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Professor Chris Thompson (MA, PhD) - postgraduate opportunities

Ion channels and vesicle trafficking

P2X receptors were identified in the 1990s as ion channels that are gated in response to extracellular ATP. They have been shown to play roles in taste sensation, bladder emptying, oxygen sensing, inflammation and pain. P2X receptors are therefore attractive drug targets and clinical trials are currently in progress to test the therapeutic value of P2X receptor antagonists.  Despite this, relative to other ion channel proteins, we know very little of the molecular structure, interacting partners, membrane trafficking, and physiological roles of P2X receptors.  Our research seeks to redress such deficits.

 

Our approach is stimulated by our recent and surprising finding that P2X receptors can be found on intracellular organelles (Nature, 2007). Recently, we have discovered that activation of a intracellular P2X receptors can result in calcium efflux required for downregulation of Rab activity and efficient vacuole fusion (Nature Cell Biology, 2014). Although Rab GTPases are known to play key roles in the delivery, docking and fusion of different intracellular vesicles, the mechanism by which spatial and temporal regulation of Rab GTPase activity is controlled has been poorly understood. Our findings suggest a novel mechanism by which localized calcium release through a vesicular ion channel controls Rab GTPase activity. Our identification of a novel calcium regulated Rab GAP protein found in a complex with the Rab and P2X receptor provides a solution to this problem. Given that P2X channels and this novel class of calcium dependent Rab GAPs are widely conserved, this work provides fundamental insights into Rab GTPase regulation in vesicular trafficking.

 

Currently, we aim to employ genetic, biochemical and cell biological approaches to further define the role of intracellular P2X receptors in vacuole fusion, infection and immunity, and to characterize the factors that regulate P2X receptor function in cells. 

 

Associated skills: Molecular biology, live cell imaging, cell culture, genetic screens, proteomics.

 

Lab website: http://thethompsonlab.wordpress.com/

 

 

  • Parkinson, K., Baines, A., Keller, T., Gruenheit, N., Bragg, L., North, R. & Thompson, C (2014). Calcium-dependent regulation of Rab activation and vesicle fusion by an intracellular P2X ion channel. Nature Cell Biology 16(1), 87-98. eScholarID:219013 | PMID:24335649 | DOI:10.1038/ncb2887

 

 

  • Baines A, Parkinson K, Sim JA, Bragg L, *Thompson CRL, North RA (2013)

Functional properties of five Dictyostelium discoideum P2X receptors.

Journal of Biological Chemistry, vol 288(29) p. 20992-1000

 

 

  • Fountain SJ, Parkinson K, Young MT, Cao L, Thompson CR, North RA. (2007). An intracellular P2X receptor required for osmoregulation in Dictyostelium discoideum. Nature, 448(7150), 200-3. eScholarID:1c6865 | PMID:17625565 | DOI:10.1038/nature05926

 

Stem cell lineage priming and self-organisation of tissue pattern

Biological processes are noisy, leading to huge amounts of cell-cell variability in gene expression. Many scientists have long argued that this variation must be dampened for biological processes such as embryonic development to be reproducible. On the other hand, heterogeneity has also been proposed to play a role in cell fate choice and the generation of developmental pattern in multicellular organisms. For example, when stem cells are exposed to a uniform concentration of a differentiation inducing signal, only some cells respond. Furthermore, these cells can sort out and self organize to generate tissue patterns. However, we know little about what generates heterogeneity, or what controls the motile properties of cells causing them to sort out.

 

Recently we found that Ras-GTPase activity sets the intrinsic response threshold to lineage specific differentiation signals thus providing a novel mechanism for heterogeneity generation and position-independent differentiation (Chattwood et al, eLife 2013).

 

Our research program is now focused on obtaining a better understanding of the molecular basis or source of this heterogeneity, as well as the effects of this heterogeneity on cell fate choice.  For this, we need to identify novel heterogeneously expressed genes that affect cell fate choice and determine the molecular source of heterogeneity. One approach is to use genetics to identify genes that affect the levels of heterogeneity. A step change has come from our ability to measure differences in cell behavior, gene expression, metabolome, proteome, etc between different cells at a whole genome level, and in real time. This quantitative analysis, together with mathematical modelling, will revolutionise our understanding of how and why heterogeneity is generated. These findings will undoubtedly change our understanding of cell fate choice, with implications for therapy and regenerative medicine.

