Academic literature on the topic 'Q Science (General) ; QH301 Biology'

Douglas Kell was Professor of Bioanalytical Science at the University of Manchester and Director of the BBSRC-funded Manchester Centre for Integrative Systems Biology before taking over as Chief Executive of the BBSRC in October 2008. He studied at the University of Oxford and then did research at Aberystwyth University. He joined UMIST (University of Manchester Institute of Science and Technology) in 2002. (UMIST merged with the Victoria University of Manchester to form The University of Manchester in 2004.)

Getting teenagers to ask good questions in science is not as easy as one would think. Many able pupils seem happy to passively absorb information without asking many questions, and to some extent the teacher might be forgiven for making the best of it by skipping through the syllabus, merrily ticking off learning objectives without losing too much sleep. While most teachers would agree that this way of learning science is not exactly ideal, questions concerning how to get pupils to become more inquisitive about science and how to foster a climate of questioning in lessons have been stagnating in the ether of secondary schools' prep rooms across the land for some time.

We introduce the concept of(γ,δ)-bifuzzy Lie subalgebra, whereγ,δare any two of{∈,q,∈∨q,∈∧q}withγ≠∈∧q, by using belongs to relation(∈)and quasi-coincidence with relation(q)between bifuzzy points and bifuzzy sets and discuss some of its properties. Then we introduce bifuzzy soft Lie subalgebras and investigate some of their properties.

D-type cyclins in plants are represented by seven conserved subgroups and play a major role in controlling cell division. Relatively little is understood of their role during seed development, although their expression pattern has been characterized and ectopic expression of CYCD3;1 has previously been shown to disrupt normal embryo development. Here the consequences of ectopic expression of CYCD7;1 using the early endosperm-specific promoter FWA in developing Arabidopsis seeds were investigated. Ectopic CYCD7;1 expression in the maternal central cell prior to fertilization, and in the endosperm from fertilization until cellularization resulted in seeds up to 45% larger. Seed enlargement was accompanied seed lethality, shown to be due to a defect of development during early and mid stages of seed development. As expected from the maternal specific expression of the imprinted FWA promoter, seed size and lethality was dependent on maternal origin of the transgene. Larger seed size was correlated to mature embryo and seed coat outgrowth, and was due to cell proliferation rather than cell elongation. In particular, embryo development was accelerated during the early stages, suggesting these may be dependent on cell division rate, whereas later stages progressed at the same rate as WT seeds. Seed-targeted CYCD7;1 expression phenocopies (1) the nucleus proliferation in the endosperm prior to fertilization observed in rbr and fis-class mutants and (2) the seed enlargement observed in paternal genome excess interploidy crosses. These suggest that CYCD7;1 may act through the RBR pathway to promote cell proliferation and modify imprinting in the endosperm, thereby influencing the parental genome balance. Mechanistically, CYCD7;1 did not interact directly with CDKA;1 but the interaction was promoted in presence of the inhibitor of CDK, ICK1/KRP1 or ICK2/KRP2 in a yeast-three-hybrid assay. However, loss of either KRP1 or KRP2 in respective mutant backgrounds did not prevent the seed enlargement phenotype.

