The following projects were available to students commening in October 2022. Projects available to students commencing in October will be published in summer 2023.
A DNA-based B-cell receptor to investigate a role for mechanical force in B-cell antigen discrimination in the immune synapse
1st Supervisor: Katelyn Spillane (Department of Physics)
2nd Supervisor: John Maher (School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre)
A B-cell mounts an antibody response by measuring the binding strength of its B-cell receptor (BCR) for antigen on the surface of an antigen-presenting cell. Bonds at the cell-cell interface are subjected to mechanical forces, but how forces influence BCR signalling leading to antigen discrimination and B-cell activation is not known. This project will establish a synthetic BCR-antigen interaction based on DNA hybridisation and use a combination of single-molecule fluorescence imaging, molecular biology, and model membrane systems to determine how B-cells discriminate antigens to mount an affinity-dependent response which is necessary for producing high-affinity antibodies.
Analysis of Cell Intercalation at the level of adhesions and tension
1st Supervisor: Jeremy Green (Centre for Craniofacial & Regenerative Biology)
2nd Supervisor: Martyn Cobourne (Centre for Craniofacial & Regenerative Biology)
Cell intercalation is critical for mechanical morphogenesis throughout the body but the cell biology of intercalation is not well understood. The Green lab has a highly tractable model system for its analysis. Using this model, the mouse molar tooth explant, this project will: 1. Apply immunofluorescence to determine the localisation and motions of cell-cell and cell-matrix adhesions to compare cell-on-cell with cell-on-matrix adhesion mechanisms; 2. Track focal of E- cadherin adhesions to assess the role of cell crawling versus junction shortening; and 3. Use super- resolution microscopy to determine what structures transmit forces from the front to the back of cells.
Determining how mechanical cues regulate muscle stem cell function during regeneration
1st Supervisor: Robert Knight (Centre for Craniofacial and Regenerative Biology)
2nd Supervisor: Susan Cox (School of Basic and Medical Biosciences, Randall Centre for Cell and Molecular Biophysics)
Stem cells respond to many inputs that that influence their response to injury, including mechanical force. Chromatin packaging and hence gene expression are affected by force, providing a mechanism for regulation of cell responses to the physical environment. This project aims to determine how mechanical signals and chromatin modifying signals interact to regulate muscle stem cell (muSC) responses to tissue injury. Mechanical tension in muSCs will be altered using optical tweezers or by over-expressing regulators of the cytoskeleton then muSC behaviour and cytoskeletal filament orientation measured using lattice light sheet microscopy in zebrafish injury models and mammalian cells.
Elucidating the antiviral mechanism of IFITM proteins.
1st Supervisor: Julien Bergeron (Randall Centre for Cell & Molecular Biophysics)
2nd Supervisor: Stuart Neil (School of Immunology & Microbial Sciences, Department of Infectious Diseases)
IFITM proteins are a family of proteins involved in innate immunity against diverse viral infection, and particularly potent against HIV, Influenza and SARS-CoV-2. They are integral membrane proteins, and have been proposed to act by preventing fusion of the viral envelopes. However, the structure of IFITM proteins, and their molecular mechanism of action, is not known.
The aim of this project is to use a combination of structural and biophysical methods (cryo-EM, HD-MS, NMR etc..) to characterize the prototypical IFITM-3 protein in lipid vesicles, and to establish how it impacts membrane fusion. Collectively, this will allow to establish the molecular basis for the antiviral activity of this family of proteins.
Engineering nuclear mechanotransduction across the nuclear pore complex (NPC) through molecular design
1st Supervisor: Sergi Garcia-Manyes (Department of Physics)
2nd Supervisor: Paula Booth (Department of Chemistry)
Mechanical forces determine a large number of biological functions. To activate force-induced transcriptional programmes, cells need to propagate mechanical stimuli from the extracellular matrix to the nucleus. The nuclear pore complex (NPC), the main gate that separates the cytoplasm and the nucleus, is capable of sensing the mechanical properties of the translocating proteins and thereby regulate their nuclear import rate. Yet the molecular mechanisms of such mechanosensitivity remain unknown. This interdisciplinary PhD project combines single molecule and single cell mechanics, together with optogenetics and confocal microscopy, to unravel the mechanisms that underpin the mechanoselectivity of the NPC, with the overarching purpose to design molecular strategies able to artificially control and regulate cellular function.
