• An introduction to Phylogenetic Path Analysis

      Gonzalez-Voyer, A.; von Hardenberg, Achaz; Estación Biológica de Doñana, Gran Paradiso National Park (Springer Verlag, 2014)
      The questions addressed by macroevolutionary biologists are often impervious to experimental approaches, and alternative methods have to be adopted. The phy- logenetic comparative approach is a very powerful one since it combines a large number of species and thus spans long periods of evolutionary change. However, there are limits to the inferences that can be drawn from the results, in part due to the limitations of the most commonly employed analytical methods. In this chapter, we show how confirmatory path analysis can be undertaken explicitly controlling for non-independence due to shared ancestry. The phylogenetic path analysis method we present allows researchers to move beyond the estimation of direct effects and analyze the relative importance of alternative causal models including direct and indirect paths of influence among variables. We begin the chapter with a general introduction to path analysis and then present a step-by-step guide to phylogenetic path analysis using the d-separation method. We also show how the known statistical problems associated with non-independence of data points due to shared ancestry become compounded in path analysis. We finish with a discussion about the potential effects of collinearity and measurement error, and a look toward possible future developments.
    • An investigation into the numerical determinants of secondary sex ratio

      Lewis, Stephen J.; Glenn, Janine; Chester College of Higher Education (2000)
      Data from the North Wales parishes of Hawarden and Northop were found previously to show seasonality for birth rate. In keeping with values reported in other studies, the annual secondary sex ratio of 105.3% was found. This sex ratio was also found to vary throughout the year in a cyclical way with a peak occuring in late summer. When male and female birth rates were investigated separately, it was found that females showed a more pronounced cyclicity than males with the peaks for both sexes occuring in the spring. A significant negative correlation between sex ratio at birth and mean day lenght (hours between sunrise and sunset) of the putative month of conception was observed. Sex ratio is a useful but derived parameter and has no independant existence upon which natural selection can be said to exert a direct influence. Therefore, the behaviour of the determinants of sex ratio should not be overlooked.
    • An investigation to determine the nutritional adequacy and individuals experience of a very low fat diet used to treat type V hypertriglyceridaemia

      Whitfield-Brown, Louisa M.; Hamer, O.; Ellahi, Basma; Burden, Sorrel; Durrington, Paul; University of Chester ; Manchester Royal Infirmary ; University of Chester ; Manchester Royal Infirmary ; University of Manchester (Wiley, 2009-05-15)
      This article discusses a study of eight patients with type V hypertriglyceridaemia on a low fat diet. The nutritional adequact of the diet and the barriers and enablers to adherence were analysed.
    • Involvement of recreational anglers in the eradication of alien brook trout from high altitude lakes

      Tiberti, Rocco; Ottino, Michelle; Brighenti, Stefano; Iacobuzio, Rocco; Rolla, Matteo; von Hardenberg, Achaz; Bassano, Bruno; Gran Paradiso National Park, University of Pavia, Università degli studi di Trento, Fondazione E. Mach, Università degli Studi di Milano, Swansea University, University of Chester (Gran Paradiso National Park Agency, 2017)
      Stocking programmes for recreational angling are primarily responsible for the spread and ecological impact of introduced sh in high-altitude, originally shless lakes. In 2013, the Gran Paradiso National Park started an eradication campaign of brook trout by intensive gill-netting. Local anglers were invited to attend two angling sessions to start the eradication before gill-netting in an experimental lake, as part of an education action devoted to these critical stakeholders. The angling sessions turned out to be a valuable help for the eradication campaign and the aim of this study is to report on the outcomes of these angling sessions. Angling techniques were highly size-selective, removing a substantial part of the adult population and of the sh biomass, but their contribution to the eradication of small sh (<15cm) was irrelevant. Therefore, angling cannot completely eradicate age-structured populations. However, there is scope to use angling sessions as a support for eradication campaigns and as an emergency measure for recent sh introduc- tions. Similar actions should be considered whenever a sh eradication programme is planned. These ndings, however, do not imply a general endorsement for angling within protected areas.
    • Is cortisol a reliable indicator of primate well-being?

