Apply to the Biosciences MRes

Follow this guide to apply for the Biosciences MRes

Stage one: review research project themes

Those applying to study MRes Biosciences at Aston University must select which extended research project they would like to complete as part of their studies. This must be clearly highlighted in your application in the personal statement section of the application. Please note admission to the programme is only after a successful interview with the project supervisor and programme director.

We offer a variety of projects each year in a wide range of specialist biosciences fields. Please take a look through the list below to find out more. If you have any questions about a specific project please contact the project supervisor directly via the contact details provided. 

    Cell and Molecular Biology

    Project Title: Breaking scars: evaluating liver matrix remodelling in vitro.

    Project Overview:
    If a tissue or organ is damaged by injury or trauma, a sequence of repair mechanisms is initiated to fix the wound and repair tissue architecture. However, in the context of chronic diseases of organs such as the liver, heart, lungs, kidney and intestines the repair process becomes dysregulated and results in fibrosis, or scarring. Tissue fibrosis is the loss of the normal epithelial and parenchymal cells within an organ and their replacement with non-functional connective tissue and extracellular matrix molecules. It is currently estimated that this organ fibrosis process is responsible for up to 45% of deaths in industrialized countries.

    There is an urgent unmet need to develop new medicines that can target fibroblast activity and breakdown the fibrotic scar to promote restore tissue homeostasis. In the context of liver fibrosis, this has the potential to allow the liver to regenerate and improve patient outcomes. However, assay systems to evaluate matrix being broken down are not well established. The aim of this project is to incorporate matrix proteins that fluoresce when cleaved to evaluate the mechanisms that regulate matrix turnover in an assay system which will be able to screen potential therapeutic candidates for “scar breaking” potential. 


    This aim will be met by the following objectives:

    • Establish optimal coating concentrations for matrix components in vitro
    • Optimize cell seeding and profibrogenic stimuli conditions to promote matrix
    • deposition and production of matrix remodelling factors
    • Screen small molecule inhibitor toolkit to evaluate active matrix remodelling

    Core Techniques:

    • Tissue culture
    • Cell health and phenotype assays
    • Immunofluorescence and microscopy imaging
    • Image analysis and coding to automate scoring
    • Matrix turnover assay

    Supervisor: Emma Shepherd


    Email

    Project Title: Development of 3D culture model of liver fibrosis to investigate therapies targeting tissue regeneration.

    Project Overview: 

    Liver disease is a leading cause of death in the UK and worldwide. The absolute number of chronic liver disease cases is estimated at 1.5 billion worldwide. Liver fibrosis is the term used to describe the accumulation of scar tissue which is produced in response to long term liver injury and inflammation. Chronic injury and inflammation drives the activation of liver myofibroblasts to synthesize and deposit matrix (scar) proteins which accumulate and replace functional liver tissue, eventually leading to organ failure. There are no licensed therapies for liver fibrosis and thus there is an urgent unmet need to identify new therapeutic targets and design systems to test their efficacy.

    Cells actively probe their extracellular environment by exerting traction forces via integrins but the mechanisms that dictate the sensing and transduction to cellular responses are poorly understood. Integrin-mediated adhesions between cells and the extracellular matrix (ECM) are fundamental for cell and tissue function. One of the main functions of cell-matrix interactions is the detection of mechanical signals linked to the rigidity of ECM or the forces transmitted from it. The ECM of healthy human liver is relatively elastic but increased liver stiffness is associated with aging and chronic diseases such as liver fibrosis. Novel models that recreate the diverse constituents and mechanical features of human liver matrix are urgently required to extend the knowledge of mechanisms underpinning regeneration.

    The aim of this project is to develop 3D liver microtissues cultured in a range of mechanical stiffnesses to model healthy and diseased liver tissue. These microtissues will provide an in vitro model of liver fibrosis to facilitate screening of novel inhibitors for efficacy in reprogramming myofibroblasts to promote healthy repair and tissue regeneration.

