Principal supervisor - Jeremy Derrick, co-supervisors Ian Kimber (Faculty of Life Sciences), Meenu Wadhwa and Robin Thorpe (NIBSC - industrial partner).

4 year BBSRC Bioprocessing Research Industry Club (BRIC) Industrial CASE Studentship

The production of anti-drug antibodies against recombinant human therapeutics can have a detrimental effect on drug efficacy and safety. Although this is generally regarded as a matter for concern within the industry, the precise immunological mechanisms responsible for generation of anti-drug antibodies remain poorly defined. Protein aggregates are believed to play an important part in this process. However, despite this, there have been comparatively few comprehensive studies of this phenomenon. Specifically, systematic investigations are lacking into how the extent and quality of protein aggregation impacts on the induction of immune responses to protein therapeutics. It is the objective, therefore, of this project to characterise the relationships between the structural characteristics of protein aggregates and the vigour and quality of induced immune responses. To address this objective we will use two independent, but complementary, experimental strategies. In the first of these we will use selected human proteins into which different extents and forms of aggregation have been engineered. Protein preparations in which aggregation patterns have been defined and confirmed by structural/biophysical characterisation will then be used for immunisation. At various periods thereafter, the vigour and quality of induced immune responses will be measured. The second experimental strategy will be to examine the influence of aggregation patterns on the recognition, internalisation and presentation of protein antigens by cultured dendritic cells (DC).  The hypothesis is that the ability of proteins with different aggregation patterns to stimulate immune responses of different vigour of quality will, at least in part, be determined by the nature of their interactions with DC. The project will provide training in immunology and protein chemistry relating to aggregate formation in biopharmaceuticals, and would suit a student with an interest in a career in the biotherapeutics industry.

Applications should be submitted no later than Friday 15 June 2012

1.         Rosenberg, A.S. The AAPS Journal 8, E501-7 (2006).

2.         Sauerborn, M. et al. Trends Pharmacol. Sci. 31, 53-59 (2009).

3.         Holgate, R.G.E. et al. Idrugs 12, 233-237 (2009).

4.         Porter, S. J. Pharm. Sci. 90, 1-11 (2001).

5.         Casadevall, N. et al. N. Engl. J. Med. 346, 469-475 (2002).

• Biochemistry
• Biomolecular Sciences
• Biotechnology
• Immunology
• Molecular Biology

Helicobacter pylori colonize the gastric mucosa of over half the world’s population. Infected individuals are predisposed to develop chronic active gastritis and peptic ulcer disease {McColl, 1997 #233} and may succumb to more severe gastric diseases, including gastric adenocarcinoma, and mucosa associated lymphoid tissue lymphomas.
This project will focus on the role of the pro-inflammatory protein Galectin-3, in the immune response to H. pylori infection. Galectin-3 recruits and activates phagocytic cells. It is up regulated and rapidly secreted by gastric epithelial cells in response to H. pylori adhesion and may play a pivotal role in stimulating an immediate influx of inflammatory cells to the site of infection.
Intriguingly, galectin-3 can adhere to H. pylori O-antigen. By sequestering secreted galectin-3, this interaction may modulate the inflammatory response and facilitate colonisation of the gastric mucosa by H. pylori. In addition, adhesion to galectin-3 may also interfere with the ability of O-antigen to adhere to its alternate ligand DC-SIGN. O-antigen-DC-SIGN interactions block development of a Th1 response which allows asymptomatic, long term colonisation to occur. By inhibiting this interaction galectin-3 may promote generation of a Th1 response which favours the onset of acute infection and the development of gastric ulcers.

Project aims
To determine the role played by galectin-3 in the pathogenesis of H. pylori disease. This overall aim encompasses several subsidiary objectives
i) To determine whether the secretion of galectin-3 by gastric epithelial cells is pivotal role to the recruitment and activation of inflammatory cells in response to H. pylori infection.
ii) To establish whether the O-antigen / galectin-3 interactions attenuate the inflammatory response to H. pylori infection.
iii) To establish whether adhesion of galectin-3 to O-antigen modulates the Th1/Th2 response by competitively inhibiting the adhesion of O-antigen to its alternative ligand, DC-SIGN.
 

• Edwards N. J., Monteiro, M., Walsh, E., Moran, A. P., Roberts, I. S., and High, N. J. (2000) Lewis X structures in the O-antigen side chain promote adhesion of Helicobacter pylori to the gastric epithelium. Mol. Microbiol. 35: 1530-1539.
• Mark Fowler, Rachael J. Thomas, John Atherton, Ian S. Roberts and Nicola J. High (2006) Galectin-3 binds to Helicobacter pylori O-antigen: it is upregulated and rapidly secreted by gastric epithelial cells in response to H. pylori adhesion. Cellular Microbiol. 8:44-54

• Immunology
• Microbiology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

In evolution, multi cellular organisms have developed an adaptive immune system, which allows specific recognition of Non-Self molecules. This adaptive immune system is important for the fight of the host against infections. The large genome sequencing effort is constantly producing new information on genes building up the element of adaptive immune system. We developed one database that collects all information related to mouse and human immunoglobulin genes automatically from sequence central databases, called VBASE2.

The aim of the project is to open this database for more species, produce automatic expert type annotation of immunoglobulin variable gene regions of many species and to add more types of genes building up the adaptive immune system. Programming language skills and experience with relational database systems would be very useful but not essential.
 

Retter I, Chevillard C, Scharfe M, Conrad A, Hafner M, Im TH, Ludewig M, Nordsiek G, Severitt S, Thies S, Mauhar A, Blöcker H, Müller W, Riblet R, (2007) Sequence and Characterization of the Ig Heavy Chain Constant and Partial Variable Region of the Mouse Strain 129S1. Journal of immunology (Baltimore, Md.: 1950) 179(4): 2419-27.

Retter I., Althaus HH., Munch R., Muller, W. (2005) VBASE2, an integrative V gene database. Nucleic Acids Research 33 (Database issue): D671-4.
 

