Prions are novel protein-only infectious agents associated with a group of transmissible neurodegenerative diseases typified by human Creutzfeldt Jakob Disease (CJD). Although CJD are rare diseases, they share many pathological features with other more common, non-infectious diseases of the brain such as Alzheimer’s Disease. In spite of its infectious nature, the majority of cases of human CJD (~80%) appear spontaneously, without any evidence of the associated infectious entity, the prion. However, the molecular basis of how prions form spontaneously into infectious amyloid-like structures is poorly understood at present. Prions are also found in the yeast Saccharomyces cerevisiae and we are using one such prion – called [PSI+] – as a model to identify what triggers the spontaneous formation of a prion in the cell.

Cells contain a sophisticated machinery of proteins, including a number of chaperones, which allows the functional state of proteins to be maintained during conditions where they would normally unfold and aggregate. We have recently shown that the Tsa1 peroxiredoxin has a novel chaperone activity which protects the protein synthesis machinery against aggregation. Peroxiredoxins are best known as antioxidants which protect against oxidative stress and this project will investigate the molecular mechanisms underlying the formation of prions during oxidative stress conditions.
 

• Sideri, T.C., Stojanovski, K., Tuite, M.F. and Grant, C.M. (2010) Ribosome-associated peroxiredoxins suppress oxidative-stress induced de novo formation of the [PSI+] prion in yeast. Proc. Natl. Acad. Sci. U A. 107:6394-6399.
• Rand, J.D. and Grant, C.M. (2006) The Thioredoxin System Protects Ribosomes against Stress-induced Aggregation. Mol. Biol. Cell. 17: 387-401.
• Trotter, E.W., Rand, J.D., Vickerstaff, J. and Grant, C.M. (2008) The yeast Tsa1 peroxiredoxin is a ribosome-associated antioxidant. Biochem. j. 412: 73-80.

• Biochemistry
• Cell Biology
• Genetics
• Molecular Biology

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

Tail-anchored (TA) proteins are characterised by a single C-terminal transmembrane anchor that acts to both target proteins to the correct subcellular compartment and retain the protein in the lipid bilayer following membrane integration. This means that tail-anchored proteins are integrated into their host membrane via a novel post-translational pathway quite distinct from the co-translational insertion of most membrane proteins. The majority of TA proteins are inserted into the endoplasmic reticulum, and different TA protein use distinct pathways for their biogenesis here (Rabu et al, 2009). A key feature of these alternative pathways is the recruitment of different cytosolic factors and molecular chaperones (Abell et al., 2007; Rabu et al., 2008; Rabu et al, 2009). We have recently identified a key role for the cytosolic protein Bat3 in loading tail-anchored proteins onto a second protein, TRC40, which delivers many TA proteins to the ER (Leznicki et al., 2010). Excitingly, Bat3 also interacts with molecular chaperones of the Hsp70 family that mediate an alternative pathway for TA protein biogenesis at the ER (Rabu et al., 2008). We speculate that Bat3 provides a previously undiscovered physical link or scaffold between two distinct routes for TA protein biogenesis. The aim of this project is to test this hypothesis and understand how Bat3 enables TA protein biogenesis in higher eukaryotes. The project will use a combination of molecular biology, in vitro transcription/translation, expression and purification of recombinant proteins, western blotting, immunofluorescence microscopy and heterologous expression in yeast.

Abell, B.M., Rabu, C., Leznicki, P., Young, J.C. & High, S. (2007). Posttranslational integration of tail-anchored proteins is facilitated by defined molecular chaperones. J. Cell Sci. 120: 1743-1751.

Leznicki, P., Clancy, A., Schwappach, B. & High, S. (2010). Bat3 promotes the membrane integration of tail-anchored proteins. J. Cell Sci. 123: 2170-2178.

Rabu, C., Wipf, P., Brodsky, J.L. & High, S. (2008). A precursor specific role for Hsp40/Hsc70 during tail-anchored protein integration at the endoplasmic reticulum. J. Biol. Chem. 283: 27504-27513.

Rabu, C., Schmid, V., Schwappach, B. & High, S. (2009). Tail-anchored protein biogenesis – the beginning for the end? J. Cell Sci. 122: 3605-3612.
 

• Biochemistry
• Cell Biology
• Membrane Trafficking
• Organelle Function

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

Mitochondrion, a vitally important organelle, plays crucial roles during many biological processes (e.g. cell growth and apoptosis), and is implicated in several human diseases and aging process. Protein import is essential for biogenesis of mitochondria, because about 99% mitochondrial proteins are synthesized in the cytosol and have to be imported into mitochondria for their function. The proteins are imported into mitochondria in unfolded forms through specific import pathways that consist of highly regulated translocase complexes. Consequently, correct import, folding, and protein-protein interactions are fundamentally important for mitochondrial biogenesis. Research in my lab focuses on understanding the molecular mechanisms of import, folding, and function of the mitochondrial intermembrane space (IMS) proteins.

One of the recent most important findings in biology is that disulphide bond formation is essential for the import and function of many mitochondrial IMS proteins. Using Tim9 and Tim10 as model proteins, we have made several important findings and contributions to this currently very hot research field. This project is aiming to understand the import and oxidative folding pathways of Tim9 and Tim10, and how Mia40/Erv1 oxidoreductase system and other biologically relevant factors affect the processes. A wide range of well-defined biophysical techniques, as well as biochemical and biological assays have been established in the lab, which will be used and further developed in this project.
 

• Ang, S.K. & Lu, H (2009). Deciphering structural and functional roles of individual disulfide bonds of the mitochondrial sulfhydryl oxidase Erv1p. The Journal of biological chemistry, 284(42), 28754-61. Full text doi:10.1074/jbc.M109.021113
• Morgan, B., Ang, S.K., Yan, G. & Lu, H (2009). Zinc can play chaperone-like and inhibitor roles during import of mitochondrial small Tim proteins. The Journal of biological chemistry, 284(11), 6818-25. Full text doi:10.1074/jbc.M808691200
• Morgan B, Lu H. (2008). Oxidative folding competes with mitochondrial import of the small Tim proteins. The Biochemical journal, 411(1), 115-22. (Faculty of 1000 Biology). Full text doi:10.1042/BJ20071476
• Lu H, Allen S, Wardleworth L, Savory P, Tokatlidis K. (2004). Functional TIM10 chaperone assembly is redox-regulated in vivo. Journal of Biological Chemistry, 279, 18952-8. Full text doi:10.1074/jbc.M313045200

• Biochemistry
• Biomolecular Sciences
• Biotechnology
• Cell Biology
• Molecular Biology
• Organelle Function
• Structural Biology

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

Carbohydrates make up most of the organic matter on earth and serve as major biological fuels. This has resulted in increasing interest in developing technology aimed at utilizing carbohydrates to produce biofuels. Lignocellulosic bioethanol production is particularly attractive in this regard since it offers an alternative source of carbohydrate to that already used as food sources. The main carbohydrate components of lignocellulose are glucose and xylose. Glucose serves as a primary biofuel for most organisms and can repress the synthesis of other carbon metabolizing enzymes through the effects of carbon catabolite repression. The objective of this proposal is to investigate the steps that limit the capacity of Saccharomyces cerevisiae to ferment xylose to ethanol and thus to identify how this process can be significantly improved, such that the utilisation of lignocellulose biomass by this organism can become a viable route to production of bioethanol. A major focus will be on the post-transcriptional control of mRNAs expressing key components of xylose metabolism. Our preliminary experiments indicate that the pathways of xylose breakdown are regulated by both transcriptional and translational mechanisms, and it is only by considering all of gene expression that we can truly understand the production of bioethanol from lignocellulose.