    Project Aims:

    • 3D culture model development and validation
    • Analysis of cellular viability and phenotype parameters to demonstrate reprogramming
    • Screening of novel compounds for efficacy as anti-fibrotic therapy

    Core Techniques:

    • Tissue culture
    • Treatment of microtissues with specific compounds/inhibitors
    • Cell health and phenotype assays
    • Immunofluorescence and microscopy imaging
    • Image analysis and coding to automate scoring
    • Matrix turnover screening assay

    Supervisor: Emma Shepherd

     Email
     

    Project Title: Stress granule dynamics in C. elegans neurodegeneration models

    Project Overview: Stress granules (SGs) are dense aggregations of proteins and mRNAs appearing in the cytosol under stress conditions. They are transient and dynamic structures and play a critical role in mRNA metabolism and translational control by modulating the stress response. RNA-binding proteins control the sequestration of mRNA within SGs upon induction of stress. SG formation represents a physiological response to stress, however chronic stresses associated with aging and neurodegenerative diseases lead to formation of persistent SGs that contribute to aggregation of disease-related proteins. SGs dynamics have been mainly studied in yeast or human cell lines and not enough information is available on stress granules in multicellular organisms. C. elegans represents a powerful model to study aging and neurodegeneration and dissect molecular mechanisms and signaling pathways contributing to pathology. An array of established C. elegans mutants can give insight into different aspects of neurodegenerative disease pathogenesis. Similarly, several tools are now available to study the role of cytoplasmic stress granules in stress response in C. elegans. The aim of this project is to use C. elegans models for neurodegenerative diseases (Alzheimer’s Disease (AD) and Parkinson’s Disease (PD)) to investigate SG dynamics and role in neurodegeneration.

    Project Aims:

    • Analyse SG dynamics in C. elegans AD and PD models using fluorescently labelled SG marker. For this objective GFP-tagged SG marker GTBP-1 will be crossed into AD and PD mutant worms and SG dynamics will be analysed using fluorescence microscopy for day 1 and day 8 old adult worms.
    • Investigate whether modulation of SG formation affects AD and PD disease phenotypes. This objective will be achieved by crossing loss-of-function mutations of SG key proteins TIAR-1 and GTPB-1 into mutant AD and PD worms and analysing the resulting phenotypes.
    • Together these objectives will allow to understand whether SGs play a crucial role in AD and PD pathogenesis and potentially suggest novel therapeutics for neurodegeneration.

    Core techniques: 

    • C. elegans maintenance and genetic crosses
    • Genotyping (PCR, agarose gel electrophoresis)
    • Light and fluorescent microscopy
    • SDS-PAGE and Western Blotting

    Supervisor: Zita Balklava

     Email

    Project Title: Molecular mechanisms of aquaporin-4 trafficking

    Project Overview: Life-threatening swelling of the brain caused by head trauma or stroke affects tens of millions of people every year. Despite this, the therapeutic options for these patients are severely limited. Aquaporin-4 (AQP4) is the water channel protein in the brain that facilitates influx of water into brain tissue and is therefore a promising drug target for prevention of death and disability following head injury and stroke. However, attempts in both academia and the pharmaceutical industry to develop drugs to directly block the AQP4 water-conducting pore have failed. We have recently discovered that AQP4 is dynamically trafficked between the plasma membrane and intracellular vesicles, and that blocking this trafficking effectively reduced swelling and improved outcomes in animal models of trauma and stroke. This means that blocking AQP4 trafficking is an alternative to directly blocking AQP4-mediated water transport, and we aim to develop new drugs for stroke and trauma patients based on this principle. To facilitate our drug discovery efforts, we need to understand the molecular mechanisms and cellular signalling pathways associated with AQP4 trafficking. In this project you will investigate AQP4 protein-protein interactions to identify new drug targets.

    Project Aims:

    • Use site-directed mutagenesis to make mutants of AQP4
    • Use pulldowns and co-immunoprecipitation followed by western blotting to identify AQP4 binding partners and the effects of mutations
    • Investigate the effects on AQP4 trafficking of inhibiting AQP4 binding partners with small molecules or siRNA

    Core techniques: Site-directed mutagenesis, mammalian cell culture, transfection, immunoprecipitation, western blotting.

    Supervisor: Philip Kitchen

     Email

     

    Project Title: Deciphering the role of metastasis-inducing proteins in placental development implantation.