Prediction of pathogen dynamics and the design of effective interventions to control and eliminate disease are key goals in epidemiology. While progress has been made towards the elimination of many infectious diseases, only two, smallpox and rinderpest, have been globally eradicated. Mass vaccination can greatly reduce the burden of vaccine-preventable diseases. However, there is relatively little scientific guidance on the optimal duration, frequency and placement of control interventions for achieving elimination. Such insights could greatly inform policy and practice. Rabies is a deadly and terrifying disease that exacts a heavy toll on human lives and national economies, with over 50,000 human deaths each year and many millions more requiring expensive life-saving post-exposure vaccines. Elimination of rabies is feasible through vaccination, and oral rabies vaccination (ORV) campaigns have eliminated fox rabies from Western Europe. However, scientific guidance could improve elimination efforts elsewhere, and is still needed for contingency planning to maintain rabies freedom and for emergency response to incursions. My thesis focuses on two pivotal questions in infectious disease ecology: what are the underlying determinants of disease persistence, and how can vaccination strategies be optimized to eliminate infection? To answer these questions, I analysed a rich and highly resolved spatial dataset of fox rabies cases and ORV efforts over three decades in Germany and neighbouring countries. The long-term, large-scale nature of these data provides a unique opportunity to improve our understanding of wildlife rabies dynamics in response to vaccination using novel spatial modeling techniques. In chapter 2, I create a metapopulation model of regional rabies dynamics that incorporates local transmission (within regions) and spatial coupling (between regions) using a hierarchical Bayesian state-space model. In chapter 3, I extend the model developed in chapter 2 to determine the best vaccination strategy, in terms of scale and duration of ORV efforts for three common epidemiological scenarios: {\bf endemic} circulation of rabies; {\bf high-risk} situations when rabies-free but neighbor endemic areas; and an {\bf endgame} scenario when only a single endemic foci remains. In chapter 4, I develop a space-time model of fox rabies dynamics and explore the effect of scale on estimates of transmission terms by aggregating rabies case data at different spatial resolutions. I then relate these estimates to the scaling of individual interactions to regional dynamics through population mixing. Collectively, the findings from this thesis contribute to our understanding of how infectious diseases persist and can be controlled through vaccination. The methods generated can be used to explore tradeoffs in the scale and duration of ORV efforts, and generate recommendations on the time horizon and investment required to achieve and maintain freedom from disease. The model developed in chapter 4 also presents the first steps to developing a highly resolved spatial model of local rabies dynamics. These findings have immediate application to the design of cordon sanitaires in Europe, and to strategies aiming to rapidly eliminate re-emergence in high-risk countries such as Greece and Turkey. The analytical and statistical framework developed in this thesis is also applicable to answering analogous questions for the elimination of dog-mediated rabies and for other vaccine preventable diseases.

Calcareous grassland, considered among the most species rich and diverse habitats in Europe, underwent wide scale loss and degradation following post 1950s agricultural intensification. Consequently, they are the focus of conservation efforts and are protected in national and international legislation (e.g. EU Habitats Directive). As elsewhere in Europe, a major cause of upland calcareous grassland loss and degradation in Britain was intensive grazing, typically with sheep. In recent years, conservation organisations have altered grazing practices in an attempt to prevent further loss and degradation by focussing management on conserving characteristic calcareous grassland vegetation. However, the impact of the contrasting grazing regimes used in this internationally important habitat on invertebrates is unknown. This study is the first to investigate the impacts of a range of established grazing regimes (low intensity sheep grazing, low intensity cattle grazing, high intensity sheep grazing and no grazing) on aspects of plant diversity and structural complexity, carabid beetle diversity, and spider diversity in upland calcareous grasslands. It also provides the first evidence based management recommendations for UK upland calcareous grasslands which incorporate both plants and invertebrates. In addition, this study is also the first to assess the biodiversity value of acid grassland and limestone heath habitat patches that occur as 3 part of the calcareous grassland matrix and are not targeted by conservation management, by examining the spider fauna in each habitat in relation to calcareous grassland. Further evidence based recommendations for the management of these non-target habitats are made for the first time.