• Biochemistry
• Biotechnology
• Genetics
• Molecular Biology

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

Plant cell walls account for most of the plant biomass and as such represent a huge source of potential novel resources. They have the advantages of being both renewable and yielding very low net CO2 emissions. Plant cell walls are currently receiving a huge amount of attention as a potential source of biofuels and could be destined to both replace oil reserves as they diminish and to do it in a manner that will contribute to reducing green house gas emissions. There are a huge number of other potential processes that exploit plant cell wall material including pulp and paper production. With the world’s population growing coupled with greater demands on land use, there is increasing pressure to generate more efficient ways of utilising plant material.

One of the challenges is to use biotechnology to alter the composition of cell walls in a way that they can be much more easily processed and used.

The project will involve using an integrated approach, molecular biology, biochemistry and genetics to improve our understanding of how different classes of genes regulate cell wall composition and to understand the role of different cell wall polymers in determining cell wall properties. The aim is to exploit this information and use genetic engineering to alter the composition and assembly of the cell wall to generate cell wall material that allows different cell wall compounds to be separated much more easily. This would greatly improve our ability to process plant cell wall material more efficiently and also greatly improving its value.
 

• Brown, D.M., Zhang, Z.N., Stephens, E., Dupree, P., and Turner, S.R. (2009). Characterization of IRX10 and IRX10-like reveals an essential role in glucuronoxylan biosynthesis in Arabidopsis. Plant J. 57, 732-746.
• Atanassov, II, Pittman, J.K., and Turner, S.R. (2009). Elucidating the Mechanisms of Assembly and Subunit Interaction of the Cellulose Synthase Complex of Arabidopsis Secondary Cell Walls. J. Biol. Chem 284, 3833-3841.
• Brown, D.M., Goubet, F., Vicky, W.W.A., Goodacre, R., Stephens, E., Dupree, P., and Turner, S.R. (2007). Comparison of five xylan synthesis mutants reveals new insight into the mechanisms of xylan synthesis. Plant J. 52, 1154-1168.
• Brown, D.M., Zeef, L.A.H., Ellis, J., Goodacre, R., and Turner, S.R. (2005). Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17, 2281-2295.

• Biochemistry
• Cell Biology
• Genetics
• Plant Sciences

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

Cell-Matrix communication is a major factor controlling growth and differentiation in eukaryotes. The extracellular matrix of plants, the cell wall, is structurally unique and needs to resist turgor pressure but is at the same time extensively remodelled during growth and development. It is also an important barrier to pathogens. We are beginning to understand how the different polysaccharide components of the wall are synthesized, but we don't understand how information on cell wall integrity is transmitted into the cell and processed on the molecular level. How is cell wall sensing cross-wired with other stress pathways and pathogen detection? What happens to the normal growth and development of the plant if we interfere with this sensory pathway?

This project will use a broad spectrum of reverse genetics, biochemistry, cutting-edge mass spectrometric techniques (quantitative phosphoproteomics, see ref.) and cell biology. We identify candidate proteins with a potential role in integrity signalling or cell wall repair via transcriptional responses to cell wall damage (microarrays from root tissue) and changes in protein phosphorylation at the plasma membrane. The phenotype of knockout or point mutants in candidate genes will be analysed in terms of development, cell wall composition and pathogen susceptibility, and the potential role of the protein (and the discovered phosphorylation sites) explored additionally with biochemical and cell biological techniques.
 

• Nühse TS, Bottrill AR, Jones AME and Peck SC, “Quantitative Phosphoproteomic Analysis of Plasma Membrane Proteins Reveals Regulatory Mechanisms of Plant Innate Immune Responses”, Plant Journal 51(5): 931-940 (2007)

• Biochemistry
• Cell Biology
• Organelle Function
• Plant Sciences

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 Lisa Swanton (Lead Supervisor, Faculty of Life Sciences), Stephen High (Faculty of Life Sciences), Roger Whitehead (School of Chemistry) and Ian Stratford (School of Pharmacy)

The reversible modification of proteins with ubiquitin represents a universal mechanism to regulate their abundance, activity and localisation. In particular, ubiquitination is a key step in the specific degradation of proteins via the ubiquitin-proteasome system. Ubiquitin is covalently cojugated to substrate proteins by E3 ligases, whilst deubiquitinating enzymes (DUBs) catalyse ubiquitin removal. Ubiquitination is linked to a number of clinically important human pathologies, and DUBs have been implicated in several diseases, including cancer and neurodegeneration. Therefore, the development of DUB inhibitors has considerable therapeutic potential. However, few cell permeable DUB inhibitors have been identified to date. This project brings together synthetic chemistry, cell biology and cellular pharmacology in a multidisciplinary approach to design and synthesise novel DUB inhibitors, which are targeted to specific subcellular localisations. A range of biochemical and cell biological assays will be used to examine the activity and cellular actions of these compounds. Such compartment-specific inhibitors will provide valuable research tools for the analysis of DUB function, and also offer a novel platform for the development of drugs to treat diseases associated with the ubiquitin-proteasome system.

• Colland, F. (2010). The therapeutic potential of deubiquitinating enzyme inhibitors. Biochem Soc Trans 38, 137-143.
• Mahon, K.P., Potocky, T.B., Blair, D., Roy, M.D., Stewart, K.M., Chiles, T.C., and Kelley, S.O. (2007). Deconvolution of the cellular oxidative stress response with organelle-specific Peptide conjugates. Chem Biol 14, 923-930.
• Kang, B.H., Plescia, J., Song, H.Y., Meli, M., Colombo, G., Beebe, K., Scroggins, B., Neckers, L., and Altieri, D.C. (2009). Combinatorial drug design targeting multiple cancer signaling networks controlled by mitochondrial Hsp90. J Clin Invest 119, 454-464.
• Cross, B.C., McKibbin, C., Callan, A.C., Roboti, P., Piacenti, M., Rabu, C., Wilson, C.M., Whitehead, R., Flitsch, S.L., Pool, M.R., High, S., and Swanton, E. (2009). Eeyarestatin I inhibits Sec61-mediated protein translocation at the endoplasmic reticulum. J Cell Sci 122, 4393-4400.
• Nolan, K.A., Scott, K.A., Barnes, J., Doncaster, J., Whitehead, R.C., and Stratford, I.J. (2010) Pharmacological inhibitors of NAD(P)H quinone oxidoreductase, NQO1: Structure/activity relationships and functional activity in tumour cells. Biochemical Pharmacology 80, 977-981.

