University of St Andrews

Project description

Violence is a major health issue in both São Paulo and Glasgow. Gang violence and street crime perpetrated by young males can have a devastating impact upon the health and well-being of individuals, communities and wider society. This PhD shall take a case study approach to violence prevention in two cities with reputations for violent crime: São Paulo and Glasgow. Following public health interventions, both cities have seen a marked decrease violent crime in recent years, however the problem endures at unacceptable levels. The student will be expected to examine the strategies adopted in both cities, and to compare and contrast their impacts. Further, the project shall identify lessons learned from each city, and suggest potential areas of policy transfer.

Availability

Co-tutelle PhD (12 months UK, 24 in Brazil)

Supervisers

• University of St Andrews Supervisor(s):

  Prof Peter Donnelly (School of Medicine)

• Brazilian University Supervisor(s):

  To be decided.

Additional notes

Prof Donnelly has a number of PhD students examining violence prevention strategies at both national and international levels. Further, Prof Donnelly has close collaborative relationships with the national Violence Reduction Unit in Glasgow, and the WHO where he sits on the committee of the Violence Prevention Alliance. These links facilitate access to on-going international violence prevention strategies, and allow observation of the interplay between academic research, policy and practice in the field.

Start date

September 2012 or February 2013

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Project description

We are living ever longer but longevity is not necessarily coupled with continuing high quality of life. One of the typical features of deteriorating life quality is decline in cognitive ability.   However, this decline is highly variable with some long-lived individuals declining very little in their cognitive abilities and others declining very early. While there is a substantial genetic component to this variation, there is increasing evidence that stress encurred during life makes a significant contribution. Identifying and quantifying those stressors is fundamental to any plans for halting or even reversing cognitive decline. Although rodents are the typical model for addressing questions of human neural and cognitive mechanisms, birds are much more amenable to the relevant experimental manipulations. The aim of this project, therefore, would be to use zebra finches as a model for examining how both early life stress (which can be manipulated from the egg stage onwards) and the stress of reproduction (zebra finches will reproduce continuously in laboratory conditions) impact on both longevity and cognitive performance. We predict that early life stressors will have major and long-lasting impacts but that these will be affected by variation in the number or quality of reproductive events during adulthood. This project would involve behavioural manipulations of birds both early in life and during their lives. The neural implications of these manipulations will also be assessed by immediate early gene expression, hormone receptor activation and volumetric measurements. The two supervisors are very experienced in the use of all of these techniques.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Drs Karen Spencer and Susan Healy, Schools of Biology, and Psychology & Neuroscience, University of St Andrews

• Brazilian University Supervisor(s):

  n/a

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

In a number of proteins, cysteine and glutamine residues can form backbone cross-links via thioester bonds, R-S-C(O)-R'.These bonds are very reactive and can be used, e.g. to promote covalent binding of the protein to nucleophilic groups on cell surfaces (e.g. carbohydrates). State-of-the-art computational methods, including quantum-mechanical/molecular-mechanical techniques [1], will be used to model the mechanisms of thioester formation and -cleavage, calling special attention to effect of the protein environment. The possible catalytic role of neighbouring residues can be identified, furnishing insights into the molecular basis of this potential binding mode of bacterial surface proteins.

Availability

Co-tutelle PhD (12 months UK, 24 in Brazil)

Supervisers

• University of St Andrews Supervisor(s):

  Prof Michael Bühl (School of Chemistry, St Andrews)

• Brazilian University Supervisor(s):

  Prof José Walkimar de M. Carneiro (Instituto de Química, Universidade Federal Fluminense, Outeiro de São João Batista, s/n, 24020-150 Niterói - RJ, Brazil)

Additional notes

To understand the chemical processes underpinning biological processes at an atomic level is a major driver for the biomolecular sciences. We wish to apply state-of-the-art modelling tools rooted in quantum chemistry to shed light on key aspects in this area, focusing to the detailed mechanism of spontaneous or enzymatic reactions of proteins. M. Bühl and Prof Carneiro have strong links, which has resulted in the following joint publication: M. T. de M. Cruz, J. W. de M. Carneiro,D. A. G. Aranda, M. Bühl, J. Phys. Chem. C 2007, 111, 11068. References: [1] R. M. Hagan, R. Björnsson, S. A. McMahon, B. Schomburg, V. Braithwaite, M. Bühl, J. H. Naismith, U. Schwarz-Linek, Angew. Chem. Int. Ed. 2010, 49, 8421.

Start date

September 2012 or February 2013

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Project description

Radiosensitisers are substances that increase the sensibility of hypoxic cells to radiation, enhancing treatment efficiency in cancer radiotherapy. Complexation to transition metals can enhance this effect, Prime tools for characterisation are NMR and EPR spectroscopy for dia- and paramagnetic complexes, respectively. We propose to use state-of-the-art quantum-chemical methods to model structures, energies, and spectroscopic properties of a variety of metal complexes (including Re(CO)₃⁺ and Cu²⁺ complexes, which have attracted recent interest), calling special attention to the effect of the solvent, water. The results promise insights into speciation of such complexes under physiological conditions, which can help to design novel metallodrugs.