Basement Membranes (BMs) are specialised extracellular matrix (ECM) structures that underlie all endothelial and epithelial cells, and provide structural support to tissues as well as influence cell behaviour and signalling. Mutations in the BMs major component collagen IV cause eye, kidney and cerebrovascular disease including intracerebral haemorrhaging (ICH). Haemorrhagic stroke accounts for 15% adult stroke and 50% paediatric stroke, and carries the worst prognosis and there are no therapeutic strategies. Mutations in the genes COL4A1/COL4A2 (collagen IV alpha chain 1 and 2) cause BM defects due to mutant protein incorporation in the BM or its absence by ER retention, and ER-stress due to intracellular accumulation of collagen IV. Despite this, the mechanism(s) of collagen IV mutations disease remain poorly characterised. To provide novel insights into mechanisms of collagen diseases, this study investigates the effect of defined engineered biointerfaces on cell behaviour/signalling, collagen secretion in COL4A2 mutant and wild-type cells. Atomic force microscopy and spectroscopy were employed together with confocal and biochemical analyses of cells cultured on engineered synthetic polymers, poly(ethyl acrylate) and poly(methyl acrylate), coated with ECM proteins, namely laminin, collagen IV and fibronectin. This enabled us to address the hypothesis that biomaterials may alter the behaviour of COL4A2+/G702D mutant cells by overcoming some of the defects caused by the mutation and rescuing the downstream effect of the ER stress. Of the ECM proteins that were used, only fibronectin was observed to undergo a drastic structural change depending on the substrate chemistry. On poly(ethyl acrylate), fibronectin was assembled into fibrillary networks upon adsorption, and these nanonetworks induced increased secretion of Col4a2 in COL4A2+/G702D cells than on poly(methyl acrylate) or control glass. The behaviour of the mutant cells appeared to be influenced by the underlying biointerface, increased levels of molecular chaperones and reduced ER area suggested an increased collagen IV folding capacity when the cells were cultured on the FN nanonetworks compared to the other surfaces. COL4A2+/G702D cells interacted with the adsorbed proteins and were able to mechanically translocate them. Enhanced formation of focal adhesions was also seen on FN-coated polymers, where ligand density and actin-myosin contractility accounted for the observed increase in cell adhesion strength. The stiffness of the mutant fibroblasts and of their ECMs was found to be 10 times lower than that of the wild-type cells; interestingly, mutant cells cultured on FN nanonetworks on poly(ethyl acrylate) were able to deposit a protein matrix with significantly higher Young modulus than on glass or poly(methyl acrylate). These findings suggest that biomaterials are able to influence the behaviour of these mutant cells through changes in the interfacial layer of adsorbed proteins presented to them. Collectively, these data provide an understanding of the effect of mutations on cell characteristic and a basis of concept that material may be employed to modulate effects of mutations of collagen/ECM molecules. Understanding the mechanisms through which these surfaces trigger a change in cell response will prove valuable for the development of new therapeutic approaches to address pathologies due to collagen IV mutations. In this respect, further investigation is needed to dissect the signalling pathways involved.

Conservation of phenotypically variable taxa such as the European whitefish (Coregonus lavaretus) can be particularly challenging. In this thesis it is argued that the recent designation of seven native C. lavaretus populations as three endemic species (C. clupeoides, C. stigmaticus and C. pennantii) by Kottelat & Freyhof (2007) are incorrect and cannot be substantiated with the results presented here. However, evidence for important infra-specific variation between populations has been found. Two native Scottish populations of C. lavaretus show considerable variation in morphology, trophic ecology and life history. The variation in these populations warrants protection, one conservation action becoming more commonly utilised in Britain is conservation translocation. It was found that there were significant differences between source and refuge populations in Scotland. The wisdom of using this conservation measure on a phenotypically plastic organism is discussed. Nevertheless the establishment of further refuge populations are considered to be a viable conservation action. Sub-structuring within the largest native Scottish population of C. lavaretus was not found. However, evidence of residence within certain basins of Loch Lomond was found through significant differences in muscle stable isotope signatures. Investigation was also made into the trophic ecology of other fish in Loch Lomond. It was found that brown trout (Salmo trutta) in Loch Lomond have a non-typical migration pattern and invasive ruffe (Gymnocephalus cernuus) now form an important part of the trophic ecology of this site. In Britain several whitefish populations have been invaded by ruffe, a species native to Britain, but not to these sites. An experiment is conducted into the protective ability against ruffe predation on C. lavaretus ova of substrates typical on spawning grounds. It was found that pebbles and gravel form the best spawning substrate. The impact this mortality may have on the life history of Loch Lomond C. lavaretus is discussed. Using information gathered in this study, recommendations for the management of Coregonus spp. are summerised. There is the potential for these recommendations to apply to other phenotypically plastic species that vary between sites such as Arctic charr (Salvelinus alpinus) and brown trout.