Bioinformatics

Genetics

Immunology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The World Health Organization has highlighted the emergence of antibiotic resistant bacteria as ‘a natural, unstoppable phenomenon exacerbated by the abuse, overuse and misuse of antimicrobials in the treatment of human illness.’ In addition to the toll on human life and increase in suffering, antimicrobial resistance costs an estimated US$4,000-5,000 million annually in the USA and €9,000 million in Europe. To combat the acute problems provoked by the emergence and spread of antimicrobial resistance, there is an urgent need to develop new compounds that act on novel genetic circuits in bacteria. One of these potential targets is the DNA segregation apparatus. The Hayes laboratory focusses on the molecular mechanisms underlying the basis of segregation using plasmids, mobile genetic elements implicated in the dissemination of antibiotic resistance, as tractable model systems. More specifically, we probe the events that lead to formation of the segrosome nucleoprotein complex at the centromere, and the role of cytoskeletal elements in precise segregation. To this end we examine segrosome dynamics of a multiresistance plasmid in the model bacterium, Escherichia coli, and in the human opportunistic pathogen Enterococcus faecium. Enterococci are among the most pernicious of antibiotic-resistant bacteria because they are inherently impervious to many antibiotics, but also because they have acquired resistance genes against antibiotics that were previously useful. We also are investigating the action of toxin-antitoxin (TA) complexes that are widely distributed in pathogenic and other bacteria. TAs induce reversible cell cycle arrest or programmed cell death in response to starvation or other adverse conditions. As the toxin components of TAs are potential intracellular 'molecular timebombs', activation of these toxins with designer drugs may be a novel antibiosis strategy. Work in the laboratory encompasses a range of cutting-edge molecular biological, biochemical and biophysical techniques that provide an excellent basis for a career in biosciences research.

• Derome A, Hoischen C, Bussiek M, Grady R, Adamczyk M, Kedzierska B, Diekmann S, Barillà D, Hayes F (2008) Centromere anatomy in the multidrug resistant pathogen Enterococcus faecium. Proc. Natl. Acad. Sci. USA 105:2151-2156.
• Barillà D, Carmelo E, Hayes F (2007) The tail of the ParG DNA segregation protein remodels ParF polymers and enhances ATP hydrolysis via an arginine finger-like motif. Proc. Natl. Acad. Sci. USA 104:1811-1816.
• Hayes F, Barillà D (2006) The bacterial segrosome: a dynamic nucleoprotein machine for DNA trafficking and segregation. Nature Rev. Microbiol. 4:133-143.
• Barillà D, Rosenberg MF, Nobbmann U, Hayes F (2005) Bacterial DNA segregation dynamics mediated by the polymerizing protein ParF. EMBO J. 24:1453-1464.
• Hayes F (2003) Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science 301:1496-1499.
 

• Biochemistry
• Biomolecular Sciences
• Biotechnology
• Gene Expression
• Genetics
• Microbiology
• Molecular Biology
• Pharmacology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Glycoconjugate vaccines have proven remarkably successful in combating a number of human diseases caused by bacterial pathogens. However the synthesis of glycoconjugates is technically challenging and is considered a “roadblock” to the further development and application of such vaccines. The recent identification, in the human pathogen Campylobacter jejuni, of a bacterial oligosaccharyltransferase involved in protein N-glycosylation has initiated novel “in vivo” approaches to glycoconjugate biosynthesis. In essence glycoconjugates can now be synthesised enzymatically rather than chemically, and this reaction can be carried out in the genetically tractable bacterium Escherichia coli. Comparative genomic analysis of emerging genome sequences from phylogenetically related bacteria has identified further N-linked oligosaccharyltransferases. This project aims to build on our exciting initial work demonstrating that these enzymes have distinct activities from the C. jejuni encoded enzyme thereby expanding their potential use in glycoconjugate biosynthesis. The project will aim to identify and functionally characterise bacterial oligosaccharyltransferases employing a multidisciplinary approach involving a range of molecular microbiological, bioinformatic, biochemical and structural approaches.

• Jervis AJ, Langdon R, Hitchen P, Lawson AJ, Wood A, Fothergill JL, Morris HR, Dell A, Wren BW and Linton D. Characterisation of N-linked protein glycosylation in Helicobacter pullorum. Journal of Bacteriology (2010) 192:
• Linton D, Dorrell N, Hitchen PG, Amber S, Karlyshev AV, Morris HR, Dell A, Valvano MA, Aebi M and Wren BW. Functional analysis of the Campylobacter jejuni N-linked protein glycosylation pathway. Molecular Microbiology (2005) 55:1695-1703.
• Szymanski CM and Wren BW. Protein glycosylation in bacterial mucosal pathogens. Nature Reviews Microbiology (2005) 3: 225-237.

• Biochemistry
• Microbiology
• Molecular Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The HIV pandemic is one of the greatest challenges facing healthcare providers across the globe today. Worldwide 33.2 million people were HIV positive at the end of 2007 with 2.5 million new cases reported that year. Highly active antiretroviral therapy (HAART), is the current treatment for HIV, however HAART does not cure HIV infection and also has several disadvantages including severe, unpleasant side effects as well as the emergence of resistance. Prevention of HIV transmission would therefore be a better approach and requires a vaccination or microbicide approach. Attempts to develop an HIV vaccine have so far been unsuccessful. New microbicides may therefore represent the best opportunity to prevent transmission of HIV, and thereby lessen the pandemic.

One source of such microbicides may be antimicrobial peptides. Dr Dobson’s group have previously developed a range of peptides based on a cationic sequence within apolipoprotein E and apolipoprotein B with broad antiviral activity, including activity against HIV, both blocking viral entry into cells and selectively disrupting the viral envelope. The peptides inhibit all strains of HIV tested, and herpesviruses. The peptides would be suitable for development as microbicides for topical application to prevent HIV transmission. This project will focus on the further development of these peptides as microbicides against HIV and HSV2.