Exploring the disease mechanisms of FUZ variants in skull development
1st Supervisor: Karen Liu (Centre Craniofacial and Regenerative Biology)
2nd Supervisor: Rivka Isaacson (Department of Chemistry)
Changes in tissue structure and signalling often lead to congenital anomalies or birth defects; however, the underlying causes are poorly understood. Here, we focus on the FUZZY gene, which controls ciliogenesis in neural crest cells. The cilium is cellular “antennae” used for sensing extracellular cues and mechanotransduction. We have identified mutations in human FUZZY associated with neural tube defects and craniosynostosis. This project links a biophysical analysis of FUZ disease variants to perturbed cell-cell and cell-environment interactions. This will have implications for understanding tissue growth and the causes of human craniofacial defects.
Force-sensing by Forcins in muscle growth
1st Supervisor: Simon Hughes (School of Biomedical Engineering & Imaging Sciences/ Randall Centre for Cell & Molecular Biophysics)
2nd Supervisor: Mark Pfuhl (School of Basic & Medical Biosciences/ School of Cardiovascular Medicine & Sciences/ Randall Centre for Cell & Molecular Biophysics)
Muscle grows in response to high force exercise, but how this ‘exercise’ effect is sensed is unknown. We recently showed that muscle myosin activity is essential for growth, implying that a sensor for physical force exists in sarcomeric muscle. Molecular genetic analysis in the optically-clear zebrafish has revealed that the Forcin gene family is necessary and sufficient for normal cellular changes in muscle growth in response to myosin. The project will test at unprecedented temporal and sub-cellular resolution how vertebrate muscle grows and the molecular and cellular mechanism/s by which Forcin activity is controlled by force and drives growth of skeletal muscle tissue.
How do nanoneedles penetrate cells?
1st Supervisor: Ciro Chiappini (Centre for Craniofacial & Regenerative Biology)
2nd Supervisor: Mark Wallace (Department of Chemistry)
Nanoneedle arrays hold significant promise as a minimally invasive method of drug delivery and sensing. Cells respond to the mechanical stimulus of nanoneedles by drastically remodeling their membrane, cytoskeleton and nucleus. Details of this interaction are starting to emerge, but to date we do not have a molecular understanding of precisely how membrane remodeling and permeability is regulated Here we will combine advanced nanofabrication techniques, with high-speed single-molecule tracking to map the membrane response to mechanical stimuli from nanoneedles.
How does lipid composition affect membrane tension in cells?
1st Supervisor: Riki Eggert (School of Biomedical Engineering & Imaging Sciences/ Randall Centre for Cell & Molecular Biophysics/ Department of Chemistry)
2nd Supervisor: Simon Ameer-Beg (School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre)
Cell membranes are key mediators of forces generated outside of the cell or within the cell, for example during cell movement or division. Cell membranes primarily consist of proteins and lipids. While we have some understanding of how proteins participate in the generation and response to force, we know very little about how lipids are involved. This interdisciplinary project will use FLIM imaging to analyse membrane tension in response to force in cells where lipids have been changed. A direct connection between lipid identity and membrane tension will be transformative in our understanding how cells regulate their mechanical environment.
Identification of new mechanical force-sensitive Vinculin binding proteins
1st Supervisor: Ryuichi Fukuda (School of Cardiovascular Medicine and Sciences)
2nd Supervisor: Mauro Giacca (School of Cardiovascular Medicine & Sciences)
Cell behavior is regulated not only by biochemical signals, but also by mechanical forces such as stretch and compression, particularly in the heart, a contractile organ. However, how cells sense forces and transform them into biological response remains unclear. We previously found that mechanical forces from cardiac contraction regulate cardiomyocyte maturation via Vinculin-Slingshot-Cofilin axis. We performed proteomic screening to identify new force-sensitive Vinculin binding proteins. In this project, we investigate whether/how cardiac contraction regulates functions of potential force-sensitive new proteins (LMO2, LRRFIP2 and ribosomal subunits), and examine whether loss of their functions is associated with cardiac disease.