GLUT4 is the insulin-regulated glucose transporter found in muscle and adipose tissue. On insulin stimulation, GLUT4 translocates from a slowly recycling storage compartment (GLUT4 storage vesicles or GSVs) to the plasma membrane. This allows glucose to enter cells by diffusion down its concentration gradient, clearing glucose from the plasma. This response is defective in the disease states of insulin resistance and type 2 diabetes. The aim of this study is to understand how GLUT4 enters GSVs, which will hopefully extend our knowledge of insulin responsive tissues. Previous studies from our lab, expressing GLUT4 in yeast, have shown that GLUT4 is subject to the same nitrogen- and ubiquitin-dependent trafficking as the yeast amino acid permease Gap1p. In my thesis I have extended these studies into 3T3-L1 adipocytes, and shown that GLUT4 is ubiquitinated in this insulin responsive cell line. A ubiquitin resistant version of GLUT4 (HA-GLUT4 7K/R) has an impaired ability to enter GSVs and does not translocate in response to insulin. However GLUT4 mutants with single ubiquitination sites outwith the large intracellular loop are ubiquitinated and traffic in an identical manner to wild type GLUT4, addressing concerns that mutation of the large intracellular loop of GLUT4 in HA-GLUT4 7K/R affects its trafficking. The GGA family of clathrin adaptor proteins have previously been implicated in sorting of newly synthesised GLUT4 into GSVs. Our lab has shown previously that the two yeast Ggas are required for ubiquitin dependent trafficking of GLUT4 in yeast, as is the case for Gap1p. I have gone on to show that the ubiquitin binding function of the GGA3 GAT domain is, at least partially, required for an in vitro interaction between GLUT4 and the VHS-GAT domains of GGA3. When expressed in adipocytes, a ubiquitin binding deficient mutant of myc-GGA3 reduces the proportion of GLUT4 loaded into a subcellular fraction enriched in GSVs, suggesting that GLUT4 ubiquitination is one of the signals for GGA dependent sorting into GSVs. As ubiquitination is usually thought of as a signal to direct lysosomal degradation, and only 0.1 % of total GLUT4 is ubiquitinated at any one time, there may be a role for a deubiquitination step in ubiquitin dependent GLUT4 traffic. Work by our collaborator (Nai-Wen Chi, UCSD) has demonstrated that the GSV cargo IRAP and its binding partner tankyrase-1 are required for normal insulin responsive GLUT4 traffic. An interaction between tankyrase and the deubiquitinase (DUB) USP25 has been demonstrated by yeast two hybrid analysis, and this DUB contains a putative tankyrase binding motif. USP25 may therefore be recruited to GSVs by IRAP, with tankyrase acting as a scaffold. I demonstrated that GST-USP25 binds tankyrase-1 from an adipocyte lysate, and that a version of the enzyme with a mutation in the putative tankyrase binding motif (GST-USP25 R1049A) does not. I also used siRNA to deplete USP25 from 3T3-L1 adipocytes, and found that this results in a reduction of GLUT4 levels in these cells. A concomitant reduction in the fold change of insulin-stimulated glucose transport into these cells suggests that GLUT4 is not sequestered in GSVs, but is rather directed to the lysosome. In summary, my data show that ubiquitination of GLUT4 is required for the transporter to be loaded into its insulin responsive compartment (GSVs). I also began to characterise the role of the ubiquitin binding GAT domain of GGA3 and the deubiquitinase USP25 in GLUT4 traffic, opening up two further avenues for research into the insulin regulated trafficking of GLUT4.

Background: This thesis examines the origins and early development of UK Biobank. This is a resource funded in 2002 by the Medical Research Council, the Wellcome Trust, the Department of Health and the Scottish Executive to gather genetic and lifestyle information from half a million participants aged 4069 years old in the UK and monitor their health for up to thirty years in order to improve the prevention, diagnosis and treatment of major diseases. UK Biobank was set up following the completion of the Human Genome Project in 2001, and was one of many established at around the same time with the goal of translating the knowledge of the human genome sequence into practical benefits for human health. (National genetic databases were also set up or proposed in Iceland, Estonia, Latvia, Sweden, Singapore, Tonga, Spain, and the United States). They, and the Human Genome Project, had raised a number of important issues about access to and ownership of genetic information. Aims: The original aim of my PhD was to examine lay and professional understandings and responses to Biobank in the light of this background. However, UK Biobank took longer than expected to reach the stage of data collection, in part because of negotiations about its organisational structure. The aim therefore changed to address the question of how and why was UK Biobank initially configured in the manner it was. Organisational structure: UK Biobank was originally set up by the funders with a ‘hub’ and ‘spoke’ model, with calls for bids from UK Universities for a central ‘hub’ charged with financial management and overall control of data and samples, and ‘spokes’ who were responsible for recruitment and data collection through primary care. The selection of both was made through the procurement rules of the EU. The hub (Manchester), six regional spokes, and the CEO (from Oxford) were all appointed simultaneously in 2003 and subsequently a Board of Directors and a number of committees were appointed. The CEO resigned in late 2004, and a new CEO and Principal Investigator was appointed in 2005, after which there were significant changes to the organisational structure. Methods: I conducted 76 oral history interviews with academic scientists directly and indirectly involved in UK Biobank, representatives of all four funding bodies, and representatives of UK Biobank Limited (the company set up to manage UK Biobank). I also conducted archival analysis of the MRC’s official documents concerning the origins and development of UK Biobank. Findings: From its beginning UK Biobank was marked by tension between academic scientists on the one hand and representatives of the funding bodies and UK Biobank Limited on the other. Academic scientists criticised the funding bodies for establishing UK Biobank in a way that departed from what I have termed ‘standard academic scientific practice’. Spokes felt they should receive some privileged access to data they would contribute to collecting, and felt that the set up did not recognise the performance indicators driving scientists and universities. Lack of clarity over who was in control of UK Biobank contributed to these tensions as both spokes and funders felt that the other exerted undue influence. Some mistrust developed between academic scientists and representatives of the funding bodies and UK Biobank Limited. Discussion: The configuration of UK Biobank was difficult for academic scientists and representatives of both the funding bodies and UK Biobank alike. Organisational issues, typical of those confronting Big Science initiatives, were largely responsible for this difficult legacy. Issues of leadership, the hub and spoke model, the sequencing of funding decisions, appointment of groups and committees and protocol development, uncertainties about who was in control, and ambiguities within the organisational structure as a whole were the most significant issues in the origins and development of UK Biobank, as the organisational changes in 2005 testify.