Specifically the study will identify more potent peptides and features associated with potency whilst retaining biocompatibility. A small a library of peptides will be screened primarily against HSV2, and ultimately against HIV, benchmarking against existing candidate microbicides. Activity will be correlated with a range of structural properties of the peptides, assessed using state of the art biophysical techniques. Additionally, the impact of formulation in standard microbicidal gels will be assessed as will the influence of physiological fluids on activity.
 

• Kelly, B.A., Harrison, I., McKnight, A. & Dobson, C.B (2010). Anti-infective activity of apolipoprotein domain derived peptides in vitro: identification of novel antimicrobial peptides related to apolipoprotein B with anti-HIV activity. BMC Immunology, 11, 13.

• Kelly BA, Neil SJ, McKnight A, Santos JM, Sinnis P, Jack ER, Middleton DA, Dobson CB. (2007). Apolipoprotein E-derived antimicrobial peptide analogues with altered membrane affinity and increased potency and breadth of activity. FEBS Journal, 274, 4511-4525.

• Dobson CB, Sales SD, Hoggard P, Wozniak MA, Crutcher KA. (2006). The receptor-binding region of human apolipoprotein E has direct anti-infective activity. J Infec Dis, 193(3), 442-450.

• Dobson C.B., Wozniak M.A. and Itzhaki R.F. (2003). Do infectious agents play a role in dementia? Trends in Microbiology, 7: 312-317.
 

• Biochemistry
• Biomolecular Sciences
• Biotechnology
• Cell Biology
• Immunology
• Microbiology
• Pharmacology
• Structural Biology

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Effective wound healing and timely restoration of skin functions is essential to prevent infection. As we age our skin’s ability to heal diminishes. Indeed, in many older individuals the process of wound healing fails entirely, leading to disease phenotypes such as leg ulcers or bed sores. Current treatments for poor wound healing are ineffective. Thus, there is an urgent need to develop new tharapies. We have identified a key role for estrogen deficiency in delayed wound healing, an effect that can be reversed by estrogen treatment. More recently we have discovered differential roles for the two murine estrogen nuclear hormone receptors during skin wound healing. Further, our comparative gene expression studies have identified numerous associated estrogen-regulated genes and processes that represent potential new targets for therapeutic manipulation to promote wound healing in elderly humans.

You will be embedded within a leading tissue regeneration research group based in new state of the art laboratory facilities in the Faculty of Life Sciences. You will be exposed to and trained in varied techniques, ranging from gene expression profiling, nano-structural quantitative data anaysis, surgery and mouse phenotyping to analysis of clinical samples and proof-of-principle clinical studies. We have strong collaborations with colleagues in the Faculty of Medicine and world-leading experts in estrogen signalling. Ultimately, this work should lead to the development of new therapies to accelerate healing.
 

• Campbell L, Emmerson E, Davies F, Gilliver SC, Krust A, Chambon P, Ashcroft GS and Hardman MJ. (2010) Estrogen promotes cutaneous wound healing via ER beta independent of anti-inflammatory activities. J Exp Med. Epub – Aug 23
• Emmerson E, Campbell L, Ashcroft GS and Hardman MJ. (2010) The phytoestrogen genistein promotes wound healing by multiple independent mechanisms. Mol Cell Endocrinol 321:184-93.
• Emmerson E, Campbell L, Ashcroft GS, Hardman MJ. (2009) Unique and synergistic roles for 17beta-estradiol and MIF during cutaneous wound closure are cell type specific. Endocrinology. 150:2749-57.
• Hardman MJ, Ashcroft GS. (2008) Estrogen, not intrinsic aging, is the major regulator of delayed human wound healing in the elderly. Genome Biol. 9:R80.
   

• Animal Biology
• Biochemistry
• Cell Biology
• Cell Matrix Research
• Developmental Biology
• Genetics
• Immunology
• Molecular Biology
• Physiology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

This project will be jointly supervised by Lydia Tabernero (Lead Supervisor, Faculty of Life Sciences), William Hope (School of Translational Medicine) and Jen Cavet (Faculty of Life Sciences)

Mycobacterium tuberculosis (Mtb), the causing agent of tuberculosis, is one of the most succesful human pathogens. This intracellualr pathogen is able to survive in host immune cells, macrophages, by defeating the innate immune system and avoiding destruction by the antimicrobial mechanisms within macrophage phagosomes. The molecular mechanims that facilitate such survival are still unclear, but manipulation of the host phosphoinositide metabolism is, in part, responsible for phagosome maturation arrest. MptpB is a secreted phosphatase, essential for survival of Mtb within macrophage phagosomes. The biological substrates of MptpB have not yet been defined, but we discovered that MptpB dephosphorylates phosphoinositides needed for specific membrane attachment of Rab proteins and EEA1 that direct phagosome maturation and fusion to lysosomes associated with bacterial killing. This suggests a potential role for MptpB in host phosphoinositide metabolism and phagosome maturation arrest offering exciting new directions for pharmacological intervention of tuberculosis. We also identified potent inhibitors of MptpB that impair the survival of Mtb in infected macrophages supporting our hypothesis. Next we want to use these inhibitors to further study the role of MptpB in pathogenesis and phagosomal maturation arrests and as targets for drug development to treat tuberculosis.
This project offers an exciting new approach to exploit virulence factors to develop novel therapies to fight tuberculosis. The project will involve a multidisciplinary approach with biochemical and structural analysis together with microbiological, cellular and imaging technologies. The collaborative nature of the project is a unique opportunity to engage in real translational research with the benefits of an interdisciplinary working environment (basic research and clinical pathology). The complementary expertise of groups involved means that the student will have a much broader and rounded up training during the PhD.
 

