Research projects

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Defining the mechanism of abscission

Supervisors: Gwyn Gould, Chris McInerny

Outline & aim: ESCRT proteins mediate membrane scission events involved in the down-regulation of ubiquitin-labelled receptors via the multivesicular body (MVB) pathway and in HIV budding from host cells. In addition, ESCRT proteins play a role in abscission, the final stage of cytokinesis. The ESCRT machinery is composed of four complexes: ESCRT-0, -I, -II and -III; and the modular composition of the ESCRT machinery is reflected in its various functions. At a precise time during cytokinesis, the ESCRT-I protein TSG101 and ESCRT-associated protein ALIX are recruited to the midbody through interactions with CEP55; TSG101 and ALIX in turn recruit ESCRT-III components. Thereafter, by a mechanism still not completely understood, ESCRT-III redistributes to the putative abscission sites, microtubules are severed and the daughter cells separate. However, the mechanisms by which this selective and specific redistribution of ESCRT proteins is regulated in space and time remain largely unsolved.

ESCRT components are phosphoproteins, so we reasoned that kinases and phosphatases are likely candidates for ESCRT regulation. We hypothesised that polo and aurora kinases and Cdc14 phosphatase may be potential regulators of ESCRT function due to their significant roles in controlling cytokinesis. This aspect of mitotic regulation of

ESCRT function will be investigated in this project, as we have shown that these kinases and phosphatases play a role; our challenge now is to define that role and to determine whether similar mechanisms operate in mammalian cells. This interface between signalling and trafficking is an important and active research theme worldwide, and you will join an active and collaborative group well versed in all the training aspects required for successful completion of a PhD.

The aim of the project is to define the role of aurora kinase, polo-like kinase and Cdc14 on ESCRT function in yeast and mammalian cells.

Techniques: Yeast genetics; molecular biology; mammalian cell culture and cell biology; high resolution imaging/confocal microscopy

References

1. M.S.Bhutta, B.Roy, G.W.Gould and C.J.McInerny Public Library of Science 1. (2014) In press. “Control of cytokinesis by polo and aurora kinases and Cdc14 phosphatase regulation of ESCRT proteins.”
2. H.Neto, A.Kaupisch, L.L.Collins and G.W.Gould. Molecular Biology of the Cell (2013) 24, 3633-3674. “Syntaxin 16 is required for early stages in cytokinesis.”

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Developing novel, combined strategies for peripheral nerve repair

Supervisor: Mathis Riehle

Outline & aim: Peripheral nerve injuries are frequently seen following trauma or malignancy, with an incidence of 300000 cases in Europe following trauma alone. These injuries often result in functional deficits, and have a high impact on the patient’s quality of life, as well as placing a heavy financial burden on the state. Despite advances in surgical treatments, motor and sensory recovery following these injuries often remains incomplete. Here we help develop materials and apply a variety of biophysical techniques ranging from ultrasonic manipulation to 3D micro fabrication and microfluidics to create artificial guidance tubes, or tissues, that aid in nerve repair, with the aim of improving and assisting the outcome of surgical nerve repair.

The materials and devices are tested in vitro using a variety of models for peripheral and central nerve repair. The projects available range from basic materials science in collaboration with chemists (Prof G Cooke, Dr R Hartley, Prof M Salmeron-Sanchez), engineers for active nerve stimulation (Prof D Cumming) acoustic placement (Prof Cummings & Dr A Bernassau), microfluidics (Dr H Yin), to applied models (Prof A Hart). The implications of the different repair strategies on the cells genomic and proteomic response is being investigated in collaboration with the Glasgow Polyomics Facility (Dr R Burchmore, P Herzyk). This work is very much interdisciplinary, and adventurous, and requires not only a good foundation in basic molecular and cell biology, but also a willingness to learn the language and science of chemists, materials scientists, engineers and surgeons.

The project will vary depending on the applicants abilities and specific interests, the techniques and supervisors mentioned below are those with whom Dr Riehle collaborates.

Techniques: Primary cell culture, molecular biology, imaging, image analysis, then depending on the specific project collaboration with engineers, chemists or physicists to make materials - synthetic organic chemistry - micro fabrication - electronic engineering - acoustic engineering.