      Skyner, Lindsay J.; Smith, Tessa E.; University of Chester (Primate Society of Great Britain, 2006-06)
    • Is Wounding Aggression in Zoo-housed Chimpanzees and Ring-tailed Lemurs related to Zoo Visitor Numbers?

      Hosey, Geoff; Melfi, Vicky; Formella, Isabel; Ward, Samantha J.; Tokarski, Marina; Brunger, Dave; Brice, Sara; Hill, Sonya P.; University of Bolton; Taronga Zoo; South Lakes Wild Animal Park; Nottingham Trent University; Chester Zoo; University of Chester (Wiley, 2016-02-29)
      Chimpanzees in laboratory colonies experience more wounds on week days than on weekends, which has been attributed to the increased number of people present during the week; thus the presence of more people was interpreted as stressful. If this were also true for primates in zoos, where high human presence is a regular feature, this would clearly be of concern. Here we examine wounding rates in two primate species (chimpanzees Pan troglodytes and ring-tailed lemurs Lemur catta) at three different zoos, to determine whether they correlate with mean number of visitors to the zoo. Wounding data were obtained from zoo electronic record keeping system (ZIMS™). The pattern of wounds did not correlate with mean gate numbers for those days for either species in any group. We conclude that there is no evidence that high visitor numbers result in increased woundings in these two species when housed in zoos.
    • Isoform-specific Ras signaling is growth factor dependent

      Hood, Fiona E.; Klinger, Bertram; Newlaczyl, Anna U.; Sieber, Anja; Dorel, Mathurin; Oliver, Simon P.; Coulson, Judy M.; Bluthgen, Nils; Prior, Ian A.; University of Liverpool; Universitätsmedizin Berlin; University of Chester (ASCB, 2019-04-11)
      HRAS, NRAS and KRAS isoforms are almost identical proteins that are ubiquitously expressed and activate a common set of effectors. In vivo studies have revealed that they are not biologically redundant; however, the isoform-specificity of Ras signaling remains poorly understood. Using a novel panel of isogenic SW48 cell lines endogenously expressing wild type or G12V mutated activated Ras isoforms we have performed a detailed characterization of endogenous isoform-specific mutant Ras signaling. We find that despite displaying significant Ras activation, the downstream outputs of oncogenic Ras mutants are minimal in the absence of growth factor inputs. The lack of mutant KRAS-induced effector activation observed in SW48 cells appears to be representative of a broad panel of colon cancer cell lines harboring mutant KRAS. For MAP kinase pathway activation in KRAS mutant cells, the requirement for co-incident growth factor stimulation occurs at an early point in the Raf activation cycle. Finally, we find that Ras isoform-specific signaling was highly context dependent and did not conform to the dogma derived from ectopic expression studies.
    • Killer cell Immunoglobulin-like Receptor 3DL1 polymorphism defines distinct hierarchies of HLA class I recognition

      Saunders, Philippa M.; Pymm, Phillip; Pietra, Gabriella; Hughes, Victoria A.; Hitchen, Corinne; O'Connor, Geraldine M.; Loiacono, Fabrizio; Widjaja, Jacqueline M.; Price, David A.; Falco, Michela; et al. (Rockefeller University Press, 2016-04-04)
      NK cells play a key role in immunity, but how HLA-I and KIR3DL1 polymorphism impacts on disease outcome remains unclear. KIR3DL1 (*001/*005/*015) tetramers were screened for reactivity against a panel of HLA-I molecules. This revealed different and distinct hierarchies of specificity for each KIR3DL1 allotype, with KIR3DL1*005 recognising the widest array of HLA-I ligands. These differences were further reflected in unctional studies utilising NK clones expressing these specific KIR3DL1 allotypes. Unexpectedly, the Ile/Thr80 dimorphism in the Bw4-motif did not categorically define strong/weak KIR3DL1 recognition. Although the KIR3DL1*001, *005 and *015 polymorphisms are remote from the KIR3DL1-HLA-I interface, the structures of these three KIR3DL1-HLA-I complexes showed that the broader HLA-I specificity of KIR3DL1*005 correlated with an altered KIR3DL1*005 interdomain positioning and increased mobility within its ligand-binding site. Collectively, we provide a generic framework for understanding the impact of KIR3DL1 polymorphism on the recognition of HLA-I allomorphs.
    • Laterality of hand function in naturalistically housed chimpanzees