Availability

Co-tutelle PhD (12 months UK, 24 in Brazil)

Supervisers

• University of St Andrews Supervisor(s):

  Prof Michael Bühl (School of Chemistry, St Andrews)

• Brazilian University Supervisor(s):

  Prof Teodorico C. Ramalho (Universidade Federal de Lavras, Campus Universitário - UFLA, Dept. de Química, 37200-000, Lavras-MG,Brasil)

Additional notes

To understand the chemical processes underpinning biological processes at an atomic level is a major driver for the biomolecular sciences. We wish to apply state-of-the-art modelling tools rooted in quantum chemistry to shed light on key aspects in this area, calling special attention to structural properties that can be probed with spectroscopic techniques. M. Bühl and Prof Ramalho have close links, which has resulted in the following two joint publications: T. C. Ramalho, M. Bühl, Magn. Reson. Chem., 2005, 43, 139; T. C. Ramalho, M. Bühl, J. D. Figueroa-Villar,R. B. de Alencastro, Helv. Chim. Acta 2005, 88, 2705.

Start date

September 2012 or February 2013

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Project description

Radiosensitisers are substances that increase the sensibility of hypoxic cells to radiation, enhancing treatment efficiency in cancer radiotherapy. Complexation to transition metals can enhance this effect, Prime tools for characterisation are NMR and EPR spectroscopy for dia- and paramagnetic complexes, respectively. We propose to use state-of-the-art quantum-chemical methods to model structures, energies, and spectroscopic properties of a variety of metal complexes (including Re(CO)₃⁺ and Cu₂⁺ complexes, which have attracted recent interest), calling special attention to the effect of the solvent, water. The results promise insights into speciation of such complexes under physiological conditions, which can help to design novel metallodrugs.

Availability

Co-tutelle PhD (12 months UK, 24 in Brazil)

Supervisers

• University of St Andrews Supervisor(s):

  Prof Michael Bühl (School of Chemistry, St Andrews)

• Brazilian University Supervisor(s):

  Prof Teodorico C. Ramalho (Universidade Federal de Lavras, Campus Universitário - UFLA, Dept. de Química, 37200-000, Lavras-MG,Brasil)

Additional notes

To understand the chemical processes underpinning biological processes at an atomic level is a major driver for the biomolecular sciences. We wish to apply state-of-the-art modelling tools rooted in quantum chemistry to shed light on key aspects in this area, calling special attention to structural properties that can be probed with spectroscopic techniques. M. Bühl and Prof Ramalho have close links, which has resulted in the following two joint publications: T. C. Ramalho, M. Bühl, Magn. Reson. Chem., 2005, 43, 139; T. C. Ramalho, M. Bühl, J. D. Figueroa-Villar,R. B. de Alencastro, Helv. Chim. Acta 2005, 88, 2705.

Start date

September 2012 or February 2013

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Project description

gamma-Aminobutyric acid (GABA) is a key neurotransmitter in the central nervous system. After pioneering studies in St Andrews of synthesis, receptor binding and quantum-chemical modelling of a singly fluorinated analog, higher fluorinated derivatives are currently being explored. We plan to perform high-level quantum-mechanical/molecular-mechanical simulations [1] of such analogs (notably the recently reported 2,3-difluoro-derivative [2]), both in water and the binding pockets of known receptors. We expect detailed insights into the way how the CF bonds affect the conformational preferences of the molecules and, hence, their affinity toward the GABA receptors, informing on potential design of new ligands for therapeutic applications.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Prof Michael Bühl (St Andrews)

• Brazilian University Supervisor(s):

  n/a

Additional notes

The project will benefit from the close proximity of Prof O'Hagan in St Andrews, a world-leading expert in organofluorine chemistry. References: [1] J. Cao, R. Bjornsson, M. Bühl, W. Thiel, T. van Mourik, Chem. Eur. J. 2012, 18, 184. [2] I. Yamamoto, M. J. T. Jordan, N. Gavande, M. RE. Doddareddy, M. Chebib, L. Hunter, Chem. Commun. 2012, 48, 829.

Start date

September 2012 or February 2013

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Project description

Resistant microorganisms represent a significant and increasing threat to human health. For example, bacterial pathogens such as MRSA and Pseudomonas aeruginosa cause significant problems in the hospital environment and the few drugs available to treat fungal infections means there is increasing difficulty with Candida and Aspergillus spp. The project will involve identifying novel combinations of antimicrobials that display potent, synergistic inhibition of a range of human pathogens. Combinations will involve existing antimicrobials currently used in clinical practice as well as antimicrobial peptides (AMPs) from a range of animal sources. Furthermore, the use of multi-drug efflux pump inhibitors, compounds that can restore or potentiate the antimicrobial effect of drugs that organisms have acquired resistance to, in combination with AMPs and existing antimicrobials will also be explored. The antimicrobial effect of combinations will be assessed in vitro but also using the wax moth larva (Galleria mellonella) in vivo model of infection. Any effective treatments thus identified would be further characterised via research on identifying the precise mode of action of the combination. A range of microbiological, genomic, proteomic and microscopic techniques would be employed to do this. It is envisaged that any effective, novel treatments would be patented and initial efficacy studies pursued in suitable mammalian models.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr. Peter J. Coote (School of Biology, BSRC).

• Brazilian University Supervisor(s):

  n/a

Additional notes

The applicant would be keen to collaborate with groups in Brazil identifying novel antimicrobial peptides from invertebrates or amphibians local to Brazilian ecosystems.

Start date

September 2012 or February 2013.