• Singh R, Rao V, Shakila H et al. Mol Microbiol 50(3), 751–762 (2003).
• Beresford N, Patel S, Armstrong J, Szoor B, Fordham-Skelton AP, Tabernero L. Biochem. J. 406(1), 13–18 (2007).
• Beresford NJ, et al. J. Antimicrob. Chemother. 63(5), 928–936 (2009).
• Lestner J.M., Howard S.J., Goodwin J., Gregson L., Majithiya, J., Jensen G.M., Hope W.W. Antimicrobial Agents and Chemotherapy (2010), 54(8):3432-41.
• Hope W.W., et al., Journal of Infectious Diseases (2007), 1;195(3):455-66.

• Biochemistry
• Biomolecular Sciences
• Microbiology
• Pharmacology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Genome damage, by “genotoxins” can lead to cancer. Animal genotoxicity tests are part of the final stage in safety assessment before novel pharmaceuticals go into clinical trials, but earlier assessments of genotoxic hazard are carried out in mammalian cell lines or bacteria: the latter tend to produce misleading ‘false positives’.
The project is part of a programme of research investigating the reasons for misleading positive results, and developing strategies for improved in vitro tests.
 

• Birrell L, Cahill P, Hughes C, Tate M, Walmsley RM. (2010). GADD45a-GFP GreenScreen HC assay results for the ECVAM recommended lists of genotoxic and non-genotoxic chemicals for assessment of new genotoxicity tests. Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 695(1-2), 87-95. 2010
• Billinton N, Bruce S, Hansen JR, Hastwell PW, Jagger C, McComb C, Klug ML, Pant K, Rabinowitz A, Rees R, Tate M, Vinggaard AM, Walmsley RM. (2010). A pre-validation transferability study of the GreenScreen HC GADD45a-GFP assay with a metabolic activation system (S9). Mutation Research, 700, 44-50 2010-07-20

• Biomolecular Science
• Biotechnology
• Cell Biology
• Environmental Biology
• Gene Expression
• Genetics
• Molecular Cancer Studies
• Toxicology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Many tissues, including skin, undergo major structural and functional changes with age, losing both elasticity and the ability to repair following injury. We have shown that fibrillin microfibrils, important components of the elastic fibre system, are degraded in aged skin and that estrogen deprivation is associated with a significant loss of microfibril tensile strength. Although estrogen is known to protect against age-associated changes in skin both the causative mechanisms and influence of this hormone on the elastic fibre system remain poorly understood.

You will be co-supervised by Dr Matthew Hardman (Faculty of Life Sciences) and Dr Mike Sherratt (Faculty of Medicine) and embedded within a leading tissue regeneration research group based in new state of the art laboratory facilities in the Faculty of Life Sciences. Your project will investigate the molecular and cellular mechanisms underlying a) accelerated skin ageing in the absence of estrogen and b) estrogen’s protective and restorative effects on skin structure and function. To achieve this you will employ a wide range of techniques including transgenic and surgical models, physiological, cellular, molecular and nano-structural analysis and clinical studies.
 

• Campbell L, Emmerson E, Davies F, Gilliver SC, Krust A, Chambon P, Ashcroft GS and Hardman MJ. (2010) Estrogen promotes cutaneous wound healing via ER beta independent of anti-inflammatory activities. J Exp Med. Epub – Aug 23
• Emmerson E, Campbell L, Ashcroft GS and Hardman MJ. (2010) The phytoestrogen genistein promotes wound healing by multiple independent mechanisms. Mol Cell Endocrinol 321:184-93.
• Sherratt MJ, Bayley CP, Reilly SM, Gibbs NK, Griffiths CE, Watson RE. (2010) Low-dose ultraviolet radiation selectively degrades chromophore-rich extracellular matrix components. J Pathol. 222:32-40
• Emmerson E, Campbell L, Ashcroft GS, Hardman MJ. (2009) Unique and synergistic roles for 17beta-estradiol and MIF during cutaneous wound closure are cell type specific. Endocrinology. 150:2749-57.
• Hardman MJ, Ashcroft GS. (2008) Estrogen, not intrinsic aging, is the major regulator of delayed human wound healing in the elderly. Genome Biol. 9:R80.
   

• Animal Biology
• Biochemistry
• Cell Biology
• Cell Matrix Research
• Developmental Biology
• Genetics
• Immunology
• Molecular Biology
• Physiology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Hepatitis C virus (HCV) poses a major threat to global human health, infecting 170 million people worldwide. It causes chronic hepatitis which can progress into fibrosis, cirrhosis and liver cancer. The virus life cycle begins when the virus successfully enters host cell. This requires the binding of virus envelope proteins to the host cell receptors, endocytosis of the virus particles and subsequent fusion of virus with host’s endosomal membrane. HCV primarily infects liver cells. To date several host cell receptors have been identified but a liver cell-specific receptor remains elusive. Much less is known about the identity of the viral peptide that mediates fusion and the fusion process itself. Understanding these processes is important for therapeutic intervention. Projects are available to study these entry processes by identifying host cell receptors and fusion peptides and selection of peptides and antibodies that will block these processes, using a range of biochemical, molecular and cellular biological and virological methods.

• Microbiology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The immune system must be primed to quickly respond to infection, but must also be tightly regulated so that self-tissues are not attacked in normal healthy individuals. A breakdown in immune system regulation can result in autoimmune diseases such as inflammatory bowel disease, diabetes and arthritis. Therefore understanding the pathways and mechanisms that keep the immune system in a resting state at times of health are vital in understanding what goes wrong to cause autoimmune disease.

This project will study pathways and mechanisms by which cells of the immune system communicate with one another to prevent autoimmune disease. Specifically, the project will focus on how the important immune cytokine TGF-beta is produced and activated by different immune cells, and how TGF-beta affects immune responses.

The project will utilise a variety of different techniques including animal models, molecular biology and cell culture models to study:

1. The mechanisms by which activation of TGF-beta by immune cells is turned on (to prevent autoimmunity).
2. The mechanisms by which the pathway is turned off (when the immune system must eliminate infection).
3. How different cells of the immune system are affected by the pathway.