      Fletcher, Alison W.; Weghorst, Jennifer A.; University College Chester ; Washington University (Psychology Press, 2005-05)
      Studies of laterality of hand function in chimpanzees ( Pan troglodytes ) have the potential to tell us about the origins of handedness in Homo sapiens . However, the data are confusing, with discrepancies present between studies done in the field and the laboratory: the former show wild chimpanzees to be unlateralised at the population level, while the latter show captive chimpanzees as lateralised at the population level. This study of 26 semi-free ranging chimpanzees of Chester Zoo, UK, aimed to investigate a situation between the wild and captivity and provided ethological data for 43 categories of spontaneous manual use and 14 categories of tool use. Other variables recorded were subordinate hand activity, whether the subject was arboreal or terrestrial, and the identity of the subject. Using switching focal subject sampling, 23,978 bouts of hand use and 1,090 bouts of tool use were recorded. No population-level handedness was present for manual non-tool use activities in the naturalistically housed chimpanzees of Chester Zoo in a similar way to studies of wild chimpanzees. However, about half of the individuals were lateralised to one side or the other for the foraging behaviours of pick up , eat , and pluck . Using a modified version of McGrew and Marchant's (1997) Laterality Framework, these results are comparable to some wild and captive populations for similar foraging tasks. Bimanuality was rare and thus prevented comparison with captive experimental studies that have reported population right handedness. Behaviour involving contact with water elicited stronger lateralisation. Chester chimpanzees were more likely to exhibit hand preferences for manual tasks with increasing age but there were no effects of sex or rearing history on hand specialisations in adult individuals. Lateralisation was biased in tool use, which evoked significant left hand preferences in half the individuals, with no effect of age. Results are discussed.
    • "Learning to speak horse": The culture of "natural horsemanship"

      Birke, Lynda; University of Chester (Brill, 2007-01-01)
      This journal article discusses the rise of "natural horsemanship" as a definitive cultural change within the horse industry.
    • Lentiviral hematopoietic stem cell gene therapy for X-linked severe combined immunodeficiency

      De Ravin, Suk S.; Wu, Xiaolin; Moir, Susan; Anaya-O'Brien, Sandra; Kwatemaa, Nana; Littel, Patricia; Theobald, Narda; Choi, Uimook; Su, Ling; Marquesen, Martha; et al. (American Association for the Advancement of Science, 2016-04-20)
      X-linked severe combined immunodeficiency (SCID-X1) is a profound deficiency of T, B, and natural killer (NK) cell immunity caused by mutations inIL2RGencoding the common chain (gammac) of several interleukin receptors. Gamma-retroviral (gammaRV) gene therapy of SCID-X1 infants without conditioning restores T cell immunity without B or NK cell correction, but similar treatment fails in older SCID-X1 children. We used a lentiviral gene therapy approach to treat five SCID-X1 patients with persistent immune dysfunction despite haploidentical hematopoietic stem cell (HSC) transplant in infancy. Follow-up data from two older patients demonstrate that lentiviral vector gammac transduced autologous HSC gene therapy after nonmyeloablative busulfan conditioning achieves selective expansion of gene-marked T, NK, and B cells, which is associated with sustained restoration of humoral responses to immunization and clinical improvement at 2 to 3 years after treatment. Similar gene marking levels have been achieved in three younger patients, albeit with only 6 to 9 months of follow-up. Lentiviral gene therapy with reduced-intensity conditioning appears safe and can restore humoral immune function to posthaploidentical transplant older patients with SCID-X1.
    • The life and works of Emily Dix, 1904-1972

      Burek, Cynthia V.; Cleal, C. (Geological Society, 2005-04-01)
      This book chapter discusses the life and career of the British palaeobotanist Emily Dix (1904-1972).
    • Lipid remodelling in the reef-building honeycomb worm, Sabellaria alveolata, reflects acclimation and local adaptation to temperature