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Project description

The proposed project aims to characterize in detail key components of the nuclear chromosomal DNA replication apparatus of the parasitic protozoa Trypanosoma brucei and Trypanosoma cruzi, and related Leishmania species, and to develop small molecular inhibitors of their functions as potential therapeutics. These organisms are the causative agents of sleeping sickness in sub-Saharan Africa (T. brucei) and Chagas disease in Central and South America (T. cruzi), "Old World" cutaneous leishmaniasis (L. major) and "New World" visceral leishmaniasis (kala-azar) in East Africa, South America and Southeast Asia (various Leishmania species). The diseases caused by these parasites affect millions of people and represent a huge percentage of the world’s disease burden; there is an urgent need to identify novel therapeutic targets and to develop effective lead compounds. Surprisingly, despite their importance as disease agents, very little is known of the enzymes and mechanisms of nuclear chromosome replication in kinetoplastid organisms – fewer than a handful of papers have been published in this area and there is vast untapped potential for drug target identification and anti-parasitic drug design. The proposed work aims to use state-of-the-art techniques to determine the molecular composition of the three replicative DNA polymerases in these organisms, to determine the three-dimensional structures of core catalytic domains of each enzyme complex, and to screen pharmacophorically-rich fragment libraries for small molecule inhibitors of their functions as a springboard for future drug discovery.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Stuart MacNeill & Dr Terry Smith

• Brazilian University Supervisor(s):

  n/a

Additional notes

The student will work in the newly built Biomedical Sciences Research Complex (BSRC), a highly interactive multi-disciplinary research facility with a secure containment level 3 facility for parasite culture.

See https://www.st-andrews.ac.uk/bsrc for details.

 

Start date

September 2012 or February 2013

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Project description

Recent research in my lab has shown that we possess inhibitory control over memory for events that have been personally experienced. Specifically, we have found that people can be trained to forget specific details about previously experienced events. Using a novel procedure called the Autobiographical Think/No-think procedure, this project will seek to explore the extent of any relationship between the ability to inhibit positively- and negatively-valenced autobiographical memories and the maintenance of conditions such as depression. There would also be scope in this project to explore some of the neurophysiological underpinnings of inhibitory control using fMRI. This project is available to an individual who possesses a good first degree in the life sciences. Familiarity with the modelling of human memory and experience in the design and running of empirical studies would also be an advantage.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Prof Malcolm MacLeod (School of Psychology & Neuroscience)

• Brazilian University Supervisor(s):

  n/a

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

Chromosomal DNA replication in all forms of life requires the complex interplay of a variety of essential and non-essential proteins factors in a temporally and spatially coordinated manner. Understanding how these processes occur in human cells, and how they are regulated, presents a major challenge to modern biology. By using simple model systems such as yeast or archaea, it is possible to gain insights into replication enzyme structure, function and regulation, insights that greatly inform our understanding of the mechanics of chromosome replication in our own cells. The proposed project focuses on the CMG (Cdc45-MCM-GINS) complex. This multisubunit complex lies at the heart of the replication machinery, unwinding double-stranded DNA ahead of the moving replication fork. The project will combine genetic and biochemical analysis of CMG helicase structure and function in a model archaeal organism, the halophile Haloferax volcanii. Unlike most archaeal models, this organism is tractable to molecular genetic methods and a wide variety of tools have been developed to facilitate this. The aim of the project will be to characterise biochemically and genetically the interactions that take place between the putative CMG components in this organism. Depending on the results of these studies, it will be possible to perform a more detailed molecular biology analysis of archaeal CMG function in vivo, to initiate a detailed structural or enzymatic analysis of the CMG in vitro, or ideally, both. Taken together, the results of these studies will ultimately offer important insights into the biology of chromosome replication in archaea and eukaryotes.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Stuart A. MacNeill

• Brazilian University Supervisor(s):

  n/a

Additional notes

The student will work in the Chromosome Replication and Genome Stability group in the newly built Biomedical Sciences Research Complex (BSRC). Research in the group is focused on understanding the molecular biology of chromosome DNA replication in eukaryotes and in archaea: see http://biology.st-andrews.ac.uk/macneill for details.

Start date

September 2012 or February 2013

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Project description

Chromosomal DNA replication in all forms of life requires the complex interplay of a variety of essential and non-essential proteins factors in a temporally and spatially coordinated manner. Understanding how these processes occur in human cells, and how they are regulated, presents a major challenge to modern biology. By using simple model systems such as yeast or archaea, it is possible to gain insights into replication enzyme structure, function and regulation, insights that greatly inform our understanding of the mechanics of chromosome replication in our own cells. The proposed project focuses on the CMG (Cdc45-MCM-GINS) complex. This multisubunit complex lies at the heart of the replication machinery, unwinding double-stranded DNA ahead of the moving replication fork. The project will combine genetic and biochemical analysis of CMG helicase structure and function in a model archaeal organism, the halophile Haloferax volcanii. Unlike most archaeal models, this organism is tractable to molecular genetic methods and a wide variety of tools have been developed to facilitate this. The aim of the project will be to characterise biochemically and genetically the interactions that take place between the putative CMG components in this organism. Depending on the results of these studies, it will be possible to perform a more detailed molecular biology analysis of archaeal CMG function in vivo, to initiate a detailed structural or enzymatic analysis of the CMG in vitro, or ideally, both. Taken together, the results of these studies will ultimately offer important insights into the biology of chromosome replication in archaea and eukaryotes.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Stuart A. MacNeill

• Brazilian University Supervisor(s):

  n/a

Additional notes

The student will work in the Chromosome Replication and Genome Stability group in the newly built Biomedical Sciences Research Complex (BSRC). Research in the group is focused on understanding the molecular biology of chromosome DNA replication in eukaryotes and in archaea: see http://biology.st-andrews.ac.uk/macneill for details.