The student will join my laboratory located within the Manchester Immunology Group and the Wellcome Trust Centre for Cell-Matrix Research within the world-class Faculty of Life Sciences at the University of Manchester, and will have access to a wide-range of expertise and facilities present within the faculty.
 

• Animal Biology
• Cell Biology
• Cell Matrix Research
• Immunology
• Molecular Biology

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Infection by gastrointestinal parasites (GI) is one of the most common types of parasitic infection in man and animals worldwide. Despite a considerable increase in our understanding of the immunoregulatory mechanisms that govern the adaptive and innate immune responses to GI parasites, progress in defining the mechanisms of protection has been slow. It is becoming clear that to remove such large multicellular pathogens from the GI tract largely revolves around the capacity of host molecules and cells to directly affect the normal metabolic activity of the parasites reducing their fitness, or indirectly alter the niche in which the parasites live making it unfavourable for parasite survival. The net result is that parasites become damaged, are not often killed by the host response but are unable to reproduce optimally and are ultimately expelled out of the host during normal intestinal transit.
Type 2 cytokine responses control a variety of cellular changes in the intestinal epithelia associated with host protection against GI nematodes. One important feature is goblet cell hyperplasia. Despite the fact that the major secreted factors from goblet cells are the gel-forming mucins a clear role for these molecules in mucosal protection against GI nematodes has only recently been identified in our laboratories. We have identified a critical role for mucins in protective immunity to the GI nematode, Trichuris muris. We hypothesise that gel-forming mucins are a major effector mechanism involved in protection against intestinal nematodes. The goals of this project are to define how gel-forming mediate protection against Trichuris muris and investigate its protective function against other intestinal nematodes.
This project will provide the student with a comprehensive training in a broad range of biochemical, immunological, proteomic, in vitro and in vivo approaches; these will include gel chromatographic, electrophoretic and centrifugal separations, tandem mass spectrometry, cell culture, immunoassay and mouse models.
 

Hasnain,, S.Z., Wang, H., Ghia, J.E., Haq, N., Deng, Y., Grencis, R.K., Velcich, A., Thornton, D.J. and Khan, W.I. Mucin Gene Deficiency in Mice Impairs Host Resistance to Enteric Parasitic Infection. Gastroenterology (2010) 138 (5):1763-71
Thornton, D.J., Rousseau, K. & McGuckin, M. (2008) Structure and function of the polymeric mucins in airways mucus. Annual Review of Physiology 70, 5.1-5.28
 

• Biochemistry
• Cell Matrix Research
• Immunology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The project will investigate the molecular and cellular basis of resistance and susceptibility to infection by gastrointestinal nematodes. Using the well established model system of whipworm infection  (Trichuris muris), the project will explore the regulation of immunity which leads to parasite expulsion and/or chronic infection using transgenic approaches in combination with analysis of the cellular immune response. The project will involve the use of a variety of techniques both in vitro and in vivo, including immunoassay, cell and tissue culture, gene expression, flow cytometry and immunohistology.

• Humphreys NE & Grencis R K (2009) Il-1 dependent IL-1R independent resistance to gastrointestinal nematodes. European Journal of Immunology, 39, 1036-45
• Artis D & Grencis RK (2008) The intestinal epithelium: sensors to effectors. Mucosal Immunology 4, 252-64.
• Humphreys NE, Xu D, Hepworth MR, Liew FY, Grencis RK, (2008) IL-33, a potent inducer of adaptive immunity to intestinal nematodes. Journal of immunology 180: 2443-9.
• McDermott JR, Humphreys NE, Forman SP, Donaldson DD, Grencis RK (2005) Intraepithelial NK cell-derived IL-13 induces intestinal pathology associated with nematode infection. Journal of immunology 175: 3207-13.
• Cliffe LJ, Humphreys NE, Lane TE, Potten CS, Booth C, Grencis RK (2005) Accelerated intestinal epithelial cell turnover: a new mechanism of parasite expulsion. Science 308: 1463-5. 

• Immunology
• Microbiology

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Antigen-specific adaptive immunity requires processing of foreign materials (antigens) by professional antigen presenting cells such as dendritic cells (DC). DCs loaded with tumour associated antigens (TAA) can be used as vaccines to stimulate anti-tumour immunity. Effective cancer vaccines must activate CD8+ cytotoxic T lymphocytes (CTLs or “killer” T cells) that can destroy tumour cells. Vaccine adjuvants are also necessary to help the immune response by increasing inflammation. Potent inflammatory adjuvant activity has been found in necrotic cell lysates which contain endogenous danger signals that can be taken up by DCs and modulate their function. A self-funded PhD project is available to investigate the efficient processing of tumour cells by DCs, for enhancing antigen cross-presentation to activate CTLs. Using a system of specific TAA and CD8+ T cells specific for the antigen, you will investigate forms of tumour cell death (apoptosis versus necrosis) and associated release of endogenous danger signals, on antigen processing, presentation, and co-stimulation to increase CTL responses. Techniques for measuring immuno-stimulatory function of DCs will include surface phenotyping by antibody staining and flow cytometry (FACS), assaying for pro-inflammatory cytokine secretion by ELISA, and assessing antigen-specific CD8+ T cell proliferation and cytotoxicity.

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The sequence of bases in DNA is not the only form of coded information in a genome. Base methylation, as well as modifications to the histones around which the DNA is wrapped, are also critical in defining the level of a gene’s expression. The study of information beyond DNA sequence is called epigenetics. Genetic and epigenetic changes can cause deleterious changes in gene expression which can lead to carcinogenesis.