Mechanochemical control of cancer cell genetic instability
1st Supervisor: Maddy Parsons (School of Basic & Medical Biosciences/ Randall Centre for Cell & Molecular Biophysics)
2nd Supervisor: Tony Ng (School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre)
Tumours are complex, heterogeneous tissues involving many cell types supported by 3D extracellular matrix (ECM). Increased ECM stiffness is a hallmark of some cancers and is sensed by cells via receptor-mediated mechano-transduction pathways. The actin cytoskeleton plays a critical role in mechano-transduction by linking cellular compartments to receptors, leading to activation of a number of mechano-sensitive signalling pathways to regulate genetic instability, proliferation and invasion. However, the mechanisms controlling mechano- sensing triggers of DNA repair remain poorly understood. This project will use state-of-the-art imaging of mechanically-tuned 3D cancer models to determine the key molecular players in force- transmission DNA repair and their role in tumour progression.
Mechanochemistry of bacterial adhesion proteins
1st Supervisor: Manuel Mueller (Department of Chemistry)
2nd Supervisor: Sergi Garcia-Manyes (Department of Physics)
Bacteria can covalently attach to diverse surfaces. To do so, they utilize (thio)ester-containing proteins which can act as ‘chemical harpoons’. Mechanical stress reconfigures the reactivity of these electrophilic groups. This project aims to systematically explore the chemoselectivity of (thio)ester cleavage against a panel of small molecule and peptide-derived N, O, and S nucleophiles under mechanical perturbations. This knowledge will then be exploited to generate new probes for bacterial adhesion proteins as well as crosslinked protein networks with useful properties.
Probing the function of the myosin regulatory light chain in vitro and in vivo, in health and in disease
1st Supervisor: Mark Pfuhl (School of Basic & Medical Biosciences/ School of Cardiovascular Medicine & Sciences/ Randall Centre for Cell & Molecular Biophysics)
2nd Supervisor: Elisabeth Ehler (School of Cardiovascular Medicine & Sciences)
The regulatory light chain (RLC) of myosin plays an important role in force generation in cardiac muscle: together with the essential light chain (ELC) it stabilizes the lever helix, it binds to myosin binding protein C (MyBP-C) and phosphorylation of its N-terminus appears to modulate muscle contraction. The last two functions have remained elusive and the N-terminus is not seen in recent cryoEM reconstructions of myosin. We plan to dissect the complex functions of RLC using a combination of NMR spectroscopy in vitro in combination with the characterization of iPSC derived genetically engineered cardiomyocytes in vivo.
Quantifying the effects of muscle fascia in transmitting muscle fibre contraction forces
1st Supervisor: Malcolm Logan (School of Basic and Medical Biosciences/ Randall Centre for Cell and Molecular Biophysics)
2nd Supervisor: Luca Fusi (School of Basic and Medical Biosciences, Randall Centre for Cell and Molecular Biophysics)
The fascial layers that surround muscle fibres in skeletal muscle tissue are essential for the integrity of this tissue and have important roles in ensuring efficient transmission of the forces of muscle fibre contraction that move the skeletal elements. Defects in the formation of these myofascial layers or failure to maintain healthy myofascia significantly impact muscle function. In this project, we will study how the fascia coordinates the forces of muscle fibre contraction to the associated tendon and how specific defects in the composition of the myofascia can impact normal muscle tissue contraction forces.
Regulation of mechanobiology in the type IV pilus of Neisseria gonorrhoeae
1st Supervisor: James Garnett (Centre for Host-Microbiome Interactions)
2nd Supervisor: Joe Atherton (School of Basic and Medical Biosciences, Randall Centre for Cell and Molecular Biophysics)
The Type IVA pilus (T4p) system is a large and complex nanomachine that coordinates both polymerisation and export of protein units into filaments on the surface of bacteria, and their disassembly and retraction. This provides bacteria with “twitching” motility, a form of translocated over surfaces, with pili exerting pulling forces of >100 pN. We have identified a new Neisseria gonorrhoeae T4p system protein, TfpC, which directly interacts with the pilus and stabilises its structure. Using structural biology (cryo-electron microscopy) and molecular microbiology approaches, this PhD will explore how TfpC regulates T4p assembly/retraction and twitching motility in N. gonorrhoeae.