• Biochemistry
• Cell Biology
• Molecular Biology
• Molecular Cancer Studies
• Organelle Function

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

This project is jointly supervised by Dr Martin Lowe (Lead Supervisor, Faculty of Life Sciences), Dr May Tassabehji (Faculty of Medical and Human Sciences) and Professor Cay Kielty (Faculty of Life Sciences)

Geroderma Osteodysplastica (GO) is an autosomal recessive disorder with clinical features of wrinkled skin, joint laxity and severe osteoporosis. GO is classified as a progeroid disorder affecting the skin and bones since these features are also observed in ageing. GO is caused by mutation of GORAB (also known as SCYL1BP1), a coiled-coil protein of unknown function localized to the Golgi apparatus. Consequently, the molecular mechanisms underlying GO are unknown. The aims of this PhD project are to determine the cellular function of GORAB and dissect the mechanisms by which loss of GORAB leads to the pathological changes observed in GO patients. An attractive hypothesis is that GORAB functions in membrane traffic at the Golgi apparatus such that loss of function mutations cause impaired glycosylation and/or secretion of extracellular matrix proteins of the skin and bone, resulting in aberrant assembly of these tissues. A major aim of the project will be to test this hypothesis. A detailed molecular dissection of GORAB function will be undertaken, and through analysis of GO patients’ cells and tissue samples we will determine the mechanisms by which its loss leads to impaired assembly of the skin and bone. The project is interdisciplinary in nature and will involve work in both the Faculty of Life Sciences and School of Medicine at the University of Manchester. The principal supervisor will be Dr Martin Lowe from FLS with co-supervision by Prof Cay Kielty (FLS) and Dr May Tassabehji (Medicine).

• Hennies, H.C. et al. (2008). Gerodermia osteodysplastica is caused by mutations in SCYL1BP1, a Rab-6 interacting golgin. Nat. Genet. 40, 1410–1412.
• Lowe, M. (2011). Structural organization of the Golgi apparatus. Curr. Op. Cell Biol. 23, 85-93.

• Biochemistry
• Cell Biology
• Cell Matrix Research
• Genetics
• Membrane Trafficking
• Organelle Function

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

Many cancers involve unregulated signalling from mitogenic receptors, so it is vital to understand how the duration of signalling is controlled. This project will look at one important aspect of this, targeting activated receptors within the lysosome.

Key questions that will be addressed include:
How do activated receptors engage the cellular machinery (the so-called ESCRT machinery) that sorts them to the lysosome?

What is the role of the novel protein tyrosine phosphatase, HDPTP, in regulating this pathway?

How does HDPTP influence signalling from epidermal growth factor receptor and other signalling receptors?
 

• Hurley, J. H. and Emr, S. D. (2006). The ESCRT complexes: structure and mechanism of a membrane-trafficking network. Annu Rev Biophys Biomol Struct. 35, 277-98.
• Doyotte et al. (2005). Depletion of TSG101 forms a mammalian `Class E' compartment: a multicisternal early endosome with multiple sorting defects. J. Cell Sci. 118, 3003-3017.
• Driskell et al. (2007). Dynein is required for receptor sorting and the morphogenesis of early endosomes. Nature Cell Biol. 9, 113-120.
• Doyotte, A., Mironov, A., McKenzie, E., and Woodman, P. G. (2008). The Bro1-related protein HD-PTP/PTPN23 is required for Endosomal Cargo Sorting and MVB Morphogenesis. Proc. Natl. Acad. Sci. USA 105, 6308-6313.
• Sorkin, A. & Goh, L. K. (2009) Endocytosis and intracellular trafficking of ErbBs, Exp Cell Res. 315, 683-96

• Biochemistry
• Cell Biology
• Membrane Trafficking
• Molecular Cancer Studies
• Organelle Function

This project has a Band 1 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.

Impaired sensory nerve regeneration in trauma or disease can lead to sensory loss. Sensory nerve injuries are commonly encountered in trauma surgery, yet despite major technical advances in repair techniques, recovery is poor. The most common cause of sensory loss due to disease is diabetic sensory polyneuropathy, which affects approximately 1.5 million people in the UK. There is no treatment or cure for this, or indeed other types of sensory neuropathy. Thus, an improved understanding of the mechanisms underlying sensory nerve outgrowth and regeneration is crucial for development of novel therapeutic strategies to improve patient outcome after sensory loss.

In response to neurotrophins and other growth factors, regenerating neurons interact with extracellular matrix (ECM) molecules (laminin, LM and fibronectin, FN) to navigate away from regions of injury in an attempt to re-innervate their target tissue. Increasing intracellular calcium modulates signal transduction in the growth cone and neurite outgrowth. In culture models of regeneration, neurite outgrowth from sensory neurons has been found to be dependent on the presence of both ECM and neurotrophic factors. Signals from the ECM are transduced to the cell interior via heteromeric integrin receptors. In addition, voltage-gated calcium channels (Cav) are also important mediators of neurite outgrowth, and evidence in various cell types, including neurons, suggests that crosstalk exists between integrin and Cav signalling.

This project aims to define the functional crosstalk between Cav and integrin receptors, which we hypothesize is essential for neurotrophic factor-mediated signal transduction and subsequent regeneration of sensory neurons. Using state of the art facilities and expertise available within The University of Manchester, the student will use biochemistry, cell biology, imaging and electrophysiology to conduct studies in cultured sensory neurons.
 

Bolsover, S. R. Calcium signalling in growth cone migration. Cell Calcium 37, 395-402 (2005).

Woodall, A.J. et al. (2008) Growth factors differentially regulate Cav channels via ERK-dependent signalling in rat sensory neurones. Cell Calcium, 43, 562-575.

Gardiner, N. J. et al. (2007) Pre-conditioning injury-induced neurite outgrowth of adult rat sensory neurons on fibronectin is mediated by mobilisation of axonal alpha5 integrin. Mol. Cell Neurosci. 35, 249-260.
 