Start date

September 2012 or February 2013

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Project description

Aspergillus fumigatus, a filamentous fungus, is the major causative agent of respiratory aspergillosis a disease that has a high fatality rate, particularly in immunocompromised individuals. The student will investigate three newly identified genes involved in nitrogen metabolism that may be important for growth under hypoxic conditions in cancerous lung tissue. The longer term ambition is to develop drugs which would target these (non-human) microbial proteins. Training would involve molecular biology techniques, protein purification, fungal culture and genetic transformation methods. Our laboratory has trained successfully a number of Brazilian students over the years.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s): Dr Sheila Unkles (School of Biology)
• Brazilian University Supervisor(s):

  n/a

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

The project will genetically and chemically validate therapeutic targets, associated with phospholipid and glycosylphosphatidylinositol anchor metabolism in the parasitic protozoa Trypanosoma cruzi, the causative agent of Chagas disease. Approximately ~100 million people in South America are at risk from Chagas disease, representing a huge disease burden; there is an urgent need to identify novel therapeutic targets and to develop novel effective lead compounds against this neglected disease.

The student will experience complementary expertise in parasite biology, drug discovery and synthetic chemistry. The project will be carried out in purpose built multi-disciplinary research facilities, including facilities for parasite culture.

Availability

Co-tutelle PhD (12 months UK, 24 in Brazil) or Full PhD (36 in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Terry K. Smith (Schools of Biology & Chemistry).

• Brazilian University Supervisor(s):

  To be decided.

Additional notes

Past connections with Brazilian research groups: i) M´ario A. C. Silva-Neto, Instituto de Bioqu´imica M´edica at Universidade Federal do Rio de Janeiro; ii) Igor Almeida and Rosa A. Maldonado, Department of Parasitology, University of Sao Paulo (USP), Brazil. No present connections.

Start date

September 2012

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Project description

Respiratory infections are the single most important cause of preventable death worldwide. Although many respiratory pathogens are know there are many still to discover and to characterize. This project will investigate a newly described organism, Mycoplasma amphoriforme found originally in immunocompromised patients but now recognized in previously healthy adults and children. The student will join a programme of research that intends to understand the pathogenicity of this organism. To date the sequence of the whole genome has been performed for multiple organisms from different countries throughout the world.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Stephen Gillespie (School of Medicine) and Nick Thompson

• Brazilian University Supervisor(s):

  n/a

Additional notes

The student will be engaged in the generation and analysis of genomic data with the aim of developing and investigating hypotheses about the pathogenicity of the organism in particular and mycoplasmas in general.   The studentship will be jointly supervised by Professor Stephen Gillespie and Professor Nick Thompson (Wellcome Genome Campus Hinxton). There will be an opportunity to collaborate with clinical colleagues in health services internationally to generate a representative collection of organisms and to evaluate improved diagnostic techniques. The student will gain extensive experience of medical microbiology applied to pathogenicity research notably in the area of genomics and proteomics. The successful candidate is likely to have achieved a First Class Honours degree in the molecular microbiology or the broad area of biomedical sciences.

Start date

October 2012

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Project description

Violence is a major health issue in both Brazil and the United Kingdom. Street crime, terrorism and collective public disorder (riots) can have a devastating impact upon the health of individuals, communities and wider society. This PhD project shall observe and evaluate public health strategies at violence prevention at major sporting events in the two countries. Specifically, the student shall retrospectively examine the efficacy of strategies employed at the London 2012 Olympic Games, and collect primary data at the 2014 World Cup in Rio de Janeiro and Glasgow 2014 Commonwealth Games. Analysis of these events shall then be used to make recommendations for violence prevention strategies at the Rio de Janeiro 2016 Olympic Games. The student will be expected to employ a range of data collection and analytic techniques (both quantitative and qualitative) in the project, and to draw theoretically from behavioural science, public health, social psychology and political science models.

Availability

Co-tutelle PhD (12 months UK, 24 in Brazil)

Supervisers

• University of St Andrews Supervisor(s):

  Prof Peter Donnelly (School of Medicine)

• Brazilian University Supervisor(s):

  To be decided.

Additional notes

Prof Donnelly has a number of PhD students examining violence prevention strategies at both national and international levels. Further, Prof Donnelly has close collaborative relationships with the national Violence Reduction Unit in Glasgow, and the WHO where he sits on the committee of the Violence Prevention Alliance. These links facilitate access to on-going international violence prevention strategies, and allow observation of the interplay between academic research, policy and practice in the field.

Start date

September 2012 or February 2013

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Project description

Why do patterns of ageing vary across different species? Identifying the causes and consequences of age-related phenotypes remain central to our understanding of variation amongst species in life-history strategies, and to addressing long-term concerns over age-related disease in humans. Moreover, there are a growing number of beneficial insect species, including parasitic wasps used in biological control, where a limiting factor to successful deployment is “shelf-life”. Using an array of genetic, genomic and whole-organism approaches the student will explore ageing in a model insect, the parasitic wasp Nasonia vitripennis. In particular, the student will address how age-related reproduction is modulated by both genes and the environment. The student will gain a broad skills-base, spanning molecular genetics, genomics, bioinformatics and behaviour.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr David Shuker and Professor Mike Ritchie (School of Biology)

• Brazilian University Supervisor(s):

  n/a

Additional notes

Biological control is central to long-term, sustainable prevention of damage to economically important crops and ornamentals. As many crop pests are arthropods, parasitic wasps play a key role in many biological control programmes. For instance, in Brazil sugarcane is a major crop (>9 million hectares). Sugarcane is attacked by a number of pests, especially the sugarcane borer Diatraea saccharalis. Biological control through release of Cotesia and Trichogramma wasps has saved millions of dollars in terms of reduced pesticide use. However, successful deployment of beneficial insects such as parasitic wasps is often hampered by developing successful mass-rearing techniques and also limitations on how long the insects can be kept alive before deployment. The Shuker lab has strong links with the entomophagous insect research communities across Europe and North America, and this project fits emerging research priorities across the globe to promote and enhance our use of beneficial insects.