      Muir, Anna P.; Nunes, Flavia L. D.; Dubois, Stanislas F.; Pernet, Fabrice; University of Chester; Ifremer Centre Bretagne; Ifremer Centre Bretagne; Ifremer Centre Bretagne (Nature Publishing Group, 2016-10-20)
      Acclimation and adaptation, which are key to species survival in a changing climate, can be observed in terms of membrane lipid composition. Remodelling membrane lipids, via homeoviscous adaptation (HVA), counteracts membrane dysfunction due to temperature in poikilotherms. In order to assess the potential for acclimation and adaptation in the honeycomb worm, Sabellaria alveolata, a reefbuilding polychaete that supports high biodiversity, we carried out common-garden experiments using individuals from along its latitudinal range. Individuals were exposed to a stepwise temperature increase from 15 °C to 25 °C and membrane lipid composition assessed. Our results suggest that S. alveolata was able to acclimate to higher temperatures, as observed by a decrease in unsaturation index and 20:5n-3. However, over the long-term at 25 °C, lipid composition patterns are not consistent with HVA expectations and suggest a stress response. Furthermore, unsaturation index of individuals from the two coldest sites were higher than those from the two warmest sites, with individuals from the thermally intermediate site being in-between, likely reflecting local adaptation to temperature. Therefore, lipid remodelling appears limited at the highest temperatures in S. alveolata, suggesting that individuals inhabiting warm environments may be close to their upper thermal tolerance limits and at risk in a changing climate.
    • Literature and science: Social impact and interaction

      Cartwright, John H.; Baker, Brian; University of Chester (ABC-CLIO, 2005-07-31)
      This book discusses the complex relationship between science and literature from Dante and Chaucer through to the twenty-first century. It focuses on science and literature in medieval times, the Elizabethan Renaissance, the seventeenth and eighteenth centuries, nineteenth-century British and American literature and science, themes in science fiction, and the twentieth-century.
    • Llandudno trail questionnaire and workshop

      Tilson, Elaine; Burek, Cynthia V.; Underwood, John; Legg, Colin; University College Chester (Association of UK RIGS Groups, 2004)
      This book chapter discusses the development and production of a geologically focused brochure based on Llandudno.
    • Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria)

      Muir, Anna P.; Biek, Roman; Thomas, R.; Mable, Barbara K.; University of Chester; University of Glasgow; Royal Zoological Society of Scotland (Wiley, 2014-01-20)
      Both environmental and genetic influences can result in phenotypic variation. Quantifying the relative contributions of local adaptation and phenotypic plasticity to phenotypes is key to understanding the effect of environmental variation on populations. Identifying the selective pressures that drive divergence is an important, but often lacking, next step. High gene flow between high- and low-altitude common frog (Rana temporaria) breeding sites has previously been demonstrated in Scotland. The aim of this study was to assess whether local adaptation occurs in the face of high gene flow and to identify potential environmental selection pressures that drive adaptation. Phenotypic variation in larval traits was quantified in R. temporaria from paired high- and low-altitude sites using three common temperature treatments. Local adaptation was assessed using QST -FST analyses, and quantitative phenotypic divergence was related to environmental parameters using Mantel tests. Although evidence of local adaptation was found for all traits measured, only variation in larval period and growth rate was consistent with adaptation to altitude. Moreover, this was only evident in the three mountains with the highest high-altitude sites. This variation was correlated with mean summer and winter temperatures, suggesting that temperature parameters are potentially strong selective pressures maintaining local adaptation, despite high gene flow.
    • Local geodiversity action plans (LGAPs) and the community – The Cheshire region LGAP

      Potter, Jacqueline; University of Chester (English Nature, 2005)
    • Local geodiversity action plans - setting to context for geological conservation

      Burek, Cynthia V.; Potter, Jacqueline; University of Chester (English Nature, 2006)
      This booklet discusses local geodiversity action plans (LGAPs) can be established to safeguard and manage the geological resources. A number of case studies are included and recommendations are made.
    • Local geodiversity action plans - sharing good practice workshop, Peterborough, 3 December 2003

      Burek, Cynthia V.; Potter, Jacqueline; Chester College of Higher Education (English Nature, 2004)
      This booklet discusses a workshop held in Peterborough in 2003 to examine good practice in the development of local geodiversity action plans (LGAPs). Six cases studies from Cheshire, County Durham and North Pennines, Leicestershire and Rutland, Staffordshire, Tees Valley, and Warwickshire.
    • A look at life

      Lewis, Stephen J.; Chester College of Higher Education (1996-11-14)