• Biomolecular Sciences
• Cell Biology
• Cell Matrix Research
• Channels & Transports
• Molecular & Cellular Neuroscience
• Neuroscience
• Pharmacology
• Physiology

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

Applications are invited for this 3 year funded studentship from the Lowe Foundation.  Informal enquiries can be made to the lead supervisor, Dr Martin Lowe

Lowe syndrome (LS), a disorder that mainly affects the brain, kidneys and eyes, is caused by mutation of a single gene, called OCRL1. Interestingly, mutation of OCRL1 also causes Dent-2 disease, which can be thought of as a milder form of LS in which kidney defects are most obvious. Renal impairment ultimately leading to renal failure is a major cause of morbidity in both LS and Dent-2. It is therefore important we understand how loss of OCRL1 leads to defects in the kidneys, but, unfortunately, we have a poor appreciation of the mechanisms involved. To better understand how the renal pathology of LS and Dent-2 is brought about, we have generated a transgenic zebrafish lacking OCRL1. We have shown that this zebrafish model recapitulates neurological features of LS, and more recently that it exhibits impaired renal function. Preliminary studies suggest that defects in endocytic trafficking are responsible for the observed defects. This PhD project aims to build upon this exciting finding to dissect the underlying mechanisms. Using a number of complimentary approaches we will investigate how loss of OCRL1 affects endocytic trafficking, and how defective endocytosis leads to the renal manifestations of LS and Dent-2. Information gained from the mechanistic studies will be used to generate a reporter zebrafish strain for high-throughput screening for drugs to treat both LS and Dent-2.

Closing date for applications: Wednesday 30 May 2012

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• Animal Biology
• Biomolecular Sciences
• Cell Biology
• Developmental Biology
• Membrane Trafficking
• Organelle Function
• Physiology

Drought is the most severe adverse environmental factor limiting plant productivity in both natural and agricultural systems and climate change is expected to exacerbate this problem. Studies have shown that severe water deficit or prolonged drought induce premature root death. Drought-induced root death has been found in various crops and forest trees (Goss and Watson, 2003). Drought-induced root death is thought to be an active response of the plants to drought, allowing them to redirect root growth to reduce the effect of drought. It is therefore important to understand this adaptative response to drought to take it into account in crop breeding and biotechnology programmes. Recent evidence suggests that root cell death under water stress corresponds to an activation of programmed cell death (PCD). Our lab specialises in identifying novel genes regulating PCD in plants, e.g Bonneau et al 2008, He et al. 2008. The student objectives will be: refine our drought model using Arabidopsis, use cell biology techniques to follow and quantify drought-induced root PCD, use mutant genetics to identify genes that modulate drought-induced root death, use transgenic lines to investigate which plant PCD pathway is activated in roots during drought-induced death.

• Bonneau L, Ge Y, Drury GE, Gallois P, (2008) What happened to plant caspases? Journal of Experimental Botany 59(3): 491-9.
• Goss MJ, Watson CA. 2003. Both drought and excess water can induce premature root death, as can the resupply of water after drought. Journal of Crop Production 8:127-155.
• He R, Drury GE, Rotari VI, Gordon A, Willer M, Farzaneh T, Woltering EJ, Gallois P, (2008) Metacaspase-8 modulates programmed cell death induced by ultraviolet light and H2O2 in Arabidopsis. The Journal of Biological Chemistry 283(2): 774-83.

• Cell Biology
• Genetics
• Molecular Biology
• Plant Sciences

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

Plants require a variety of essential metals for normal growth and development. These metals including zinc, iron, copper and manganese have a number of cellular functions such as enzyme and protein co-factors. Metal transport proteins play a critical role in regulating the accumulation of essential metal nutrients into plants, in partitioning these metals throughout the cell, and in providing tolerance mechanisms to metal stress. Recent work in this lab has begun to identify proteins involved in the cellular homeostasis of some of these metals from model plant species. These include transporters which are important for mediating metal accumulation into internal organelles which can be stores for potentially toxic metals, and regulatory proteins. This project will further characterise the mechanism and function of these metal homeostatic proteins. Manipulation of these genes may be able to improve metal storage and environmental metal stress tolerance in plants. The project will therefore also examine the impact of altered expression of wild type and engineered metal transporters which may have biotechnological potential. This project will provide training in a variety of biochemical, molecular biology and plant biology techniques.

• Edmond C et al (2009) Comparative analysis of CAX2-like cation transporters indicates functional and regulatory diversity. Biochemical Journal 418: 145-154
• Mei H et al (2009) Root development under metal stress in Arabidopsis thaliana requires the H+/cation antiporter CAX4. New Phytologist 183: 95-105
• Mills R et al (2008) ECA3, a Golgi-localised P2A-type-ATPase, plays a crucial role in manganese nutrition in Arabidopsis. Plant Physiology 146: 116-128
• Pittman JK et al (2004) Functional and regulatory analysis of the Arabidopsis thaliana CAX2 cation transporter. Plant Molecular Biology 56: 959-971
• Pittman JK (2005) Managing the manganese: molecular mechanisms of manganese transport and homeostasis. New Phytologist 167: 733-742

• Biochemistry
• Biotechnology
• Channels & Transporters
• Environmental Biology
• Molecular Biology
• Organelle Function
• Plant Sciences

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

Zebrafish are an excellent model for investigating early development. In recent years, this organism has also emerged as a powerful model for investigating a wide variety of pathological conditions including cancer and neurodegenerative disorders, and for studying processes such as stem cell regeneration and angiogenesis. This project will utilise zebrafish to investigate the X-linked disorder called Oculocerebrorenal Syndrome of Lowe (OCRL or Lowe syndrome), which is characterised by defects in the eyes, brain, and kidneys. Lowe syndrome is brought about by mutation of OCRL1, a lipid phosphatase that functions in membrane traffic and intracellular signalling. The aim of this project is to determine the mechanisms responsible for the kidney problems observed in Lowe syndrome patients. It will utilise a mutant zebrafish line we have recently generated to determine the role of OCRL1 both in kidney development and in kidney function in embryos and juvenile animals. The project will use molecular biology techniques including PCR and DNA cloning, developmental biology techniques, fluorescence and electron microscopy, and methods to investigate kidney function in vivo.

• Lowe, M. (2005). Structure and Function of the Lowe Syndrome Protein OCRL1. Traffic 6,711-719.
• Lieschke, G.J., and Currie, P.D. (2007). Animal models of human disease: zebrafish swim into view. Nat. Rev. Genet. 8, 353-367.
• Schurman, S.J., and Scheinman, S.J. (2009). Inherited cerebrorenal syndromes. Nat Rev Nephrol. 5, 529-538

• Animal Biology
• Biomolecular Science
• Developmental Biology
• Membrane Trafficking
• 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.