Regulation of physical forces and membrane remodelling to repair ruptured nuclei
1st Supervisor: Juan Martin-Serrano (School of Immunology & Microbial Sciences, Department of Infectious Diseases)
2nd Supervisor: Monica Agromayor (School of Immunology & Microbial Sciences, Department of Infectious Diseases)
The nuclear compartment is highly dynamic and its integrity is constantly challenged by mechanical forces. Transient nuclear envelope ruptures during interphase (NERDI) occur when mechanical stress is generated by cytoskeletal forces, and NERDI repair requires membrane remodelling activities to reseal the nucleus. However, for repair to be effective, mechanical strain imposed by the cytoskeleton needs to be relieved from the nucleus to counteract intranuclear pressure. Here we will combine cell biology, advanced microscopy and atomic force microscopy/magnetic tweezers to reveal the molecular mechanisms that coordinate membrane remodelling with mechanical forces regulation to facilitate nuclear envelope repair and maintain genome stability.
The biological and physical interactions controlling suture morphology and function
1st Supervisor: Abigail Tucker (Centre for Craniofacial & Regenerative Biology)
2nd Supervisor: Owen Addison (Centre for Oral, Clinical & Translational Sciences)
Skull growth in vertebrates is coordinated by sutures, soft tissue structures that separate the bones and act as growth centres. These sutures respond to mechanical stimulation, stimulating growth in different planes in order to create complex interlocking patterns, allowing the skull to respond to stress. Stem cells housed within the sutures act as reservoirs for bone growth, homeostasis and repair. How mechanical force impacts sutures anatomy and organization and how such force is interpreted by suture stem cells is largely unknown. In this interdisciplinary project we bring together these areas to understand suture biomechanics and interactions that shape the skull.
The contribution of L-selectin and ezrin interaction in regulating the mechanobiology of neutrophil phagocytosis.
1st Supervisor: Aleksandar Ivetic (School of Cardiovascular Medicine & Sciences)
2nd Supervisor: Katelyn Spillane (Department of Physics/ Randall Centre for Cell & Molecular Biophysics)
Neutrophil phagocytosis is a biomechanical process that is absolutely essential to host survival from infection. In contrast, the process of incomplete/frustrated phagocytosis can
have detrimental effects in vital organs such as the heart during myocardial infarction (MI) or the brain during stroke. We have strong evidence to suggest that the cell adhesion molecule, L-selectin, and its intracellular binding partner, ezrin, play an important role in regulating neutrophil phagocytosis. Using cell lines and animal models, this PhD will explore the individual and combined contribution that ezrin and L-selectin play in regulating neutrophil tension, force exertion and reactive oxygen species production in mechanisms of normal and frustrated phagocytosis.
Understanding the dynamic regulation of extracellular matrix structure and mechanics during embryogenesis
1st Supervisor: Brian Stramer (Faculty of life science and medicine, Randall)
2nd Supervisor: Susan Cox (School of Basic and Medical Biosciences, Randall Centre for Cell and Molecular Biophysics)
The extracellular matrix (ECM) is a polymer scaffold that is essential for tissue function. Its mechanical properties are dynamically controlled during normal physiology and disease, however it is unclear how its pliability is regulated. This dearth of knowledge is related to ECM complexity and the difficulty of analysing ECM structure and mechanics within living organisms. Here we will exploit our unique capacity to live image and genetically dissect ECM components and quantify ECM mechanical properties within developing Drosophila. This will allow us, for the first time, to understand how changes in ECM organisation and mechanical properties controls tissue structure and growth.
Understanding the mechano-regulation of ovarian ageing
1st Supervisor: Kim Jonas (School of Life Course Sciences/ Department of Women & Children’s Health)
2nd Supervisor: Eileen Gentleman (Centre for Craniofacial & Regenerative Biology)
Ovarian ageing is a naturally occurring process resulting in declining and cessation of fertility at menopause. The ovary ages chronologically faster than other organs, however the mechanisms governing ovarian ageing remain elusive. There is increasing evidence that the extracellular matrix is dynamically modulated during ovarian ageing. This project aims to determine how ovarian stiffness changes across the reproductive lifespan of the ovary. We will use a combination of atomic force microscopy, mechano-modulation of ovarian follicle cultures, immunohistochemistry and qPCR to interrogate the aim. The outcome of which will provide key insights into the mechano-regulation of the ovary across its lifespan.