Molecular and Cellular Medicine PhD research projects

Supervisor: Genever, Prof Paul

Analysis of mesenchymal stromal/stem cell sub-populations

Human mesenchymal stromal/stem cells (MSCs) are found in adult tissues such as bone marrow and are able to differentiate into osteogenic, chondrogenic and adipogenic tissues. There is intense interest in determining how MSCs may be used in future cell-based therapies, including gene therapy, immunotherapy and tissue engineering, and as in vitro models for fundamental research and drug discovery. However, little is known about MSC identity and research is often performed on heterogeneous mixtures of different MSC sub-populations. Using a process of telomerase-based immortalisation and cell cloning, we have generated several different MSC lines that represent different “types” of MSCs. For example, some MSC lines demonstrate tri-lineage, whereas other are bi-potent, uni-potent or nulli-potent. This project will examine the differentiation characteristics of these MSC lines to determine how they reflect MSC sub-populations in vivo.

Supervisor: Pegine Walrad

None currently

Supervisor: Paul Kaye

For application requirements, process, and guidelines please see the postgraduate study pages of the Department of Biology website (http://www.york.ac.uk/biology/postgraduate/). New available studentships are announced on these web pages, the Departmental site and on FindAPhD.

Supervisor: Adrian Mountford

 

 

For application requirements, process, and guidelines please see the postgraduate study pages of the Department of Biology website (http://www.york.ac.uk/biology/postgraduate/). New available studentships are announced on these web pages, the Departmental site and on FindAPhD.

Supervisor: Southgate, Professor Jenny

 

Self-funded PhD Studentship (example below)

Project Title

Homeostatic mechanisms in human urothelium: balancing of tissue regeneration and differentiation with implications for regenerative medicine and cancer

The urothelium is the self-regenerating epithelium that lines the bladder, where it is highly specialised to function as a urinary barrier.  Although normally a mitotically-quiescent tissue, urothelium shows a rapid and highly regenerative response to damage.  Whether there is a specific progenitor or stem cell population remains controversial, as no such cell has been unequivocally identified. An alternative hypothesis is that all cells remain capable of switching into a regenerative phenotype, irrespective of differentiation state.  The project will examine this hypothesis in a well-established cell culture system, using a combination of cell and molecular biology approaches to examine the role of cell:cell interactions, downstream signal transduction and epigenetic regulation.  

Supervisor: Professor Jennifer Southgate (Biology JBU)

Please contact Professor Jennifer Southgate:  Jennifer.southgate@york.ac.uk  if you would like to discuss this or other self-funded projects that may be available.

 

 

 

Supervisor: Ungar, Dr Daniel

Connecting vesicle targeting with SNARE complex assembly (2015-16)

The 2013 Nobel prize in Medicine was awarded for the discovery of the protein factors involved in intracellular vesicle transport. Vesicle transport is critical for processes such as neurotransmitter release or insulin regulated GLUT4 secretion, and therefore impacts on areas like neuroscience and diabetes. Yet the regulation of the final step of vesicle trafficking, the fusion of the two membranes is not well understood. It is well known that a SNARE complex that bridges the two membranes has to form to fuse these membranes, but how SNARE complex formation is regulated is an important open question. We would like to understand how the process of vesicle targeting regulates SNARE complex formation and thereby membrane fusion. During vesicle targeting the first contact between the vesicle and target membrane are made, and therefore this is a key site for vesicle trafficking specificity – where does a vesicle end up in the cell. Large multisubunit tethering complexes (MTCs) coordinate vesicle targeting throughout the cell, one working at the Golgi apparatus is the COG complex. COG is important for the sorting of Golgi-resident proteins, most notably glycosylation enzymes, but also Golgi SNAREs. COG is known to interact with several Golgi SNAREs, yet if this interaction is involved in regulating SNARE complex formation is not established. We will use biochemical SNARE assembly assays with purified COG to address this question. Mutant COG complexes will also be generated, which cannot bind SNAREs, and tested both in the biochemical assay and for their ability to alter sorting within the Golgi. Golgi sorting will be assessed by analyzing the glycosylation potential for cells using a mass spectrometric glycan profiling method. Thus this project will combine biochemical, cell biological, glycobiological and mass spectrometric methods for the analysis of an important cell biological problem.

Miller VJ, Ungar D (2012) Re’COG’nition at the Golgi. Traffic, 13, 891-897

Co directors - Nia Bryant

Supervisor: Elliott, Dr Chris J H

Understanding the role of LRRK2 in Parkinson’s disease (2015-16)

The most common genetic cause of Parkinson’s disease (PD) is a mutation in the LRRK2 gene, G2019S. We have developed a new fly model, which exploits the homology of between fly and human. The proboscis extension response (PER)  shows a marked decline in performance with G2019S expression, but not with other mutations in LRRK2. This loss of function is most marked when G2019S is expressed in the dopaminergic neurons. It can be rescued by drug application. We will use the extensive fly genetic toolbox to test the function of G2019S as a dominant negative kinase mutation,  and to screen candidate genes which slow degeneration. We will support this by using drug application (L-DOPA, kinase inhibitors, glycolytic upregulation). This will provide a new view of LRRK2 neurophysiology in the whole organism, in a way that has not been possible in mouse models.