Non-native proteins are continually generated by errors in biosynthesis, adverse environmental conditions, and genetic mutation. Removal of such aberrant proteins is essential for cellular function, and a failure to degrade misfolded proteins can result in the accumulation of toxic protein aggregates, including those associated with Alzheimer’s, Parkinson’s and Huntington’s diseases. Protein quality control (QC) systems monitor the proteome, identify non-native polypeptides and either promote (re)folding to a native state or initiate degradation. The best characterised of these is the endoplasmic reticulum (ER) QC system, which scrutinises both soluble and transmembrane proteins before they are allowed to exit the ER and proceed along the secretory pathway. The aim of this project is to examine how proteins with defective transmembrane domains are recognised by the ER QC, sorted from those that are properly folded, and ultimately targeted for degradation. The project will involve a range of range of cell-based techniques (mammalian cell culture, transient and stable transfection, RNA interference, fluorescence microscopy), together with complementary biochemistry (electrophoresis, protein purification, cross-linking) and molecular biology (molecular cloning, PCR, mutagenesis) methods.

• Alcock, F. and Swanton, E. (2009). Mammalian OS-9 is upregulated in response to endoplasmic reticulum stress and facilitates ubiquitination of misfolded glycoproteins. J Mol Biol 385, 1032-42.
• Hegde, R. S. and Ploegh, H. L. Quality and quantity control at the endoplasmic reticulum. Current Opinion in Cell Biology 22, 437-446.
• Roboti, P., Swanton, E. and High, S. (2009). Differences in endoplasmic-reticulum quality control determine the cellular response to disease-associated mutants of proteolipid protein. J Cell Sci 122, 3942-53.
• Swanton, E., Holland, A., High, S. and Woodman, P. (2005). Disease-associated mutations cause premature oligomerization of myelin proteolipid protein in the endoplasmic reticulum. Proc Natl Acad Sci U S A 102, 4342-7.

• Biochemistry
• Cell Biology
• Membrane Trafficking
• Organelle Function

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

Proteomics analysis of disease pathways offers a way to decipher the underlying pathogenesis allowing the development of novel drugs for the treatment of the disease. In this project we will exploit the power of proteomics to define the mechanisms responsible for the X-linked disorder Oculocerebrorenal Syndrome of Lowe (OCRL or Lowe syndrome), which is characterised by defects in the eyes, brain, and kidneys. Lowe syndrome is brought about by mutation of OCRL1, a lipid phosphatase that functions in membrane traffic and intracellular signalling. Protein complexes containing OCRL1 from a variety of human tissues will be analyzed using mass spectrometry for identification of specific binding partners. This will be combined with comparative proteomics of wild-type zebrafish and a mutant lacking OCRL1, allowing us to map the disease pathway for Lowe syndrome. Proteins identified using these approaches will be characterized in detail to decipher how loss of OCRL1 leads to Lowe syndrome, and help design drugs for the treatment of the disorder. The project will use mass spectrometry based proteomics, cell culture, PCR and DNA cloning, and fluorescence and electron microscopy.

• Lowe, M. (2005). Structure and Function of the Lowe Syndrome Protein OCRL1. Traffic 6,711-719.
• Aebersold, R., and Mann, M. (2003). Mass spectrometry-based proteomics. Nature 422, 198-207.
   

• Animal Biology
• Biomolecular Sciences
• Developmental Biology
• Membrane Trafficking
• Molecular and Cellular Neuroscience
• 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.

Mitochondria are essential organelle playing a central role in many biological processes. For example, mitochondria perform a central task in the biogenesis of all cellular iron–sulfur (Fe-S) proteins. Not only mitochondrial Fe-S proteins, all cytosolic and nuclear Fe-S protein maturation depends strictly on the function of the mitochondrial Fe-S cluster assembly and export machineries. However, little is known about how a ‘Fe/S’ cluster is exported from mitochondrial matrix to the cytosol is unknown. Evidence suggests that Erv1, an essential component of the MIA pathway is not only required for protein import into mitochondria, but also involved in export of ‘Fe/S’ from mitochondria. Our preliminary study suggests that Mia40 may be able to bind a Fe-S cluster as well. This PhD project will investigate the correlation between Mia40/Erv1 function and biogenesis of cellular iron–sulfur proteins. A wide range of biological, biochemical, and biophysical methods will be used to address the issue comprehensively. The project will be co-supervised and carried out in well equipped labs in the Manchester Multidisciplinary Biocentre. This study will provide important insights into mitochondrial function that are inextricably linked to many human diseases and ageing process.

Lill R. (2009) Function and biogenesis of iron-sulphur proteins. Nature 460:831-8 (Review) 

Lange H. et al. (2001) An essential function of the mitochondrial sulfhydryl oxidase Erv1p/ALR in the maturation of cytosolic Fe/S proteins. EMBO Rep. 2:715-20. 

Ang, SK. & Lu, H (2009). Deciphering structural and functional roles of individual disulfide bonds of the mitochondrial sulfhydryl oxidase Erv1p. The Journal of biological chemistry, 284: 28754-61.

Biochemistry

Biomolecular Sciences

Biotechnology

Cell Biology

Molecular Biology

Organelle Function

Structural Biology

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

Proteins are synthezised in cells by large complex molecular machines termed ribosomes. Whilst ‘nascent proteins’ are still being made by the ribosome they already engage with factors which ensure they fold correctly and/or are targeted to specific locations within the cell (eg. endoplasmic reticulum/secretion, mitochondria, plastids). If this process goes wrong, this can lead to production of misfolded proteins and/or the mislocalization of proteins, which is frequently associated with disease, exemplified by cystic fibrosis.
A delicately balanced interplay exists to ensure the correct factors interact with the ribosome at the right time to ensure correct nascent polypeptide folding and targeting. The project will investigate the molecular mechanisms, which underpin this interplay. Experimental approaches used include a combination of genetics, cell biology and biochemistry using both yeast as a genetically-tractable model system and mammalian-based cell-free assays.
 

• Pool M.R. (2009) A trans-membrane domain inside the ribosome exit tunnel triggers RAMP4 recruitment to the Sec61p translocase. J. Cell Biol. 185: 889-902.
• Kramer G. et al. (2009) The ribosome as a platform for co-translational processing, folding & targeting of newly synthesized proteins. Nat. Struct. Mol. Biol. 16: 589-597.
• Halic M. et al. (2006) Signal recognition particle receptor exposes the ribosomal translocon binding site. Science 312: 745-747.

• Biochemistry
• Cell Biology
• Membrane Trafficking
• Organelle Function

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

Oxidative stress is a major biological problem which has a causal relationship with many disease processes including cancer, neurodegenerative and cardiovascular diseases. All organisms are exposed to reactive oxygen species (ROS) during the course of normal aerobic metabolism or following exposure to radical-generating compounds. In addition, the generation of ROS by neutrophils and macrophages is an important component of immunological defences against pathogens. ROS cause wide-ranging damage to macromolecules eventually leading to cell death.