 

Associated skills: Molecular biology, live cell imaging, cell culture, next generation sequencing.

 

Lab website: http://thethompsonlab.wordpress.com/

 

  • Chattwood A, Nagayama K, Bolourani P, Harkin L, Kamjoo M, Weeks G, *Thompson CRL. (2013)

Developmental lineage priming in Dictyostelium by heterogeneous Ras activation. 

eLife, vol 2:e01067.

 

  • Blagg SL, Battom S, Annesley S, Keller T, Parkinson K, Wu M-F, Fisher P and *Thompson CRL (2011)

Cell type specific filamin complex regulation by a novel class of HECT ubiquitin ligase is required for normal cell motility and patterning

Development, vol 138 p. 1583-93

 

Chattwood A, Thompson CR.

Dev Growth Differ. 2011 May;53(4):558-66. doi: 10.1111/j.1440-169X.2011.01270.x.

 

Whole genome sequencing to identify candidate genes governing social behaviour in Dictyostelium discoideum

Although the Darwinian idea of ‘survival of the fittest’ is central to our understanding of the diversity of life on this planet, the evolution and maintenance of cooperative behaviour remains a conundrum. This is because when cooperating individuals perform some sort of costly act to help one another, they run the risk of disruptive cheaters that do not pay their fair share of the cost. In other words, if cheating is a better strategy, how is cooperative behaviour maintained within populations.

To address these problems, we use a simple system for the study of cooperative behaviour, the soil dwelling social amoeba D. discoideum. Under favourable conditions, D. discoideum amoebae exist as single celled individuals that grow and divide by feeding on bacteria. Upon starvation, however, up to 100,000 amoebae aggregate and cooperate to make a multicellular fruiting body consisting of hardy spores supported by dead stalk cells. Stalk cells thus sacrifice themselves to help the dispersal of spores, raising the question of why selection does not lead to unchecked cheating by individuals that do not pay their fair share of the cost of stalk production. Indeed, we have recently found that even within a small number of different D. discoideum strains, different social strategies, including facultative partner specific cheating and coercion, could be detected.

However, the key will be to extend this work to address patterns of genetic variation at the molecular genomic level in natural populations.

Through this PhD studentship we aim to reach this important goal. The project will have 3 stages:

 

1. Genome sequencing: Whole genome sequence data will be generated for many different naturally occurring D. discoideum isolates

 

2. Bioinformatic analysis of this sequence data: This will allow you to test whether genetic variation is associated with patterns of phenotypic variation. Through this you will identify ‘social genes’ and the potential role of all of these genes as generators of biodiversity. Finally, these data will allow broader questions regarding the selective forces driving genome evolution and the emergence of social traits to be addressed.

 

3. Molecular genetics: Using cutting edge developmental genetics techniques (e.g. transformation, knockouts and forced expression of functional variants) you will test hypotheses about the functional consequences of sequence variation on social behaviour.

In summary, this project will address major questions in evolutionary, developmental and environmental ecology. It will utilise hugely multidisciplinary approach by combining next generation sequencing, bioinformatic exploration of sequence variation, together with molecular and developmental genetics. Consequently it will undoubtedly provide an unprecedented opportunity for training in multidisciplinary approaches to biological questions.

 

Associated skills: Bioinformatics, next generation sequencing, molecular biology, cell culture, genetic screens, proteomics.

 

 

 

 

 

  • Parkinson K., Buttery N.J., Wolf J.B. and Thompson C.R.L (2011) A simple mechanism for complex social behaviour. PLoS Biology, vol9 e1001039

 

  • Buttery N.J., Thompson C.R.L, Wolf J.B. (2010) Complex genotype interactions influence social fitness during the developmental phase of the social amoeba Dictyostelium discoideum. Journal of Evolutionary Biology