Supervisor: Chawla, Dr Sangeeta

Role of redox-signalling and oxidative stress in the regulation of neuronal transcription factors (2016-17)

Synaptic activity-induced changes in neuronal gene expression programs direct neuronal differentiation during development and alter connectivity of adult neurons in response to emotional and sensory stimuli. The Class IIa HDACs, HDAC4 and HDAC5 are transcriptional co-repressors that regulate the activity of the myocyte enhancer factor-2 (MEF2) family of transcription factors. Under basal conditions Class IIa HDACs reside in the nucleus and repress MEF2 transcriptional activity. Derepression of MEF2 factors involves synaptic activity-induced nuclear export of Class IIa HDACs through phosphorylation of two conserved serine residues in their N-termini.   Recently, reactive oxygen species (ROS) have been implicated in mediating nuclear export of Class IIa HDACs in muscle through the oxidation of conserved cysteines in HDAC4 and HDAC5. Moreover, HDAC5 displays phosphorylation-independent cyclical changes in subcellular localization (Fogg et al, 2014). This PhD project will examine whether ROS signalling influences HDAC4/5 subcellular localization in primary hippocampal neurons in response to synaptic activity and in response to oxidative stress. It will investigate whether there is an interaction between HDAC4/5 cysteine oxidation and phosphorylation. The project will employ a range of cellular, molecular and biochemical techniques to assess HDAC4/5 localization, phosphorylation and cysteine oxidation in neurons.

References

FoggPCM, O'NeillJS, DobrzyckiT, CalvertS, LordE, LordRL, ElliottCJH, SweeneyST, HastingsMHand Chawla S (2014).  Class IIa histone deacetylases are conserved regulators of circadian function. Journal of Biological Chemistry 289, 34341-34348.

Supervisor: Blanco, Dr Gonzalo

CRISPR/CAS mediated gene therapy of adult muscle (2015-16)

CRISPR/CAS is rapidly becoming the tool of choice for custom designed genome alterations in vitro and in vivo. Genome editing mediated by these nucleases has been used to efficiently modify endogenous genes in a wide variety of cell types and organisms. The primary objective of this project is to edit the genome of adult muscles using an efficient and mild electroporation protocol in vivo to deliver CRISPR/CAS vectors. To evaluate the translational potential of this technology we will use as experimental paradigm the well-characterized mouse muscular dystrophy ky-kyphoscoliosis. The distinctive pathology and overt phenotype displayed by ky/ky mice will greatly facilitate assessment of the genomic modification in adult mice. The KY protein deficiency results and typical dystrophic changes in slow type muscles (Blanco et al, Hum Mol Gen, 2001; Baker et al, Exp Cell Res, 2010), general muscle weakness of supporting muscles and chronic spinal deformity. In this project, the ky mutation will be reversed to wild type by providing a CRISPR/CAS vector designed to cause a double strand breaks near the mutation together with a homologous recombination template with the correct ky sequence. The functional changes of the genomic modification of paraspinal and hindlimb muscles will be assessed at molecular, cellular and whole organismal levels.

Co directors - Paul Genever

 

 

Supervisor: Sweeney, Dr Sean T

Identifying enhancers and suppressors of Frontotemporal Dementia in a Drosophila model (2015-16)

Frontotemporal Dementia (FTD) is a major cause of early onset dementia. Characterised by atrophy of the frontal and temporal lobes with loss in language and social function, FTD incidence has a strong dominant genetic component. A number of loci have been mapped. Among these is CHMP2B encoding a subunit of ESCRTIII, a complex required for endosomal function. We have used mutant CHMP2B to perform genetic screens in Drosophila for enhancers and suppressors of an FTD related phenotype in the fly eye. We have preliminarily mapped 29 loci, three of which we have identified and characterised in detail: a regulator of the Toll innate immune pathway (Ahmad et al., 2009, PNAS), a component of phagosome maturation (Lu et al., 2013, Mol Cell) and a regulator of the endosomal recycling pathway (paper in preparation). This project will focus on fine mapping and identifying other loci from the screen. Once identified, fly genetics, cell biology and physiology will be used to define the cellular function of such proteins critical to FTD onset and progression. This project is a collaboration with Professor Fen-Biao Gao of the Department of Neurology, University of Massachusetts, Worcester. Exchanges between labs may play an important part of the project.

Supervisor: Nathalie Signoret

 

For application requirements, process, and guidelines please see the postgraduate study pages of the Department of Biology website (http://www.york.ac.uk/biology/postgraduate/). New available studentships are announced on these web pages, the Departmental site and on FindAPhD.