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Projects available for October 2019

Abstracts of research projects offered for October 2019

The research interests of all the members of the Department are available at www.phar.cam.ac.uk/research.

Candidates are advised to read these research interest pages in conjunction with this information.

 

Dr Matthew Harper:
Platelet heterogeneity in cardiovascular disease

Not all cells behave in the same way, even when they are seemingly of the same type. Heterogeneity in signalling may lead to important biological differences in cell behaviour that may be important in understanding and treating disease.

Platelets play a critical role in arterial thrombosis and myocardial infarction, which is a major cause of death in the UK. During thrombosis, platelets adhere to a ruptured atherosclerotic plaque and become activated. Platelets are short-lived, with a circulating life of 7 – 10 days. Platelets in circulation are a mix of young recently-released platelets, and older platelets. Young platelets are also known as ‘reticulated platelets’. It has been suggested that they are more active and less sensitive to some anti-platelet drugs.

In this project we will study these reticulated platelets. Are they really more active than older platelets? What accounts for their increased activity and drug resistance? Do they play a special role in thrombosis? Are reticulated platelets a potential drug target? To answer these questions, we will use a range of approaches including flow cytometry, fluorescence imaging, protein biochemistry and proteomics.

Keywords: cardiovascular disease; heart attack;  cell signalling; cell heterogeneity; thrombosis

 

Dr Matthew Harper, Dr Graham Ladds and Dr Taufiq Rahman
Novel regulators of cardiovascular G protein-coupled receptors

G protein-coupled receptors (GPCRs) form the largest protein family in the human genome with ~30% of marketed drugs targeting these receptors. GPCRs are key regulators of the cardiovascular system and attractive drug targets. We aim to develop novel small molecule regulators of cardiovascular GPCRs, both as chemical tools to better understand the biology of these receptors and as potential lead compounds. Our collaborative projects use a wide range of techniques, from in silico molecular modelling, through screening and signalling studies in well-characterised receptor expression systems, to understanding the physiological and pathological effects in primary cardiovascular cells. 

Please contact Dr Harper, Ladds or Rahman to discuss the projects offered. Note that these projects are currently unfunded. We particularly welcome applicants who would make strong candidates for prestigious scholarships, such as Gates Cambridge, Cambridge Trust, Vice Chancellor’s Awards, or similar (see www.graduate.study.cam.ac.uk/finance/funding for more details and deadlines). Funded PhD studentships will be advertised separately.

 Keywords: GPCR; in silico; cardiovascular disease; thrombosis

 

Dr Laura Itzhaki:
Tandem-repeat proteins: Folding, function, role in disease and therapeutic intervention

The major focus of our research is a class of proteins with very distinctive architecture, known as tandem-repeat proteins (e.g. ankyrin, tetratricopeptide and armadillo repeats). These proteins are frequently deregulated in human diseases such as cancers and respiratory and cardiovascular diseases. The individual modules of repeat proteins stack in a linear fashion to produce highly elongated, superhelical structures, thereby presenting an extended scaffold for molecular recognition. The term ‘scaffold’ implies a rigid architecture; however, as suggested by their Slinky spring-like shapes, it is thought that repeat arrays utilise much more dynamic and elastic modes of action. For example: stretching and contraction motions to regulate the activity of a bound enzyme; reversible nanosprings to operate ion channels; proteins that wrap around their cargoes to transport them in and out of the nucleus. The modular architecture of repeat proteins makes them uniquely amenable to the dissection of their biophysical properties as well as the rational redesign of these properties. We are interested in understanding how the process of folding and unfolding of this distinctive protein class directs their functions in the cell.  We are also looking at small molecule and peptide-based approaches to target these proteins for therapeutic benefit; examples include the development of inhibitors of ankyrin-repeat proteins gankyrin for the treatment of liver cancer and inhibitors of tankyrase for the treatment of breast cancer. Lastly, we are exploiting the design-ability of repeat proteins with the goal of creating artificial proteins with applications in medicine and nanotechnology.

Research in our group is at the interface between biology and chemistry; we also have close collaborations with computational groups and synthetic chemistry groups in Cambridge, and therefore students will be able to learn a broad range of techniques and approaches, including protein engineering, biochemistry and biophysical analysis including single-molecule techniques, cell biology and medicinal chemistry.

Key words: protein engineering, protein folding, cancer, biotherapeutics

 

Dr Catherine Lindon:
Ubiquitin-mediated signalling in cell division

Cellular proteostasis depends on ubiquitin-mediated targeting of proteins for destruction at the proteasome, and is a critical element in cell cycle control.

PhD projects are available

(1) to investigate the dynamic relationship between destruction and function of the Aurora kinases, important cell cycle regulators and common drivers in cancer

(2) to identify sites of ubiquitin modification in substrates, and the nature of the ubiquitin chains they are modified with, to further understanding of “the ubiquitin code"

(3) to decipher ubiquitin pathways controlling specific substrates (such as Aurora kinases) throughout the cell cycle

These projects will involve time-lapse imaging of living cells to measure substrate proteolysis and localization, and to examine the functional outcomes of ubiquitination, alongside biochemical strategies to ‘capture’ ubiquitination events in different cell cycle phases. Students will receive training in a wide range of cell culture and molecular cell biology techniques, cellular imaging and quantitative image analysis.