Start date

September 2012 or February 2013

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Project description

Splicing snRNPs are essential components of the spliceosome required for pre-mRNA splicing in all cell types. They have a complex structure comprising a core of RNA (snRNA), which is highly modified, bound to numerous proteins including a core ring of Sm proteins. This structure results in a biogenesis pathway involving numerous steps that take place in various regions of the cell. The way in which splicing snRNPs traffic through the cytoplasm and nucleus of the cell is not fully understood but is of great importance both for understanding the basic biological function of the cell and for elucidating the pathologies of a number of neurodegenerative conditions, including Spinal Muscular Atrophy (SMA), in which defects in snRNP biogenesis are implicated.

We aim to combine the use of fluorescently tagged Sm proteins and advanced quantitative mass spectrometry approaches to track the progress of newly made snRNPs within the cell throughout their biogenesis and to identify cellular proteins involved in each of the different stages. The project will involve molecular biology, cell culture, advanced fixed and live cell microscopy and protein analysis.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Judith Sleeman, Dr Catherine Botting (School of Biology)

• Brazilian University Supervisor(s):

  n/a

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

Multiple stressors, including those form climate change, industrialization, fisheries and high levels of human population, on marine and coastal ecosystems can result in major changes in biodiversity. Some indicators suggest that most of these changes will lead to a greater prevalence of invasive species and the possibility that marine ecosystems could be less resilient to perturbation. This may result in an overall erosion of the goods and services supplied by coastal and marine ecosystems. A major challenge to this field is the development of underlying theory of ecosystem structure and function. In order to tackle this we need well developed case studies and also use, or build, ecosystem models to examine the stability and resilience of these ecological systems. These systems could include everything from coastal and benthic to pelagic. The projects(s) will involve specific studies of perturbed and unperturbed marine and coastal ecosystems and the use of validated ecosystem models to examine the potential dynamics of these systems.

Availability

Co-tutelle PhD (12 months UK, 24 in Brazil)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Maria Dornelas, Professor David Paterson, Professor Chris Todd, Professor Ian Johnston, Prof Anne Magurran and Professor Andrew Brierley

• Brazilian University Supervisor(s):

  To be confirmed.

Additional notes

The work will be conducted within the Scottish Oceans Institute (http://soi.st-andrews.ac.uk/) at the University of St Andrews.

Start date

September 2012 or February 2013

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Project description

Awareness of memory ability, metamemory, shapes how we interact with the world. In those with memory deficits, accurate metamemory enables the use of compensatory strategies. Conversely, inaccurate metamemory means that compensatory strategies may not be employed so willingly or effectively. Metamemory therefore has potential for significant impact on perceived health and quality of life. There is debate about how metamemory should be conceptualised, and consequently, whether or not it systematically declines with healthy ageing. The student will test a range of participants for memory and metamemory ability and develop a mathematical model of metamemory. The goal will be to establish how metamemory varies across a full range of the healthy population.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Akira O’Connor (School of Psychology & Neuroscience)

• Brazilian University Supervisor(s):

  n/a

Additional notes

Dr O’Connor is a member of the SINAPSE pooling initiative for Scottish neuroscience research. Funds allowing, there may be the opportunity to assess neural correlates of memory/metamemory using fMRI and/or EEG at the Clinical Research Centre, Ninewells Hospital.

Start date

September 2012 or February 2013

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Project description

Lack of physical activity contributes to ill health and is a problem encountered globally. There is a need to explore novel interventions to encourage physical activity particularly among sedentary individuals. Cognitive biases are known to affect physical activity levels as well: for instance, research shows that people systematically underestimate how much they will enjoy exercising. In this project, the doctoral student will have the chance to explore factors and cognitive biases influencing physical activity with particular attention to inactive people with a view to develop and test novel and brief interventions that can be cost effective and easily applied in sport settings.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Gozde Ozakinci (School of Medicine)

• Brazilian University Supervisor(s):

  n/a

Additional notes

Health Psychology Group is a research active group that focuses on intervention development and testing and communication related issues. The doctoral student will be joining a lively and supportive group of staff and postgraduate students that use the ory to develop and test effective interventions for health behaviours. In addition, active research connections with School of Psychology will mean that the student will have an added advantage to benefit from expertise that exists across Schools.

Start date

September 2012 or February 2013

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Project description

Microsporidia are intracellular eukaryote parasites that are pathogenic in AIDS patients and responsible for economically important diseases in bees and fish. Infection is achieved through a polar tube that penetrates the membrane of the host cell. The student will aim to discover the intracellular mechanisms and proteins involved in polar tube assembly. The project will involve protein biochemistry, high-resolution electron tomography and quantitative immuno-electron microscopy. Our long-term aim is to identify key proteins/processes and develop drugs that could target microsporidial infection.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr John Lucocq (School of Medicine)

• Brazilian University Supervisor(s):

  n/a

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

As the 2011 Lancet series on health in Brazil highlighted, the country has made great advances in improving child and maternal health overall. However, there are two areas which remain of concern: the medicalisation of childbirth (namely, the high prevalence of caesarean delivery for non-medical reasons) and the prevalence of illegal abortions.   Abortion is a hugely contentious issue, involving as it does issues relating to religion, culture, and society, and the government in Brazil are currently debating the issue. This project will not seek to answer the moral question of the “rightness” or otherwise of abortion but rather seek to investigate the health-related problems and resource burden posed by illegal abortions in Brazil. In this project the student will examine both the legislation and health burden associated with illegal abortions in Brazil, and then carry out a comparison with other South American countries, and European countries with similar cultural/religious beliefs, to determine if lessons can be learnt from other countries and what the most appropriate and realistic means of addressing this problem might be.