Chemical carcinogens that affect the DNA genome may cause mutations, chromosome breakage or chromosome mis-segregation and are called genotoxic carcinogens. Such agents also induce the GADD45a gene which is involved in the cellular response to genome damage, which is largely effective in either repairing damage, or ensuring that cells with damaged genomes commit suicide. In this way the risk of carcinogenesis is reduced. Our laboratory developed a cell line in which GADD45a regulation is linked to green fluorescent protein expression. Cells exposed to genotoxic carcinogens glow greener than normal cells. This GADD45a-GFP assay is used to detect potential carcinogens amongst new compounds being developed for example as pharmaceuticals, pesticides and herbicides etc (1). At present there are no routine assays available to detect “epimutagens”,

Work in our laboratory has shown that the GADD45a-GFP reporter is up-regulated by compounds that affect the acetylation status of histones. Whilst this might be because such compounds also lead indirectly to DNA damage, it might equally reflect a change in the epigenetic regulation of the gene. Other studies add to this suspicion. The GADD45a gene has a “CpG Island” spanning its promoter. Such regions are subject to epigenetic down-regulation by DNA methylation, and in some tumour cells, this part of the GADD45a genes is methylated. This reduces the ability of cells to commit suicide making them more resistant to genotoxic anticancer drugs (2). Interestingly, the GADD45a protein itself is implicated within the process of demethylation, associated with DNA repair (3). Together these observations provide the basis for this PhD project in which the potential for GADD45a expression to serve as a model for the study of epigenetic regulation will be investigated.

1. Hastwell et al., 2009 Mutagenesis 24 (455-463)
2. Al-Romaih et al., 2008 Neoplasia 10 (471-480)
3. Barreto et al., 2007 Nature 445 (671-675)

Biotechnology

Gene Expression
Genetics
Molecular Cancer Studies
Toxicology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Dendritic cells (DCs) direct immune responses by responding to pathogens and directing the appropriate T cell action. A key question is how DCs initiate immunity in tissue sites. The intestine is a major site of infection and diseases that affect millions worldwide yet comparatively little is known about how intestinal DC function particularly large intestinal DCs. The gut is lined by a continuous epithelial barrier which must be breached for pathogens to attack. In the large intestine, we have observed a rapid recruitment of DCs to the gut epithelium which is strongly associated with resistance to many infectious diseases. However, if the influx of DCs into the gut is uncontrolled, chronic inflammation can result. The aim of this project is to define mechanisms involved in DC migration to the epithelium in infection.
 

Ashcroft AJ, Cruickshank S, Croucher PI, Perry MJ, Rollinson SJ, Lippitt JM, Child JA, Dunstan C, Morgan GJ, Carding SR. Colonic Dendritic Cells, colitis and T cell-mediated bone destruction are modulated by recombinant Osteoprotegerin. Immunity. 2003 19: 849-861.

Cruickshank SM, Deschoolmeester ML, Svensson M, Bazakou A, Logunova L, Little MC, Howell G, English N, Mack M, Grencis RK, Else KJ, Carding SR. Rapid Dendritic Cell Mobilisation to the Large Intestinal Epithelium is Associated with Resistance to Trichuris muris Infection. 2009 Journal of Immunology 182: 3055-62.
 

• Immunology

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The canonical pathway of translation of cellular genes is cap-dependent. An alternative form of translation, mediated by means of an internal ribosome entry site (IRES) element, was first reported in viruses and more recently, in a subset of cellular genes that are involved in cellular processes determining cell fate e.g. apoptosis, proliferation, mitosis, angiogenesis. To be able to translate via an alternative mechanism allows evasion of translational control under stress conditions that would otherwise compromise cap-dependent translation, resulting in differential up-regulation of viral genes and select cellular genes. Projects are available to understand how HCV and cellular IRES-mediated translation is regulated under stress conditions and its role in the pathogenesis of HCV-associated diseases, using a range of biochemical, molecular and cellular biological and virological methods.

• Gene Expression
• Microbiology
• Molecular Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Structural studies greatly enhance our understanding of molecular function and mechanisms. We have been studying the molecular mechanisms of protein synthesis and its control in eukaryotic cells. Protein synthesis is a multistep process that relies on a dynamic series of protein-protein and protein-RNA interactions necessary to assemble ribosomes, factors, tRNAs and mRNA. This project will use recombinant protein expression systems to purify specific protein complexes and then use electron microscopy techniques to obtain images to gain insight into the structures of these molecules that are critical for protein synthesis and its control and which are important for human health and disease. For example, mutations in eIF2B cause a genetically inherited brain disease, while regulation of eIF2B activity is critical for a wide variety of cues, including: nutritional responses, stress, fighting viral infections, and long-term memory.

Protein complexes and co-complexes will be generated by purification from yeast cells engineered to overexpress the target proteins. Samples will be prepared by a combination of the negative stain and cryo techniques, and images collected on the transmission electron microscope. Structures of the complexes will be reconstructed in three dimensions.

Analysis of the complex and co-complexes will provide new information to assign the positions of subunits and build a 3D model. Where possible, models of individual subunits/domains generated from Xray crystallography and/or homology modelling will be fitted by density docking into the three dimensional EM maps. Known disease state mutations will then be mapped onto the structures. These experiments will allow deeper understanding and provide insight into the structure/functions of these factors and guide future functional experimentation.
 

• Martin D. Jennings and Graham D. Pavitt. (2010). eIF5 has GDI activity necessary for translational control by eIF2 phosphorylation. Nature, 465(7296), 378-381.
• Pavitt GD, Proud CG. (2009). Protein synthesis and its control in neuronal cells with a focus on vanishing white matter disease. Biochem Society Transactions, 37, 1298-1310.
• Mohammad-Qureshi SS, Haddad R, Hemingway EJ, Richardson JP, and Pavitt GD (2007) Critical contacts between the eukaryotic initiation factor 2B (eIF2B) catalytic domain and both eIF2beta and 2gamma mediate guanine nucleotide exchange. Molecular and Cellular Biology 27(14): 5225-34.
• Roseman, A.M., Berriman, J.A., Wynne, S.A., Butler, P.J.G. & Crowther R.A. (2005). A structural model for hepatitis B virus core maturation. Proc. Natl. Acad. Sci. USA 44, 15821-15826.
• Roseman, A.M., Chen, S., White, H., Braig, K. & Saibil, H.R. (1996). The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL. Cell 87, 241-251.