Cells must be able to maintain their intracellular homeostasis in the face of changing conditions. Typically, they respond by invoking complex regulatory mechanisms including a global inhibition of translation. This reduction in protein synthesis may prevent continued gene expression during potentially error-prone conditions as well as allow for the turnover of existing mRNAs and proteins whilst gene expression is reprogrammed to deal with the stress. We have shown in the yeast Saccharomyces cerevisiae that oxidative stress brings about a rapid inhibition of protein synthesis including an inhibition of translation initiation that is dependent on phosphorylation of the initiation factor eIF2 by the Gcn2 protein kinase. Additionally, translation is inhibited at the post-initiation phase in a Gcn2-independent manner. The aim of this project is to identify how oxidative stress regulates the translation machinery to control protein synthesis.
 

• Shenton, D., Smirnova, J.B., Selley, J.N., Carroll, K., Hubbard, S.J., Pavitt, G.D., Ashe, M,P. and Grant, C.M. (2006) Global translational responses to oxidative stress impact upon multiple levels of protein synthesis. J. Biol. Chem. 281: 29011-29021.
• Mascarenhas, M., Edwards-Ingram, L. C., Zeef, L., Shenton, L., Ashe, M. P., and Grant, C. M. (2008) Gcn4 is required for the response to peroxide stress in the yeast Saccharomyces cerevisiae Mol. Biol. Cell 19: 2995-3007

• Biochemistry
• Cell Biology
• Genetics
• Molecular Biology

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

Cytoplasmic dynein is a microtubule motor whose function is vital for processes as diverse as spindle assembly, chromosome movement, and the transport of membranous organelles. Dynein is also needed to position the mitotic spindle, and this is vitally important for correct development of tissues during embryogenesis and for tissue homeostasis. Its activity as a membrane motor is similarly important in neuronal morphogenesis. Complete loss of dynein function leads to embryonic lethality, but even slight alterations in its activity can cause neurodegenerative diseases (Levy & Holzbaur, 2006). Several different proteins or protein complexes have been identified that play roles in regulating dynein activity or in its interactions with cargo, including dynactin, LIS1, Nudel and Nde (e.g. Lam et al. 2010) and huntingtin (HTT), the protein whose mutation causes Huntington’s Disease (Caviston & Holzbaur, 2009).
In this project, we will investigate the role of HTT in dynein-driven membrane movement using light microscopy of living cells, and using in vitro assays in which dynein-driven membrane movement along microtubules is reconstituted. We will investigate whether HTT is required for dynein and its other regulators to associate with the membrane, and establish a heirarchy of interactions. Since HTT also interacts with the microtubule motor kinesin-1 (which moves in the opposite direction along microtubules compared to dynein), we will also determine in parallel any effects on kinesin-1 activity and membrane binding. This project will involve a broad range of cell biological, biochemical and molecular biological techniques. Together, these studies will determine the role of HTT in microtubule motor protein function.
 

• Lam, C., Vergnolle, M.A.S., Thorpe, L., Woodman, P.G. and Allan, V.J. (2010). Functional interplay between LIS1, NDE1 and NDEL1 in dynein-dependent organelle positioning. J. Cell Sci. 123:202-212
• Levy, J.R. & Holzbaur, E.L.K. Cytoplasmic dynein/dynactin function and dysfunction in motor neurons. Int. J. Dev. Neurosci. 24:103-111
• Caviston, J.P. and Holzbaur, E.L. (2009) Huntingtin as an essential integrator of intracelleular vesicular trafficking. Trends Cell Biol. 19:147-155

• Biochemistry
• Cell Biology
• Membrane Trafficking
• Molecular & Cellular Neuroscience
• Molecular Biology
• Organelle Function

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

Microtubule motors are molecular machines that drive the movement of a wide range of cargoes along microtubule tracks within eukaryotic cells. They are crucial for cell division, migration, and proper development, as well as for continued day-to-day cell functions such as secretion and endocytosis. Their importance is seen most clearly in neurons, where they transport components needed for growth, survival and continued neuronal function over distances of a metre or more. Indeed, neurons are particularly sensitive to slight changes in motor protein function, which over years lead to build up of material in “traffic jams” within neurons, and cause neuronal cell death. Many diseases such as Alzheimer’s, Huntington’s, and motor neuron disease have been linked to defects either in motor proteins themselves or their regulators. As we age, cognitive function slowly declines, even in the absence of disease states. The aim of this project is to determine how microtubule motor activity changes during ageing, since a decrease would lead to impaired neuronal function. If it declines, then identifying drugs that enhance motor activity could provide a means of countering impaired neuronal function in the future.
The specific objectives of the project are:
1. To determine how the motor properties, composition and regulation of the microtubule motors kinesin-1 and dynein in brain changes with age, using young and old mouse brain as a source of material.
2. To determine whether the movement of membranes in the endocytic pathway changes with age in fibroblast cell lines made from young and old human donors. We will use sophisticated live cell imaging approaches and automated particle tracking to analyse the movement of endosomes quantitatively.
 

This project will provide multi-disciplinary training in biochemical approaches, light microscopy of living cells, cell culture and related techniques. There will be a strong emphasis on mathematical approaches for analysing complex endosome dynamics.

• Allan, V.J. (2011). Cytoplasmic dynein. Biochem. Soc. Trans. 39:1169-1178
• Driskell, O.J., Mironov, A., Allan, V.J. and Woodman, P.G. (2007). Dynein is required for receptor sorting and the morphogenesis of early endosomes. Nature Cell Biol. 9:113-120.
• Flores-Rodriguez, N., Rogers, S.S., Kenwright, D.A., Waigh, T.A., Woodman, P.G. and Allan, V. J. (2011) Roles of dynein and dynactin in early endosome dynamics revealed using automated tracking and global analysis. PLoS ONE, 6:e24479.
• Hirokawa, N, Niwa, S and Tanaka, Y. (2010) Molecular motors in neurons: transport mechanisms and roles in brain function, development and disease. Neuron. 68:610-638.

• Biomolecular Sciences
• Cell Biology
• Membrane Trafficking
• Neuroscience
• Organelle Function

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

The endoplasmic reticulum (ER) is a major site for the synthesis of secretory and membrane proteins, and relies on the Sec61 translocon for the cotranslational transport of these proteins into and across its membrane (Cross et al., 2009). We have a long-standing interest in the quality control function of the ER, a process that ensures that misfolded proteins are retained and degraded within the cell (see Alcock & Swanton, 2009; Roboti et al., 2009). The small molecule eeyarestatin I was first identified as an inhibitor of a specific aspect of ER quality control, and we have synthesised the compound and investigated its effects upon cultured cells. In addition to previously reported effects (see Wang et al., 2009 and references therein) we find that eeayrestatin inhibits Sec61 mediated translocation both in vitro and in vivo (Cross et al., 2009). This novel, and unexpected, finding has led us to formulate the hypothesis that it is this inhibition of ER translocation that results in the ability of the compound to induce an ER stress response (Cross et al., 2009; Wang et al., 2009). Co-treatment of cultured cells with both eeyarestatin and small molecules inhibitors of proteasomal degradation exacerbates the ER stress response (Wang et al., 2009; our unpublished data), and this drug combination has been reported to display enhanced toxicity for cancer cells and that eeyarestatin I may provide a basis for novel anticancer agents.