Availability

Co-tutelle PhD (12 months UK, 24 in Brazil)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Morven Shearer, School of Medicine, University of St Andrews

• Brazilian University Supervisor(s):

  To be decided.

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

As the 2011 Lancet series on health in Brazil highlighted, the country has made great advances in improving child and maternal health overall. However, there are two areas which remain of concern: the medicalisation of childbirth (namely, the high prevalence of caesarean delivery for non-medical reasons) and the prevalence of illegal abortions.   In this project the student will investigate the reasons underlying the overuse of caesarean delivery in Brazil, and compare approaches to child birth and choice in the UK with those of their home country and the subsequent impact on maternal and child health, as well as the burden on health care resources.

Availability

Co-tutelle PhD (12 months UK, 24 in Brazil)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Morven Shearer, School of Medicine,

• Brazilian University Supervisor(s):

  To be decided.

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

The rise in multiple drug resistance appears unstoppable. We are short of novel agents to treat patients with resistant organisms and current methods to identify patients infected with MDR strains are expensive and require expensive high containment laboratories that are beyond the reach of man hospitals in low and middle income countries. A new technological solution rapidly identifies organisms that are resistant to rifampicin, an important drug in the treatment regimen. This approach has two problems, the individual test cost is high and it tells the physician what he or she is not able to treat the patient with. We are developing a low cost high speed antibiotic susceptibility device that will be able to produce results in 48 hours (compared with two weeks) and will be able to be used in the facilities usually available in hospital laboratories in low and middle income countries. Moreover, it will have a flexible format that allows a range of antibiotic agents to be tested simultaneously which means that the physician will be able to build a successful regimen

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Professor Stephen Gillespie and Dr Mario Giardini (School of Medicine)

• Brazilian University Supervisor(s):

  n/a

Additional notes

This studentship will allow the student to assist in the evaluation of this new device that has the potential to bring susceptibility testing to district level. The student will work to develop and evaluate the device in the laboratory and in the field working with clinicians and clinics internationally.

Start date

October 2012

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Project description

Zinc is crucial to normal immune function, where deficiencies lead to several known abnormalities in cellular immune responses. Despite this, very little is currently known of its precise roles at the cellular and molecular level. This project will focus on two aspects, which will provide core observations on how zinc influences immune responses. 1) Zinc as a regulator of immune complex clearance. Collectively, complement proteins form part of the body’s innate immune system and are involved in removal of pathogens and immune complexes. The first component of the system is a protein called C1q. It is thought that activation of C1q is controlled in a zinc-dependent manner via its interaction with another protein called histidine-rich glycoprotein (HRG). It has been presumed that zinc acts as a signaling molecule, whereby zinc released from blood cells binds to HRG, causing dissociation of C1q to initiate activation of the complement cascade. Here we will examine zinc release from monocyte-derived dendritic cells (DC: key antigen presenting cells) and its impact on C1q activation using model systems consisting of DC preparations and purified proteins. 2) The role of zinc in exosome formation. Exosomes are small (50-150 nm) secreted vesicles that have a wide range of biological functions based on their ability to deliver signals and cargo to cells at both neighbouring and distant sites. They are under intense investigation as novel therapeutics, and have already passed Phase I clinical trials as mini-cancer vaccines. The homeostasis of zinc in dendritic cells is altered upon antigen stimulation, and leads to a decrease in intracellular concentration. We will use human monocytes and monocyte-derived DC to modify their ability to uptake zinc, and determine the effects on exosome secretion, their contents and biological function.

 

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Alan J. Stewart & Dr Simon J. Powis, School of Medicine, University of St Andrews

• Brazilian University Supervisor(s): n/a

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

Gonadal hormones (such as testosterone and estrogen) can impact upon the development of the brain, leading to sex differences in brain structure and function. While previous research on rodents has shown that the brain is sensitive to the effects of gonadal hormones during prenatal and perinatal periods of life, this project will investigate the hypothesis that adolescence is also a period of life when gonadal hormones influence brain development and subsequent behaviour. Psychopharmacological techniques will be used to suppress gonadal hormones during adolescence in rats, and the effects on long-term behavioural and brain development will be examined. Techniques will include the use of hormone antagonists, ELISA hormone assays, immunohistochemistry and detailed behavioural analysis. The results will provide novel insights into why human males and females are differentially susceptible to a range of mental health disorders.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Gillian Brown (School of Psychology & Neuroscience)

• Brazilian University Supervisor(s):

  n/a

Additional notes

The field of behavioural neuroendocrinology has a strong history in Brazil and is gaining influence at an international level, as exemplified by the First Brazilian International Symposium on Integrative Neuroendocrinology (2011). The student would gain experience of the neuroendocrinology community within the UK through membership of the British Society for Neuroendocrinology. Within St Andrews, the student would become a member of the Institute of Behavioural and Neural Sciences (IBANS), which supports interdisciplinary research across Psychology, Biology, Chemisty and Medicine. In the School of Psychology, PhD students receive advanced training in statistical techniques and experimental design, and all students gain generic skills training. PhD students attend seminars, present their research at conferences and workshops, and often experience public engagement activities, all of which provide an excellent foundation for their future careers.