References

1. Cortese, B., Gigli, G., & Riehle, M. (2009). Mechanical Gradient Cues for Guided Cell Motility and Control of Cell Behavior on Uniform Substrates. Advanced Functional Materials, 19(18), 2961–2968
2. Donoghue, P. S., Sun, T., Gadegaard, N., Riehle, M. O., & Barnett, S. C. (2013). Development of a Novel 3D Culture System for Screening Features of a Complex Implantable Device for CNS Repair. Molecular Pharmaceutics. doi:10.1021/mp400526n
3. Caldwell, S. T., Maclean, C., Riehle, M., Cooper, A., Nutley, M., Rabani, G., … Cooke, G. (2014). Protein-mediated dethreading of a biotin-functionalised pseudorotaxane. Organic & Biomolecular Chemistry, 12(3), 511–6. doi:10.1039/c3ob41612g
4. Gesellchen, F., Bernassau, a L., Déjardin, T., Cumming, D. R. S., & Riehle, M. O. (2014). Cell patterning with a heptagon acoustic tweezer - application in neurite guidance. Lab on a Chip, 19, 2266–2275. doi:10.1039/c4lc00436a
5. Martin, C., Dejardin, T., Hart, A., Riehle, M. O., & Cumming, D. R. S. (2013). Directed Nerve Regeneration Enabled by Wirelessly Powered Electrodes Printed on a Biodegradable Polymer. Advanced Healthcare Materials, 1–6. doi:10.1002/adhm.201300481
6. Nikukar, H., Reid, S., Tsimbouri, P. M., Riehle, M. O., Curtis, A. S. G., & Dalby, M. J. (2013). Osteogenesis of mesenchymal stem cells by nanoscale mechanotransduction. ACS Nano, 7(3), 2758–67. doi:10.1021/nn400202j

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Molecular mechanics of clustering and gating in plant ion channels

Supervisor: Michael Blatt

Outline & aim: The organisation of ion channels in eukaryotic membranes is intimately connected with their activity, but the mechanics of the connections are, in general, poorly understood. Both in animals and plant, many ion channels assemble in discrete clusters that localise within the surface of the cell membrane. The clustering of the GORK channel — responsible for potassium efflux for stomatal regulation in the model plant Arabidopsis — is intimately connected with its gating by extracellular K+. Recent work from this laboratory yielded new insights into the processes linking K+ binding within the GORK channel pore to clustering of the channel proteins.

This project will explore the physical structure of GORK that determines its self-interaction as a function of the K+ concentration with the aim of understanding its integration with the well-known mechanics of channel gating.

Techniques: The student will gain expertise in molecular biological methods, and a deep grounding in the concepts of membrane transport, cell biology and physiology. Skills training will include in-depth engagement in molecular biology, protein biochemistry and molecular genetic/protein design, single-cell imaging and fluorescence microscopy, and single-cell recording techniques of electrophysiology using heterologous expression in mammalian cell systems and in plants.

References

1. Lefoulon, et al. (2014) Plant Physiol 166, 950-75
2. Eisenach, et al. (2012) Plant J 69, 241-51
3. Dreyer & Blatt (2009) Trends Plant Sci 14, 383-90

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Photoregulation of plant hormone trafficking and signalling

Supervisor: John Christie

Outline & aim: The phytohormone auxin (indole acetic acid) is instrumental for directing and shaping plant growth and form. Understanding how this chemical growth regulator controls plant development will have important implications for manipulating plant growth for agronomic gain. Auxin trafficking is profoundly influenced by many abiotic factors, including light. For instance, phototropin receptor kinases (phot1 and phot2) function to redirect auxin fluxes that are required to reorientate plant growth toward or away from light. The phot1-interacting protein Non-Phototropic Hypocotyl 3 (NPH3) is essential for establishing these light-driven auxin movements. However, the mode of action of NPH3 and how it functions to regulate transporter activity remains poorly understood.

This project aims to spatially dissect the site(s) of NPH3 action and how it impacts the subcellular trafficking and function of known auxin transporter proteins implicated in phototropism. Work is also focussed on characterising a newly identified NPH3 protein (NPH3-like, NPH3L) that interacts directly with phot1. Functional characterisation of NPH3, NPH3L and its homologues will provide new insights into the photoregulation of auxin trafficking and signalling associated with phototropism and other phototropin-mediated responses.

Techniques: This proposal is focused on characterising the molecular processes that integrate light and phytohormone signalling, two important agronomic processes associated with manipulating plant growth and optimising photosynthetic efficiency. Both these research areas fall squarely within the strategic priorities of Food Security, Living with Environmental Change and Crop Science. The project will provide excellent training in a range of techniques associated with molecular biology, cell biology, genetics and biochemistry. Training will also be given in key skills including teaching, project-management and science communication. Additionally, the student will have the opportunity to attend and present their research at the international photobiology meetings e.g. Gordon Research Conference in Photosensory Receptors and Signal Transduction, Galveston, Texas in 2016 (which I will chair).

References

1. CHRISTIE, J.M. (2007) Phototropin blue-light receptors. Annu. Rev. Plant Biol. 58, 21-45.
2. Sullivan, S., Thomson, C.E., Kaiserli, E. and Christie J.M. (2009) Interaction specificity of Arabidopsis 14-3-3 proteins and phototropin receptor kinases. FEBS Lett. 583, 2187-2193.
3. Christie, J.M., Richter, G., Yang, H., Sullivan, S., Thomson, C.E., Lin, J., Tiapiwatanakun, B., Ennis, M. Kaiserli, E., Lee, O.R., Adamec, J., Peer, W.A. and Murphy, A.S. (2011) Phot1 inhibition of ABCB19 primes lateral auxin fluxes in the shoot apex required for phototropism. PLoS Biol., 9(6): e1001076.
4. CHRISTIE, J.M. and MURPHY, A.S. (2013) Shoot phototropism in higher plants: New light through old concepts. Am. J. Bot. 100, 35-46.