Breast cancer is the third most common cause of cancer death in the UK, accountable for more than 11000 deaths in 2010 alone (www.cancerresearchuk. org). Developmental pathways commonly required for normal development are often hijacked during tumour progression, so a better understanding of mammary gland development is necessary to fully understand the roots of breast cancer. The Runx gene family are known to be important regulators of development in different lineages. In particular RUNX1 and RUNX2 have been widely studied in the context of haematopoiesis and osteogenesis respectively, but their role in epithelial tissue is much less well understood. In this thesis a role for RUNX1 and RUNX2 in mammary development and breast cancer has been identified. The first part of this study is focused on characterizing the expression and function of the Runx genes in the mammary epithelium. RUNX1 and RUNX2 protein levels fluctuate during embryonic and adult mammary development, and an in vivo conditional knockout strategy shows that both genes are important for maintenance of mammary epithelium homeostasis. Moreover, combined loss of RUNX1 and RUNX2 significantly perturbs the normal mammary architecture with an expansion of the basal population in vivo and the appearance of preneoplastic lesions in aged mammary glands. An exciting new role for RUNX2 in mammary stem cells has also been revealed showing that RUNX2 is important for the regenerative potential of mammary epithelial cells in vitro. Evidence is also presented to indicate that RUNX2 could be linked to regulation of quiescence and Wnt signalling in the stem cell compartment and during transformation. Finally, the role of these genes in breast cancer is discussed demonstrating involvement of RUNX1 and RUNX2 specifically in the triple negative (ER-PR-HER2-) subtype. In particular, for the first time, RUNX1 is revealed as an independent prognostic indicator correlating with poor prognosis in triple negative tumours. Meanwhile, evidence from various mouse models demonstrates that RUNX2 may be specifically involved in the squamous metaplastic form of this disease.

Signalling from Fibroblast Growth Factor Receptors (FGFRs) is under tight control by a wide variety of extrinsic and intrinsic regulatory mechanisms, many of which remain poorly defined. Sproutys and their related Spred proteins constitute two such families of signalling regulators with multiple developmental roles as well as potential tumour suppressive functions. However, the molecular mechanisms of these proteins have remained unclear and subject to many unresolved controversies. Using a mass spectrometry approach, several novel interacting partners of Sprouty with roles in endocytosis are identified here, suggestive of a potential endocytic-related function for Sproutys. In addition, comprehensive analysis of Sprouty phosphorylations and their dynamics by mass spectrometry reveal previously unknown but potentially crucial sites that might regulate Sproutys function. Next, a novel late-endosomal protein that directly binds to Spred is identified using a different approach. Neighbor of BRCA1-1 (NBR1) is shown to be necessary for attenuation of FGF signaling by Spred, and this is demonstrated to be via modulation of the trafficking itinerary of FGFRs. Finally, NBR1 is established as a novel regulator of RTK trafficking and signalling, and the interplay between its various regions for protein localisation and function is revealed.