Start date

September 2012 or February 2013

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Project description

The last twenty years are seeing a remarkable development in the fields of photonics, of electronics and of biomedical engineering. This excitingly unique technological combination has only just begun to show its potential, and is stimulating and transforming the vision and practice of research and clinical medicine. Light offers the unique possibility to access, simultaneously, both the morphology and the chemistry of biological samples. This allows, in principle, to identify the specific cell types present in the samples, key issue to effective diagnostics in a number of diseases. This PhD studentship will focus on the development of light-based technologies for in-field diagnosis and monitoring of tuberculosis (TB).

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Stephen Gillespie and Mario Giardini (School of Medicine)

• Brazilian University Supervisor(s):

  n/a

Additional notes

One third of the world population is infected with Mycobacterium tuberculosis and, of these, 5-10% will develop TB throughout their life. Light-based technologies are intrinsically robust, can be miniaturised, and lend themselves to be implemented in inexpensive disposable units, thus simplifying the management of the large number of dangerous samples coming from the TB patients. They are therefore extremely attractive for real-life, in-field clinical situations. This PhD studentship will provide the exciting opportunity to work in a multidisciplinary team on the frontier between microbiology and engineering. All aspects, from manipulating cells and cell cultures, to designing and building instruments, to testing them in-field, to liaising with medical and industrial Partners, will be explored.

Start date

October 2012

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Project description

The student will develop a new experimental approach to social learning research, drawing on niche construction theory and developmental systems theory. The method comprises the integration of subjective, perceptual and behavioural data in an experimental game context. The goal will be to investigate the processes involved in the development of the knowledge and skills in the observer throughout the social learning process.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s): Prof Kevin Laland (School of Biology)
• Brazilian University Supervisor(s):

  n/a

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

Fluorinated compounds make up 20% of pharmaceutical products. Replacing fluorine for hydrogen does not have a significant steric effect but it suppresses adventitious metabolism, influences pK_a of functional groups and alters solution conformation. The C-F bond is polar and subject to strong stereoeletronic effects. A series of bioactive neurotransmitter analogues will be explored, combining experiment (synthesis, NMR, X-ray) with theory to evaluate the influence of varied fluorine substitution with a focus on neuroactive compounds GABA and NMDA. The student will prepare/synthesise and analyse appropriate compounds in St Andrews and carry out the theory studies in Lavras.

Availability

Co-tutelle PhD (12 months UK, 24 in Brazil)

Supervisers

• University of St Andrews Supervisor(s):

  Prof David O'Hagan (School of Chemistry, St Andrews)

• Brazilian University Supervisor(s):

  Prof Matheus P Freitas (Universidade Federal de Lavras, Campus Universitário - UFLA, Dept. de Química, 37200-000, Lavras-MG,Brasil)

Additional notes

D. O'Hagan has hosted Prof. Freitas during his recent fruitful visit in St Andrews, which, in collaboration with M. Bühl, has resulted in the following two publications: Joint publications: D. O'Hagan, M. P. Freitas, M. Bühl, Chem. Commun., 2011, 48, 2433; M. P. Freitas, M. Bühl,D. O'Hagan, R. A. Cormanich, C. F. Tormena, J. Phys. Chem. A, 2012, 116, 1677.

Start date

September 2012 or February 2013

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Project description

Crick (1984; PNAS81:4586-4590) wrote, “If the thalamus is the gateway to the cortex, the reticular complex might be described as the guardian of the gateway”. The reticular complex, or thalamic reticular nucleus (TRN), is a sheet of GABA-ergic cells, interposed between thalamus and cortex. It receives collateral projections from both thalamocortical and corticothalamic fibres, but the projections of TRN are only to thalamus. As such, the TRN is privy to the information passing between cortex and thalamus and positioned such that it could filter this information. By its projections into thalamus, the TRN could ‘open’ selected thalamic channels to cortex and close others. Such a function defines the requirements of a substrate of attention. In our studies of the TRN in rats, our aim has been to understand how the brain might solve the problem of selection of inputs with the intention of understanding how and why this might sometimes fail: from errors arising from normal lapses of attention, to functional pathologies of attention arising from brain dysfunction or disease. This project will take a multidisciplinary approach employing behavioural and electrophysiological techniques coupled with pharmacologically selective agents. The aim of the project is to characterize the role played by GABA and nicotine in information transmission in the TRN, with a view to understanding the potential significance of this pathway to the attentional and cognitive deficits in schizophrenia.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Prof Verity J Brown and Dr Eric M Bowman (St Andrews),

• Brazilian University Supervisor(s):

  n/a

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

Crick (1984; PNAS81:4586-4590) wrote, “If the thalamus is the gateway to the cortex, the reticular complex might be described as the guardian of the gateway”. The reticular complex, or thalamic reticular nucleus (TRN), is a sheet of GABA-ergic cells, interposed between thalamus and cortex. It receives collateral projections from both thalamocortical and corticothalamic fibres, but the projections of TRN are only to thalamus. As such, the TRN is privy to the information passing between cortex and thalamus and positioned such that it could filter this information. By its projections into thalamus, the TRN could ‘open’ selected thalamic channels to cortex and close others. Such a function defines the requirements of a substrate of attention. In our studies of the TRN in rats, our aim has been to understand how the brain might solve the problem of selection of inputs with the intention of understanding how and why this might sometimes fail: from errors arising from normal lapses of attention, to functional pathologies of attention arising from brain dysfunction or disease. This project will take a multidisciplinary approach employing behavioural and electrophysiological techniques coupled with pharmacologically selective agents. The aim of the project is to characterize the role played by GABA and nicotine in information transmission in the TRN, with a view to understanding the potential significance of this pathway to the attentional and cognitive deficits in schizophrenia.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Prof Verity J Brown and Dr Eric M Bowman (St Andrews),