This project will use eeyaretatin I, and a set of related compounds, to study the effects of the drug on both Sec61 function and the ER stress response. Our goal is to understand what contribution the different reported targets of eeyarestatin I make to its effect on cells, and how its toxicity is enhanced in combination with other drugs. A through understanding of the molecular targets and cellular consequences of eeyarestatin treatment will be an essential starting point for any long term application as part of an anticancer therapy. The project will involve a combination of molecular biology and in vitro analytical systems, together with complementary mammalian cell culture and microscopy based imaging techniques.
 

Alcock, F. & Swanton, E. (2009). Mammalian OS-9 is upregulated in response to endoplasmic reticulum stress and facilitates ubiquitination of misfolded glycoproteins. J. Mol Biol. 385: 1032-42.

Cross, B.C.S., McKibbin, C., Callan, A.C., Roboti, P., Piacenti, M., Rabu, C., Wilson, C.M., Whitehead, R., Flitsch, S.L., Pool, M.R., High, S. and Swanton, E. (2009). Eeyarestatin I inhibits Sec61-mediated protein translocation at the endoplasmic reticulum. J. Cell Sci. 122: 4393-4400.

Roboti, P., Swanton, E. & High, S. (2009). Differences in endoplasmic reticulum quality control determine the cellular response to disease-associated mutants of proteolipid protein. J. Cell Sci. 122: 3942-3953.

Wang, Q. et al (2009). ERAD inhibitors integrate ER stress with an epigenetic mechanism to activate BH3-only protein NOXA in cancer cells. Proc.Natl.Acad.Sci.USA 106: 2200-2205.
 

• Biochemistry
• Cell Biology
• Membrane Trafficking
• Organelle Function

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 Philip Woodman (Lead Supervisor), Lydia Tabernero and Stuart Pickering-Brown

Many neurodegenerative diseases are linked to defects in ubiquitin homeostasis/protein folding and/or endosomal trafficking. We have recently identified that UBAP1, a novel risk factor for frontotemporal lobar degeneration (FTLD) (1), is a component of the Endosomal Sorting Complex Required for Transport (ESCRT) pathway (2). This pathway is a series of ubiquitin-recognising protein complexes (ESCRTs 0-III) that orchestrate the sorting of endocytosed signalling receptors to the multivesicular body (MVB), a key transport stage on the lysosomal, degradative pathway (3).

We have shown that UBAP1 is a component of the ESCRT-I complex. ESCRT-I has been shown to perform several cellular roles in addition to endosomal sorting, and this diversity may be linked to the existence of isoforms for several ESCRT-I components. Importantly, we have found that UBAP1 is an isoform of one of these ESCRT-I subunits, and defines the population of ESCRT-I that acts at the endosome (2). UBAP1 is a multidomain protein. It has a tandem C-terminal UBA domain that binds ubiquitin, and a central domain that binds His Domain Protein Tyrosine Phosphatase (HDPTP), a regulator of ESCRT-dependent MVB sorting that we have recently identified (4). It also has an N-terminal region responsible for incorporating UBAP1 into the endosome-specific ESCRT-I complex. Hence, UBAP1 has a central position in organising the MVB sorting of ubiquitinated receptors. Although UBAP1 mutations are linked to FTLD, UBAP1 itself is ubiquitously expressed, and we have shown it is essential for EGF receptor trafficking to the MVB and lysosome (2). We will therefore be able to undertake a detailed structure-function analysis of UBAP1 and understand how it interacts with ESCRT-I and HDPTP. These studies will bring insight into the mechanism of action of UBAP1 and provide clues about how FTLD-associated mutations affect UBAP1 function.

1. Rollinson, S., Rizzu, P., Sikkink, S., Baker, M., Halliwell, N., Snowden, J., Traynor, B.J., Ruano, D., Cairns, N., Rohrer, J.D., et al. (2009). Ubiquitin associated protein 1 is a risk factor for frontotemporal lobar degeneration. Neurobiol Aging 30, 656-665.
2. Stefani, F., Zhang, L., Taylor, S., Donovan, J., Rollinson, S., Doyotte, A., Brownhill, K., Bennion, J., Pickering-Brown, S., and Woodman, P. (2011). UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting. Current Biology 21, 1245–1250.
3. Woodman, P. G., and Futter, C. E. (2008). Multivesicular bodies: co-ordinated progression to maturity. Curr. Opin. Cell Biol. 20, 408–414.
4. Doyotte, A., Mironov, A., McKenzie, E., and Woodman, P. (2008). The Bro1-related protein HD-PTP/PTPN23 is required for endosomal cargo sorting and multivesicular body morphogenesis. Proceedings of the National Academy of Sciences 105, 6308-6313.

Biochemistry
Biomolecular Sciences
Cell Biology
Membrane Trafficking
Molecular & Cellular Neuroscience
Molecular Biology
Organelle Function

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

 Mutations in the gene encoding torsinA cause a neurological disease known as torsion dystonia. The function of torsinA is not yet known, but it is essential for survival and is expressed in the endoplasmic reticulum (ER) of most animal tissues. TorsinA and part of the AAA+ superfamily of ATPases, and is most closely related to the Clp/Hsp100 family of chaperones. It has been suggested that torsinA may also posess a chaperone-like activity in vivo. The aim of this project is to test the hypothesis that torsinA and its close relative torsinB, function as chaperones in the ER of mammalian cells. The results of these studies will be of general significance in terms of understanding the role of torsinA at the ER, as well as providing important insights into the molecular mechanisms that underlie torsion dystonia. The project will involve a range of range of cell-based techniques (mammalian cell culture, transient and stable transfection, RNA interference, fluorescence microscopy), together with complementary biochemistry (electrophoresis, protein purification, cross-linking) and molecular biology (molecular cloning, mutgenesis, in vitro transcription and translation) methods.

• Alcock, F. and Swanton, E. (2009). Mammalian OS-9 is upregulated in response to endoplasmic reticulum stress and facilitates ubiquitination of misfolded glycoproteins. J Mol Biol 385, 1032-42.
• Callan, A. C., Bunning, S., Jones, O. T., High, S. and Swanton, E. (2007). Biosynthesis of the dystonia-associated AAA+ ATPase torsinA at the endoplasmic reticulum. Biochem J 401, 607-12.
• Granata, A., Schiavo, G. and Warner, T. T. (2009). TorsinA and dystonia: from nuclear envelope to synapse. Journal of Neurochemistry 109, 1596-1609.
• Roboti, P., Swanton, E. and High, S. (2009). Differences in endoplasmic-reticulum quality control determine the cellular response to disease-associated mutants of proteolipid protein. J Cell Sci 122, 3942-53. 