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Regulation of plant nuclear architecture by light

Supervisor: Eirini Kaiserli

Outline & aim: Light is essential for plant growth, development and photoprotection. One of the primary sites where light regulates major cellular processes is the nucleus. We are interested in elucidating how light stimulates the accumulation of photoreceptors and signalling components in nuclear micro-domains to regulate gene expression, chromatin remodelling and DNA damage repair. The student will investigate how nuclear compartmentalisation correlates with changes in the expression of growth promoting genes in response to light.

Techniques: A series of approaches will be used depending on the interests and background of the applicant: Gene expression analysis (qRT-PCR, ChIP), molecular cloning, protein interactions studies (Y2H, co-immunoprecipitation), protein characterisation (heterologous expression and purification), cell biology (confocal microscopy), plant genetics and plant physiology.

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Overview

The Centre for the Cellular Microenvironment at Glasgow is a new entity (2018) arising from the merger of the Centre for Cell Engineering (CCE) and the Microenvironments for Medicine (MiMe).

Our goal is to apply the knowledge gained from our research to address key issues affecting (stem) cell biology. Our research is centred on exploring how cells respond to their environment by changes in behaviour, differentiation, metabolism and various aspects of development. 

The Centre for the Cellular Microenvironment at Glasgow adopts an interdisciplinary approach across the School of Molecular Biosciences in the College of Medical, Veterinary & Life Sciences and the Bioengineering Group in the School of Engineering, which is part of the College of Science & Engineering. Cell-environment interactions, cell signalling, stem cell biology, cell, and protein structure and function at interfaces, bioengineering of gene regulation by microenvironments, nanoparticle technologies, synthetic biology to guide cell adhesion, cell sorting and translational approaches to take finding to clinical application.

Research topics are allied to ongoing research within the Centre for the Cellular Microenvironment. Some projects are related to basic science and other projects are more focused on translational aspects of our research, but all projects integrate with our existing research themes. A variety of multidisciplinary research approaches are applied within these research programmes, including biomedical engineering, protein engineering, biochemistry, molecular biology, biophysics, polyomics (genomics, transcriptomics, proteomics, metabolomics), biomaterials, bioinformatics and synthetic biology, as well as cellular imaging of biological functions.

Specific areas of interest include:

• bioengineering the microenvironment
• engineering approaches to control gene expression
• bio-engineered interfaces
• biomaterials, scaffolds and 3D printing
• protein structure and function
• protein engineering and application
• cell sorting and characterisation
• stem cell maintenance and differentiation
• nanoparticles for theranostics

Specific areas of application are:

• bone repair
• nerve repair
• sourcing of rare cells
• blood Brain Barrier
• mesenchymal stem cell niche
• haematopoietic stem cell niche

See Glasgow Biomaterials Seminar for an idea about recent and current projects.

Our PhD programme provides excellent training in cutting edge technologies that will be applicable to career prospects in both academia and industry. Many of our graduates become postdoctoral research associates (Canada, USA, Europe and UK) while others go on to take up positions within industry either locally (e.g. Collagen Solutions, BioGelX) or overseas (e.g. Medtronic). We have strong national and international connections with many academic and industrial collaborators. Funds are available through the College of Medical, Veterinary & Life Sciences or the College of Science & Engineering (depending on primary alignment) to allow visits to international laboratories, or industry where part of your project can be carried out. This provides an excellent opportunity for networking and increasing your scientific knowledge and skill set.

Study options

PhD

• Duration: 3/4 years full-time; 5 years part-time

Individual research projects are tailored around the expertise of principal investigators.

Integrated PhD programmes (5 years)

Our Integrated PhD allows you to combine masters level teaching with your chosen research direction in a 1+3+1 format. 

International students with MSc and PhD scholarships/funding do not have to apply for 2 visas or exit and re-enter the country between programmes. International and UK/EU students may apply.

Year 1

Taught masters level modules are taken alongside students on our masters programmes. Our research-led teaching supports you to fine tune your research ideas and discuss these with potential PhD supervisors. You will gain a valuable introduction to academic topics, research methods, laboratory skills and the critical evaluation of research data. Your grades must meet our requirements in order to gain entry on to your pre-selected PhD research project. If not, you will have the options to pay outstanding MSc fees and complete with masters degree only.

Years 2, 3 and 4

PhD programme with research/lab work, completing an examinable piece of independent research in year 4.

Year 5

Thesis write up.

MSc (Research)

• Duration: 1 year full-time; 2 years part-time