbourhoods, one in which new productive systems are embedded into the city, at a small-scales. These include a peak-load hydro-electric project in Ligoneal; a productive landscape in Glen Cairn and a city-wide energy refurbishment utilising neighbourhood waste streams.

The three projects illustrate different ways in which place-based solutions can enact urban transformation through a process of rigorous visualisation of process, and its attendant changes in content and form of the neighbourhood, These designs, based around a process-based strategy plan, allow for a roadmap for development to be created that could change the modus operandi of an area over a relatively short period of time,. The paper demonstrates that even modest investments of productive technologies at a local scale can fundamentally change the form and the economic and environmental operation of the city in the future, and create a new resilient city, one that can have resilience built-in. This resilience allows the neighbourhood to be less externally dependent on resources, economically active and more socially just.

MESAS

MESAS is an urban intervention that promotes the relationship with everyday sound through indispensable pieces of furniture for the domestic, the professional and the playful in our lives – the table. Different uses and contexts determine the many variations in form; from dinning, to coffee tables, kitchen, garden, meeting, bar, side or game tables. The MESAS project, by artists Pedro Rebelo and Ricardo Jacinto was conceived for Rua Direita in Viseu and consists of a sequence of tables suspended throughout the street, which reveal experiences and memories through sound. The materiality, context and utility of each table articulate sonorities that include the manipulation of objects on their tops or the conversations happening around them, as well their impact on the soundscapes of the places in which they are situated. The project makes audible these particular experiences through a set of sound installations associated with places such as the jewellery, the school, or the tailor’s.

'When I Land in Islamabad I Feel Home and When I Land in Heathrow I Feel Home': Gendered Belonging and Diasporic Identities of South Asian British Citizens in London, in Leicester and in North England

According to Deleuze and Guattari (1987) ‘de-territorialization’ is followed by a moment of re-territorialization. This moment, however, has to be regarded as a continuing educational process that becomes a different spatial site of social practices. It is argued in this chapter that regional, local as well as global identification override national and mono-ethno cultural identities, while shaping particular notions of gendered belonging and creating specific diasporic practices. Based on a sample of interviews with professional and academic South Asian British citizens in London, in Leicester, and in a number of Northern English cities gendered and generational patterns in terms of local diasporic identities are explored. Apart from multiple cultural belonging, foremost, territorial bonds and notions of group loyalty collapse at a point where temporary migration and settlement alternate in individual biographies.

Chromatin immunoprecipitation (ChIP) methodology and readouts

The identification of direct nuclear hormone receptor gene targets provides clues to their contribution to both development and cancer progression. Until recently, the identification of such direct target genes has relied on a combination of expression analysis and in silico searches for consensus binding motifs in gene promoters. Consensus binding motifs for transcription factors are often defined using in vitro DNA binding strategies. Such in vitro strategies fail to account for the many factors that contribute significantly to target selection by transcription factors in cells beyond the recognition of these short consensus DNA sequences. These factors include DNA methylation, chromatin structure, posttranslational modifications of transcription factors, and the cooperative recruitment of transcription factor complexes. Chromatin immunoprecipitation (ChIP) provides a means of isolating transcription factor complexes in the context of endogenous chromatin, allowing the identification of direct transcription factor targets. ChIP can be combined with site-specific PCR for candidate binding sites or alternatively with cloning, genomic microarrays or more recently direct high throughput sequencing to identify novel genomic targets. The application of ChIP-based approaches has redefined consensus binding motifs for transcription factors and provided important insights into transcription factor biology.

Using particle dispersal models to assist in the conservation and recovery of the overexploited native oyster (Ostrea edulis) in an enclosed sea lough

Oyster populations around the world have seen catastrophic decline which has been largely attributed to overexploitation, disease and pollution. While considerable effort and resources have been implemented into restoring these important environmental engineers, the success of oyster populations is often limited by poor understanding of site-specific dispersal patterns of propagules. Water-borne transport is a key factor controlling or regulating the dispersal of the larval stage of benthic marine invertebrates which have limited mobility. The distribution of the native oyster Ostrea edulis in Strangford Lough, Northern Ireland, together with their densities and population structure at subtidal and intertidal sites has been documented at irregular intervals between 1997 and 2013. This paper revisits this historical data and considers whether different prevailing environmental conditions can be used to explain the distribution, densities and population structure of O. edulis in Strangford Lough. The approach adopted involved comparing predictive 2D hydrodynamic models coupled with particle tracking to simulate the dispersal of oyster larvae with historical and recent field records of the distribution of both subtidal and intertidal, populations since 1995. Results from the models support the hypothesis that commercial stocks of O. edulis introduced into Strangford Lough in the 1990s resulted in the re-establishment of wild populations of oysters in the Northern Basin which in turn provided a potential source of propagules for subtidal populations. These results highlight that strategic site selection (while inadvertent in the case of the introduced population in 1995) for the re-introduction of important shellfish species can significantly accelerate their recovery and restoration.