• Biochemistry
• Biomolecular Sciences
• Gene Expression
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Neisseria meningitidis is the causative agent of meningococcal meningitis and a serious public health problem in developed and developing countries. The outer membrane proteins from N. meningitidis carry out a variety of functions for the bacterium, including transport of small molecule solutes and adhesion to host cell surfaces. They are also important to public health because they are potential vaccine components. This project seeks to determine the structures of these proteins by X-ray crystallography and/or NMR, and to understand how their functions are delivered at the molecular level. It will also examine how the outer membrane proteins interact with immune system molecules, such as antibodies, and how they recognize host cell surface receptors. The work will involve protein expression, purification, structural analysis by X-ray crystallography or NMR and analysis of ligand or protein binding. The studentship would suit a graduate in Biochemistry, Chemistry or a related discipline who wishes to apply their skills to the study of bacterial pathogenicity.

• Prince, S.M., Achtman, M. & Derrick, J.P. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 3417-3421. Crystal structure of the OpcA integral membrane adhesin from Neisseria meningitidis.
• Bond, P.J., Derrick, J.P. & Sansom, M.S.P. (2007) Biophys. J. 92, 23-25. Membrane Simulations of OpcA: Gating in the Loops?
• Bennett, J. S., Callaghan, M. J., Derrick, J. P. and Maiden, M. C. J. (2008) Microbiology 154, 1525-1534. Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.
• Cherezov, V., Liu, W., Derrick, J. P., Luan, B., Aksimentiev, A., Katritch, V. and Caffrey, M. (2008) Proteins 71, 24-34. In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin.

• Biochemistry
• Biomolecular Sciences
• Microbiology
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Metal ion availability plays a vital role in our innate defences against bacterial infection. Bacterial pathogens must compete with their host for essential metals while redox active metals can contribute to their killing by our immune defences. Metal levels alter dramatically between mucosal surfaces, the gastrointestinal tract, circulating fluids and different intracellular environments and several lines of evidence now support the notion that changing metal availabilities (eg Fe, Zn, Cu, Mn & Ni) within a host can alter pathogen survival and select for bacterial virulence determinants. Our laboratory is uncovering the various survival strategies employed by bacterial pathogens to adapt to metal fluxes during infection, with current studies focusing upon the mechanisms of metal sensing and homeostasis in the intracellular pathogen Mycobacterium tuberculosis (the causative agent of TB) and the food-borne pathogen Salmonella sp. PhD projects are available to characterise novel metal sensing and metal homeostatic proteins from these organisms and examine their contributions to virulence. The student will join the Molecular Microbiology Group based in the new Michael Smith Building at the University of Manchester with state of the art facilities, and will receive a broad training in molecular biology, protein biochemistry, cell biology and microbiology (techniques will include DNA and RNA manipulation, protein expression and purification, mammalian cell culture and infection experiments). This training will provide an excellent basis for a career in biosciences research.

• Osman D, Waldron KJ, Denton H, Taylor CM, Grant AJ, Mastroeni P, Robinson NJ & Cavet JS (2010) Copper homeostasis in Salmonella is atypical and copper-CueP is a major periplasmic metal complex. Journal of Biological Chemistry 285.
• Taylor CM, Osman D & Cavet JS (2009) Differential expression from two iron-responsive promoters in Salmonella enterica serovar Typhimurium reveals the presence of iron in macrophage-phagosomes. Microbial Pathogenesis 46: 114-118.
• Beresford NJ, Mulhearn D, Szczepankiewicz B, Liu G, Johnson ME, Fordham-Skelton A, Abad-Zapatero C, Cavet JS & Tabernero L (2009) Inhibition of MptpB phosphatase from Mycobacterium tuberculosis impairs mycobacterial survival in macrophages. Journal of Antimicrobial Chemotherapy 63: 928-936.
• Osman D & Cavet JS (2008) Copper homeostasis in bacteria. Advances in Applied Microbiology 65: 217-247.
• Campbell DR, Chapman KE, Waldron KJ, Tottey S, Kendall S, Cavallaro G, Andreini C, Hinds J, Stoker NG, Robinson NJ & Cavet JS (2007) Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. Journal of Biological Chemistry 282: 32298-322310.

• Biochemistry
• Cell Biology
• Gene Expression
• Immunology
• Microbiology
• Molecular Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Escherichia coli is responsible for a number of extra-intestinal life threatening infections including septicaemia, pyelonephritis and neonatal meningitis. A key virulence factor is the expression of a polysaccharide capsule or K antigen. The capsule plays a key role in conferring resistance to the innate host response. There are projects in two general areas. The first is to study how capsule gene expression is regulated by environmental stimuli and correlate this to the different environments encountered by the bacterium in the host during infection. This project will involve using molecular genetics including techniques such as cloning, PCR, Q-RTPCR, micro-arrays. The second project aims to understand the role of the capsule as a mediator of the host inflammatory response. Specifically this will involve looking at the effect of purified capsular polysaccharides on the chemokine and cytokine response of epithelial cells. This second project is predominantly a cell biology based project and will a involve techniques such as tissue culture, ELISAs and QRT-PCR.

• Corbett, D., Roberts I. S. (2008).
• Capsular Polysaccharides in Escherichia coli. Adv. Applied Micro. 65:1-25.
• Corbett, D., Roberts, IS. (2009).
• The role of microbial polysaccharides in host-pathogen interaction. F1000 Biology Reports 2009, 1:30 (doi: 10.3410/B1-30)

• Biochemistry
• Gene Expression
• Microbiology
• Molecular Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

In normal physiology, the polymeric mucins MUC5AC and MUC5B provide the organizing framework of the airways mucus gel and are major contributors to its properties. However, much of our knowledge of mucins has been gained after isolation under conditions that have disrupted their native interactions in mucus. Thus, we have no adequate description of their 3D-organisation within mucus and how this changes in obstructive airway diseases such as asthma, cystic fibrosis and chronic obstructive pulmonary disease. Such interactions are key to understanding the architecture of mucins, their rheological and transport properties.