Key words: Cell cycle, mitosis, ubiquitin, cancer

 

Dr Paul Miller:
Taking control of GABAA receptors

GABAA receptors are pentameric ligand-gated ion channels (pLGICs) and the principal mediators of inhibitory neurotransmission in the central nervous system (CNS). Small molecule PAMs such as benzodiazepines (e.g. Valium) and non-benzodiazepines (e.g. Zolpidem) are used to treat generalized anxiety disorder, epilepsy, muscle spasm and insomnia. Critically, different subtypes are associated with distinct roles in addiction, sedation, anxiety, and nociception. Unfortunately, the selectivity of small molecule PAMs remains unsatisfactory, and for clinical drugs this contributes to dependence, amnesia, ataxia, tolerance and withdrawal. This barrier restricts the generation of therapeutics to better treat these established indications, and to target novel illnesses linked to GABAA receptor dysfunction, such as postpartum depression, autism, neuropathic pain and stroke. My research is aimed at using biochemical, protein engineering and structural biology approaches to develop novel modulators of GABAARs with unique selectivity and pharmacological properties, and to test these in relevant systems to uncover novel subtype specific roles in neuronal function and to realise the therapeutic potential. Projects require the application of computational, structural, pharmacological and electrophysiological approaches to study, identify, develop and optimize such modulators.

These projects are currently unfunded, and so I particularly welcome applicants who would make strong candidates for prestigious scholarships, such as Gates Cambridge, Cambridge Trust, Vice Chancellor’s Awards, or similar (see www.graduate.study.cam.ac.uk/finance/funding for more details and deadlines).

Keywords: GABA, X-ray crystallography, ion channels, benzodiazepines

 

Dr Ewan Smith:
Sensing the microbiota: Toll-like receptors in colonic sensory function in health and disease

Sensory neurones enable the body to detect and respond to both its internal and external environment. Sensory neurones innervating the gastrointestinal (GI) tract detect both mechanical and chemical stimuli, and recent work from our lab has identified 7 different colonic sensory neurone subtypes through unbiased RNA-sequencing (Hockley et al, Gut, in press). Two of these subtypes mutually exclusively express Toll-like receptor 4 and Toll-like receptor 5 (Tlr4 and Tlr5), both of which are known to be activated by bacterial products. In recent times there has been much focus on the microbiota and how it interacts with the rest of the body. We propose that Tlr4- and Tlr5-mediated sensing of bacterial products plays an important role in health and disease, especially, during epithelial infiltration of bacteria in the colon wall. For example, Tlr5 detects flagellin, the principal component of bacterial flagella and anti-flagellin antibodies are upregulated in irritable bowel syndrome (IBS).

Techniques used include: single-cell qRT-PCR, primary neuronal culture, immunohistochemistry, real-time fluorescence imaging, electrophysiology, and behaviour.

Key words: visceral pain, microbiota, neurobiology

 

Prof. Colin Taylor:
Structure and functions of Ca2+ channels within dynamic organelles

How does Ca2+, an element and the simplest of all intracellular messengers, selectively regulate so many cellular activities? We address this question by examining how the behaviour of intracellular Ca2+ channels, notably IP3 receptors, and the organelles in which they reside lead to complex changes in intracellular Ca2+ concentration. We are exploring the structural basis of IP3 receptor gating and the contribution of dynamic intracellular organelles to shaping cytosolic Ca2+ signals. The ER, where most IP3 receptors reside, forms intimate contacts with most other organelles. Dynamic regulation of these interactions may be as important as receptor-regulated formation of IP3 in determining how cells generate and respond to cytosolic Ca2+ signals. Furthermore, IP3 receptors move within the ER. We do not understand the relationships between these dynamic IP3 receptors and the much smaller number of immobile IP3 receptors that appear to generate most Ca2+ signals. What licences immobile IP3 receptors to respond? We apply super-resolution optical and electrophysiological methods alongside gene-editing with CRISPR/cas9 of native signalling proteins to explore, often at the single-molecule level, the structural basis of IP3 receptor activation and the dynamics of Ca2+-handling organelles. We apply these methods to both 'work-horse' cells like HEK293 cells, and to primary cells: bronchial and vascular smooth muscle (cAMP/Ca2+ interactions controlling contraction), fibroblasts, astrocytes (spatial organization of intracellular ATP provision) and glioma cells (migration and invasion). Our work, including that of PhD students, is supported by extensive national and international collaborations with chemists, structural biologists and mathematicians, and with partners in industry.

Keywords: Cell signalling, patch-clamp recording, super-resolution microscopy, gene-editing, ion channel, Ca2+, cyclic AMP, intracellular organelles, smooth muscle, fibroblast, astrocyte, glioma.

 

Dr Hendrik van Veen:
Mechanisms of multidrug transport in microorganisms and cancer cells

Multidrug transporters mediate the extrusion of a broad range of drugs from the cell, away from intracellular targets on which these drugs act. These membrane transporters modulate the toxicity and pharmacokinetics of drugs in organisms ranging from bacteria to man, and are a cause of drug resistance in pathogenic microorganisms and cancers. Using structural and biochemical tools, we work on interesting questions: how are drugs recognised by multidrug transporters and how is metabolic energy coupled to transport? Is drug transport the primary physiological role of these systems? Can we use novel mechanistic insights to generate inhibitors and new drugs that bypass recognition and thus improve the drug-based treatment of diseases? Please, contact Dr Hendrik van Veen to discuss the projects offered.

Key words: Antimicrobial and anticancer drug resistance, membrane transporters, drug efflux, drug recognition, mechanisms of transport, multidrug transport.