• Brazilian University Supervisor(s): n/a

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

The human MHC class I molecule HLA-B27 is strongly linked to the inflammatory arthritic condition ankylosing spondylitis (AS). 90% of patients with AS express HLA-B27. Recent genetic studies have also identified a role in the disease process for ERAP1, a proteolytic enzyme which is involved in the assembly of HLA-B27. This project will use a variety of cellular, biochemical and molecular biological approaches to study the role that both HLA-B27 and ERAP1 play in AS.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Simon Powis, School of Medicine, University of St Andrews

• Brazilian University Supervisor(s):

  n/a

Additional notes

The student appointed in this project will be based in the new Medical and Biological Sciences Building in St Andrews, which provides excellent research facilities. The student will join a highly research active Principal Invesitigator and research group working on the immune system. The student will also be able to attend postgraduate training courses, attend conferences and receive skills training for future career development. 1. Campbell, E.C., Fettke, F., Bhat, S., Morley, K. and Powis, S.J. (2011) Expression of MHC class I dimers and ERAP1 in an ankylosing spondylitis patient cohort. Immunology, 133, 379-385; 2. Antoniou, A.N., Guiliano, D.B., Lenart, I., Burn, G. and Powis, S.J. (2011) The oxidative folding and misfolding of human leukocyte antigen-B27. Antioxidants and Redox Signalling, 15, 669-84; 3. Lenart, I., Guiliano, D.B., Burn, G., Campbell, E.C., Morley, K., Fussell, H., Powis, S.J. and Antoniou, A.N. (2012) The MHC class I heavy chain structurally conserved cysteines 101 and 164 participate in HLA-B27 dimer formation. Antioxidants and Redox Signalling, 16,33-43.

Start date

September 2012 or February 2013

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Project description

Transcription factor IIH (TFIIH) is a 10 subunit protein complex essential for both transcription initiation and Nucleotide Excision Repair (NER) in eukaryotes. Mutations in subunits of TFIIH, in particular the helicases XPB and XPD, lead to a spectrum of genetic diseases including xeroderma pigmentosum and trichothiodystrophy, characterised by extreme sensitivity to sunlight. Because of its intrinsic complexity, the structure of TFIIH and role of each subunit in transcription and repair is not completely understood, with progress dependent on studies of subunits conserved in archaea. In this PhD project, available to any individual with a good first degree in the life sciences, you will build on recent progress in the reconstitution of TFIIH from the fission yeast Schizosaccharomyces pombe. Biochemical, genetic and structural studies of the complex and individual sub-complexes will be used to define their functions, mechanisms and interactions in DNA repair and transcription.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Professor Malcolm White (School of Biology)

• Brazilian University Supervisor(s):

  n/a

Additional notes

n/a

Start date

September 2012 or February 2013

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Project description

Apart from Man, marine mammals have probably evolved the most advanced form of acoustic communication of any species. This ability is particular to cetaceans that use active sound production underwater. Through the development of acoustic monitoring systems that can be deployed on the animals or using sub-sea and surface-mounted systems it has been possible to open a up a whole new field in marine mammal passive acoustic measurement. This can be directed towards testing models of social structure and the functional typology of cetacean vocalizations as well as simply allowing these animals to be surveyed to assess their distribution and abundance. The project(s) will involve the application of these methods to study marine mammals either within coastal regions of Brazil or in the Amazon Basin.

Availability

Co-tutelle PhD (12 months UK, 24 in Brazil)

Supervisers

• University of St Andrews Supervisor(s):

  Dr Luke Rendell, Professor Peter Tyack; Dr Vincent Janik; Dr Mark Johnson; Dr Patrick Miller

• Brazilian University Supervisor(s):

  n/a

Additional notes

The work will be conducted within the Sea Mammal Research Unit (SMRU) which is a part of the Scottish Oceans Institute at the University of St Andrews but operates globally. SMRU is a globally-leading centre for marine mammal research and it is responsible for developing many of the current technologies used to study marine mammals including both instruments and software tools. It has a close working relationship with industry , through its commercial arm SMRU Ltd.

Start date

September 2012 or February 2013

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Project description

Alzheimer’s disease is characterised by deficits in episodic memory. Much is known about the molecular and genetic basis of the disease but in order to translate this knowledge into pharmacological or genetic treatments a viable animal model must be developed. This has so far proved to be difficult as many researchers do not accept that animals possess episodic memory. This project would aim to validate a currently used animal model of episodic memory in humans. The student will examine whether similar behavioural manifestations are present in both humans and rodents performing the episodic memory task. They will go on to test whether these behavioural manifestations are correlated with episodic memory use in humans. This project has the potential for great impact by providing a link between the learning and memory literature in systems neuroscience and drug discovery research in pharmaceutical companies.

Availability

Full PhD (36 months in UK)

Supervisers

• University of St Andrews Supervisor(s):

  Dr James Ainge (School of Psychology & Neuroscience)

• Brazilian University Supervisor(s):

  n/a

Additional notes

James Ainge is a member of the Alzheimer’s Research UK (ARUK) network and as such is in regular contact with researchers at the forefront of basic and clinical research into the disease. The student would have the opportunity to expand the research either by testing a clinical population of Alzheimer’s patients or by examining the molecular and genetic factors underlying the disease. Current related work includes a project grant from ARUK, in collaboration with Prof Frank Gunn-Moore, to examine endophilin-1, a gene which is up-regulated in Alzheimer’s disease.

Start date

February 2013

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