This studentship will address the hypothesis that organisation of the mucus gel is defective in obstructive airways disease, resulting in mucus with sub-optimal transport properties and leading to tethering (adhesion) to the epithelial surface. We will focus on this fundamentally important problem to address the following questions:

• How are mucins organized within mucus?
• Is this altered in disease?
• What is the nature of mucin/mucus adhesion to the epithelial surface?

To answer these questions we are working together with clinical colleagues and Faculty members and we will apply a number of state-of-the-art methodologies; these include airway epithelial cell culture, advanced polymer imaging using electron microscopy, mass spectrometry and mucin characterization and quantification. This work is a vital first step in understanding the nature of mucin organization and interactions within mucus. It is anticipated that greater understanding of these processes will lead to better application of current mucus-altering therapies to treat obstructive lung disease and ultimately development of novel agents.

Kirkham, S., Kolsum, U., Rousseau, K., Singh, D., Vestbo, J. & Thornton, D.J. (2008) MUC5B is the major mucin in the gel-phase of sputum in chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 178, 1033-1039.

Thornton, D.J., Rousseau, K. & McGuckin, M. (2008) Structure and function of the polymeric mucins in airways mucus. Annu. Rev. Physiol. 70, 5.1-5.28.

Rosenberg MF, O'Ryan LP, Hughes G, Zhao Z, Aleksandrov LA, Riordan JR, Ford RC. The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR): Three-dimensional structure and localization of a channel gate. J Biol Chem. (2011) 286(49), 42647-54.

• Biochemistry
• Cell Matrix Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Gram-negative pathogenic bacteria, such as Neisseria, Pseudomonas and Vibrio, produce long, thin protein fibres, or pili, from their surfaces. Pili have been shown to be major virulence determinants. They have a number of functions, including binding to specific receptors on the surfaces of the cells of the infected host. In addition, type IV pili also exhibit dynamic behaviour: they are capable of rapid retraction, generating a powerful motor force in the process. The process of retraction has been linked to the ability of bacteria to spread out on certain types of surfaces, a property which influences their ability to cause infection. At least a dozen different proteins are known to be involved in the assembly and disassembly of the pilus fibre, but the way in which they act together as a molecular motor is poorly understood. The overall aim of this project is to understand this process at the molecular level; to do so, we aim to introduce a systems-based approach to the study of pilus biogenesis, developing a quantitative model for the way the retractile machine works. Such work could ultimately help in the development of inhibitors of the process. The studentship would suit a graduate in Microbiology, Biochemistry, Chemistry or a related discipline.

• Collins, R.F., Frye, S.A., Kitmitto, A., Ford, R.C., Tønjum, T. & Derrick J.P. (2004) J. Biol. Chem. 279, 39750-39756. Structure of the Neisseria meningitidis outer membrane PilQ secretin complex at 12 Ångstrom resolution.
• Collins, R.F., Frye, S.A., Balasingham, S., Ford, R.C., Tønjum, T. & Derrick J.P. (2005) J. Biol. Chem. 280, 18923-18930. Interaction with type IV pili induces structural changes in the bacterial outer membrane secretin PilQ.
• Golovanov, A.P., Balasingham, S., Tzitzilonis, C., Goult, B.T., Lian, L.Y., Homberset, H., Tønjum, T. & Derrick J.P. (2006) J. Mol. Biol. 364, 186-195. The Solution Structure of a Domain from the Neisseria meningitidis Lipoprotein PilP Reveals a New Beta-Sandwich Fold.
• Derrick JP. (2008) Structure 16, 1441-1442. A pilot sheds light on secretin assembly.
• Karuppiah, V., Hassan, D., Saleem, M. and Derrick, J.P. (2010) Proteins 78, 2049-2057. Structure and oligomerization of the PilC type IV pilus biogenesis protein from Thermus thermophilus.

• Biochemistry
• Biomolecular Sciences
• Microbiology
• Molecular Biology
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Intestinal nematode worm infection imposes an enormous economic burden on society globally. Indeed the World Health Organisation has shown that worm infection is one of the most significant factors that traps developing countries into poverty. No effective vaccines exist to prevent infection of humans with gut worms. Mice can be protected against infection with murine nematode parasites by vaccination. The project investigates the mechanisms underlying the protection mediated by vaccination of mice normally susceptibility to the intestinal nematode parasite Trichuris muris. Understanding vaccine-induced immunity in the mouse will inform the development of vaccines for use against these sorts of parasites in man. The project uses transgenic approaches and a variety of contemporary immunological methodologies including cell and tissue culture, immunohistochemistry, flow cytometry, gene expression analyses and immunoassay.

Dixon H., Little MC., and Else KJ. (2010) The protective Th2 response following subcutaneous vaccination against T. muris. International Journal for Parasitology 2010 May;40(6):683-93.

d’Elia R., Behnke JM, Bradley JE., and Else KJ. (2009) Regulatory T cells: a role in intestinal helminth survival and the control of host pathology. Journal of Immunology 182, 2340-2348

deSchoolmeester ML., Martinez Pomares L., Gordon S and Else KJ. (2009) The mannose receptor is not important in the expulsion of Trichuris muris. Immunology 126(2), 246-55.

deSchoolmeester ML., Manku H. and Else KJ (2006) The innate immune response of colonicepithelial cells to a nematode parasite does not differ between mouse strains that ultimately develop differentially polarised adaptive immune responses. Infection and Immunity, 74, 6280-6286

Little MC, Bell LV, Cliffe LJ and Else KJ. (2005) The characterization of intraepithelial lymphocytes, lamina propria leukocytes and isolated lymphoid follicles in the large intestine of mice infected with the intestinal nematode parasite Trichuris muris. Journal of Immunology 175, 6713-6722.
 

• Animal Biology
• Immunology

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.