Museum City - Improvisation and the narratives of space

This paper provides four viewpoints on the narratives of space, allowing us to think about possible relations between sites and sounds, reflecting on how places might tell stories, or how practitioners embed themselves in a place in order to shape cultural, social and/or political narratives through the use of sound. I propose four viewpoints that investigate the relationship between sites and sounds, where narratives are shaped and made through the exploration of specific sonic activities. These are:
- sonic activism
- sonic preservation
- sonic participatory action
- sonic narrative of space

I examine each of these ideas in turn before focusing in more detail on the final viewpoint, which provides the context for discussing and analysing a recent site-specific music improvisation project, entitled ‘Museum City’, a work that aligns closely with my proposal for a ‘sonic narrative of space’.
The work ‘Museum City’ by Pedro Rebelo, Franziska Schroeder, Ricardo Jacinto and André Cepeda specifically enables me to reflect on how derelict and/or transitional spaces might be re-examined through the use of sound, particularly through means of live music improvisation. The spaces examined as part ‘Museum City’ constitute either deserted sites or sites about to undergo changes in their architectural layout, their use and sonic make-up. The practice in ‘Museum City’ was born out of a performative engagement with[in] those sites, but specifically out of an intimate listening relationship by three improvisers situated within those spaces.
The theoretical grounding for this paper is situated within a wider context of practising and cognising musical spatiality, as proposed by Georgina Born (2013), particularly her proposition for three distinct lineages that provide an understanding of space in/and music. Born’s third lineage, which links more closely with practices of sound art and challenges a Euclidean orientation of pitch and timbre space, makes way for a heightened consideration of listening and ‘the place’ of sound. This lineage is particularly crucial for my discussion, since it positions music in relation to social experiences and the everyday, which the work ‘Museum City’ endeavoured to embrace.

Ischemic A/D transition of mitochondrial complex I and its role in ROS generation

Mitochondrial complex I (NADH:ubiquinone oxidoreductase) is a key enzyme in cellular energy metabolism and provides approximately 40% of the proton-motive force that is utilized during mitochondrial ATP production. The dysregulation of complex I function – either genetically, pharmacologically, or metabolically induced – has severe pathophysiological consequences that often involve an imbalance in the production of reactive oxygen species (ROS). Slow transition of the active (A) enzyme to the deactive, dormant (D) form takes place during ischemia in metabolically active organs such as the heart and brain. The reactivation of complex I occurs upon reoxygenation of ischemic tissue, a process that is usually accompanied by an increase in cellular ROS production. Complex I in the D-form serves as a protective mechanism preventing the oxidative burst upon reperfusion. Conversely, however, the D-form is more vulnerable to oxidative/nitrosative damage. Understanding the so-called active/deactive (A/D) transition may contribute to the development of new therapeutic interventions for conditions like stroke, cardiac infarction, and other ischemia-associated pathologies. In this review, we summarize current knowledge on the mechanism of A/D transition of mitochondrial complex I considering recently available structural data and site-specific labeling experiments. In addition, this review discusses in detail the impact of the A/D transition on ROS production by complex I and the S-nitrosation of a critical cysteine residue of subunit ND3 as a strategy to prevent oxidative damage and tissue damage during ischemia–reperfusion injury.

The neoliberalisation of the Cathedral Quarter and its contestations

Over time Belfast has been well researched as a site of ethnosectarian conflict, segregation and fear see (Boal et al 1976) and (Gaffiken and Morrisey 2011). The study of socio-spatial patterns of ‘ethnocracy’ is useful, but this article will argue how it is equally important to understand local forms of urban restructuring in terms of global processes that are linked to neoliberalism. To better understand the neoliberal urbanisation of Belfast this article is organised into two parts. The first part will demonstrate how the Northern Ireland State has sought legitimacy in the free market as ‘therapy’ for the production of neutral socio-spatial formations such as the Cathedral Quarter. Secondly it will examine this performance of neoliberal urbanism, as it ‘actually exists’ and demonstrate how market-led renewal has been extended through the clustering and non-sectarian interests, ‘soft’ arrangements of urban governance, cultural re-branding strategies, economic development incentives, and the development of various flagship projects. Critically this place-based grounding of neoliberalism is useful, as it also allows for the contestations of neoliberal urbanism to become real rather than just theoretical. The second part of the article will draw attention to the responses of local, and sometimes marginal, interests that have looked to challenge, adapt and, at times, divert the extension of market-led renewal. To be clear, this article does not want to overstate the performance of such interests. Nor does it want to claim that they significantly impact or obstruct the wider neoliberal urbanisation of Belfast. Instead it is interested in their behaviours and their different methods of working to explore what may be constituted as ‘alternative’, at least in the locality of the Cathedral Quarter. By studying how and why these interests have responded to the extension of neoliberal urbanism over time, it may just be possible to provide a better platform to articulate what more progressive forms of urban resistance might look like.

Quantification of the smoking-associated cancer risk with rate advancement periods: meta-analysis of individual participant data from cohorts of the CHANCES consortium

BACKGROUND: Smoking is the most important individual risk factor for many cancer sites but its association with breast and prostate cancer is not entirely clear. Rate advancement periods (RAPs) may enhance communication of smoking related risk to the general population. Thus, we estimated RAPs for the association of smoking exposure (smoking status, time since smoking cessation, smoking intensity, and duration) with total and site-specific (lung, breast, colorectal, prostate, gastric, head and neck, and pancreatic) cancer incidence and mortality.

METHODS: This is a meta-analysis of 19 population-based prospective cohort studies with individual participant data for 897,021 European and American adults. For each cohort we calculated hazard ratios (HRs) for the association of smoking exposure with cancer outcomes using Cox regression adjusted for a common set of the most important potential confounding variables. RAPs (in years) were calculated as the ratio of the logarithms of the HRs for a given smoking exposure variable and age. Meta-analyses were employed to summarize cohort-specific HRs and RAPs.

RESULTS: Overall, 140,205 subjects had a first incident cancer, and 53,164 died from cancer, during an average follow-up of 12 years. Current smoking advanced the overall risk of developing and dying from cancer by eight and ten years, respectively, compared with never smokers. The greatest advancements in cancer risk and mortality were seen for lung cancer and the least for breast cancer. Smoking cessation was statistically significantly associated with delays in the risk of cancer development and mortality compared with continued smoking.

CONCLUSIONS: This investigation shows that smoking, even among older adults, considerably advances, and cessation delays, the risk of developing and dying from cancer. These findings may be helpful in more effectively communicating the harmful effects of smoking and the beneficial effect of smoking cessation.