• Biochemistry
• Cell Biology
• Membrane Trafficking
• Organelle Function

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.

In excitable cells, such as neurons and muscle, physiological responses depend upon the density of ion channels at the cell surface. The factors which control the numbers and distributions of such channels are poorly understood, but, if manipulated could lead to new therapies to correct diseases such as epilepsy and sleep disorders. 

Work in this laboratory is aimed at identifying the mechanisms which control the trafficking and distributions of voltage-gated calcium and potassium channels. One such channel - the N-type voltage-gated calcium channel (Cav2.2) – is a multi-subunit complex, intimately involved in synaptic transmission and dendritic integration. This project aims to test the hypothesis that the surface expression and distribution of Cav2.2 channels is controlled by an orchestrated intersection of discrete physiological signals and trafficking mechanisms acting upon different task-specific subunit components. To test this hypothesis our goal is to define the kinetics, and regulation of Cav2.2 expression, in response to cell stimuli e.g. growth factors and electrical activity, using novel cell biological strategies that permit the visualisation of Cav2.2 assembly, trafficking and distribution in live cells.

This project lies at the interface of several disciplines including cell and molecular biology, pharmacology, physiology and neurobiology and would be suitable for students with a background in any of the above fields. 

 

• Jones, V., Rodriguez, J., Verkhratsky, A., Jones, O. (2009) A lentivirally-delivered photoactivatable GFP to assess continuity in the endoplasmic reticulum of neurones and glia. Pflugers Archiv-European Journal of Physiology (In Press, ePUb March 19th)
• Mckeown L, Burnham MP, Hodson C, Jones OT. (2008) Identification of an evolutionarily conserved extracellular threonine residue critical for surface expression and its potential coupling of adjacent voltage-sensing and gating domains in voltage-gated potassium channels. J. Biol. Chem. 283:30421-304332.
• Jones, V.C., McKeown, L., Verkhratsky, A., Jones, O.T., (2008) LV-pIN-KDEL: a novel lentiviral vector for probing the dynamics and morphology of the endoplasmic reticulum in live neurones. BMC Neuroscience, 9:10. 
• Bernstein, G.M., Jones, O.T. (2006) Kinetics of Internalization and Degradation of N-type Voltage-Gated Calcium Channels: Role of the alpha2/delta Subunit. Cell calcium, 41, 27-40.
• McKeown, L., Robinson, P., Greenwood, S.M., Hu, W., Jones, O.T. (2006) PIN-G - A novel reporter for imaging and defining the effects of trafficking signals in membrane proteins. BMC Biotechnology, 6:15.

• Biotechnology
• Cell Biology
• Channels & Transporters
• Integrative Neurobiology & Behaviour
• Membrane Trafficking
• Molecular & Cellular Neuroscience
• Neuroscience
• Systems Neuroscience

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

Worldwide crop production is under increasing pressure to meet the needs of a growing populations food and industrial requirements. Plants unlike animals have the ability to produce their own food via photosynthesis. Photosynthesis produces carbohydrates, such as starch, and other important food products such as amino acids, proteins and fats. The major site of these biosynthetic processes is within the family of organelles known as plastids. This PhD will focus on understanding the role and regulation of specific processes within the plastid using a combination of molecular and proteomic approaches. Such studies will provide a clear insight into how different aspects of plastid metabolism contribute to, for example, crop yield. Such information can be combined with biotechnological methods to develop crops able to cope with changing environmental conditions. For example, photosynthetic ferredoxin NADP+ oxidoreductase (pFNR) is an enzymes involved in photosynthesis. pFNR helps the plant cope with environmental conditions such as drought, salinity and temperature stress. Depending on environmental conditions, there are different forms of this enzyme present in the plant. This variation in pFNR forms and the way they function affects the overall ability of the leaf to produce carbohydrates, fats and proteins and therefore crop yield. A PhD undertaken to study this enzyme would provide an understanding of how pFNR forms vary within the plant. This is important because it will help us to understand how photosynthesis is regulated and may lead to an increase in overall yield of the plant.

.

• Moolna A and CG Bowsher (2010). The physiological importance of photosynthetic NADP+ oxidoreductase (FNR) isoforms in wheat. J Exp Bot (in Press).
• Tickle P, MM Burrell, SA Coates, MJ Emes, IJ Tetlow and CG Bowsher (2009). Characterisation of plastidial starch phosphorylase in Triticum aestivum L. endosperm. J Pl Phys 166, 1465-1478.
• Bowsher CG (2008). Chloroplast – the biosynthetic powerhouse?. Biological Sciences Review 21.
• Bowsher CG, M Steer, AK Tobin (2008). Plant Biochemistry. Garland Science 500pp
• Bowsher CG, AE Lacey, GT Hanke, DT Clarkson, LR Saker, I Stulen and MJ Emes (2007). The effect of Glc6P uptake and its subsequent oxidation within pea root plastids on nitrite reduction and glutamate synthesis. J Exp Bot 58, 1109-1118.

• Biochemistry
• Biomolecular Science
• Environmental Biology
• Gene Expression
• Membrane Trafficking
• Molecular Biology
• Organelle Function
• Plant Sciences

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

Microalgae are a diverse group of photosynthetic freshwater or marine organisms that are widely studied with regard to their ecology or as model organisms in biological research. It is apparent that there is increasing potential in using microalgae for a variety of processes, particularly when coupled with powerful molecular techniques that allow their genetic engineering and manipulation. There is particular interest in the use of microbes in sustainable biotechnology - the development of novel ‘green’ processes for solving some of the world’s urgent needs such as for renewable energy resources and for environmental clean-up. Recent projects in the lab are investigating the use of microalgae for bioremediation purposes, such as through the accumulation of toxic metals like cadmium, or the potential of microalgae as a sustainable resource for producing biofuel. This project will further investigate and develop these organisms for sustainable bioenergy or bioremediation strategies. The project will provide training in a variety of experimental techniques including molecular biology, biochemical and cell biology skills.

• Pittman JK et al (2010) The potential of sustainable algal biofuel production using wastewater resources. Bioresource Technology in press ( doi:10.1016/j.biortech.2010.06.035)
• Dean AP et al (2010) Using FTIR spectroscopy for rapid determination of lipid induction in response to nitrogen limitation in freshwater microalgae. Bioresource Technology 101:4499-4507
• Pittman JK et al (2009) A cation-regulated and proton gradient-dependent cation transporter from Chlamydomonas reinhardtii has a role in calcium and sodium homeostasis. Journal of Biological Chemistry 284:525-533
   

• Biotechnology
• Environmental Biology
• Microbiology
• Molecular Biology
• Plant Sciences

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