    Project Overview: Our lab has, over the years, been interested in different protein markers whose aberrant expressions relate to increased cellular motility. These proteins are key and now considered to be significant markers for cellular metastasis and poor prognosis when related to cancer biology. Recently we have shown that these same factors also play vital roles in regulating motility of specific cells known as trophoblasts in a much more physiological context, that of placental development during the stage of implantation.

    This project aims to further elucidate how these proteins regulate both cellular motility and invasion in trophoblasts, using an array of both molecular and cellular biology techniques including tissue culture, gene expression manipulation and imaging.

    Project Aims: 

    • Grow and manipulate trophoblast cells
    • Regulate expression and analyse localisation of the metastasis inducing protein studied
    • Study changes in motility markers by fluorescent microscopy including focal adhesion, filopodia, lamellipodia.
    • Analysed changes in overall cell migration and invasion

    Core Techniques: 

    • Tissue culture
    • Gene expression manipulation and/or treatment with specific compounds/inhibitors
    • Immunofluorescence and microscopy imaging
    • Migration and invasion assays (Boyden chambers)

    Supervisor: Stephane R. Gross 

    Email

    Project Title: Investigating the effect of lipoxidation on mammalian cell function.

    Project Overview: Lipoxidation is the covalent modification of proteins by lipid oxidation products such as short-chain aldehydes, which can be formed under conditions of oxidative stress, for example in inflammatory conditions. It is thought that lipoxidation can change the activity and localization of cellular proteins, and thus the behaviour of the cells. This may be important in determining the balance of cell proliferation, apoptosis or altered metabolic responses in cancer. This project will build on our previous research with pyruvate kinase in this area. 

    The project will involve treatment of the breast cancer cell line MCF-7 with different lipid oxidation products to analyse changes in cell morphology, viability, metabolic status and stress responses. Enzymatic assays will be used to investigate changes in activity of pyruvate kinase, glyceraldehyde-3-phosphate dehydrogenase or the signalling phosphatase PTEN, all of which are known to be redox-sensitive. Alterations at a proteomic level will also be determined.

    Project Aims: 

    • To determine which lipid oxidation products alter the balance of cell proliferation versus cell death.
    • To determine if pyruvate kinase, glyceraldehyde-3-phosphate dehydrogenase or PTEN are inhibited or activated by lipoxidation.

    Core techniques: Mammalian cell culture; enzymatic assays; SDS-PAGE; western blotting; mass spectrometry.

    Supervisor: Corinne M. Spickett

    Email

     

    Project Title: Novel polymers to extract and purify membrane proteins.

    Project Overview:

    Membrane proteins are vitally important, controlling what enters and leaves a cell, mediating cellular communication and cell identification. It’s estimated that half of all prescribed drugs bind to membrane proteins. However, their membrane environment can make it challenging to study their structure & function. Detergents have been used to solubilise membrane proteins from the lipid bilayer, but they can alter protein structure and function, as well as stripping away important lipids. In the last 10 years styrene-maleic acid co-polymer (SMA) has been used instead of detergents to extract small discs of bilayer containing the membrane protein, termed SMALPs (SMA lipid particles). Thus, enabling the solubilisation and purification of a membrane protein whilst maintaining its lipid environment. This polymer approach has revolutionised the study of membrane proteins, making them technically much simpler to work with, but it does still have some limitations. In addition, we still do not fully understand how SMALPs work. This project will investigate novel polymer variants to try to overcome these limitations and/or figure out how they work.

    Project Aims: Individual projects will be tailored to the applicant’s interests but could include:

    • Screening a series of polymer variants for solubilisation and purification of a range of membrane proteins.
    •  Kinetic analysis of disc formation.
    • Biophysical characterisation of the polymer-lipid-discs.
    • Investigating the structure and function of a specific membrane protein.
    • Examining the lipids that co-purify with a specific protein.
    • Reconstituting proteins from SMALPs into other systems

    Core Techniques: Bacterial protein expression, solubilisation, purification, SDS- PAGE, Western blotting, light scattering, fluorescent and enzymatic assays.

    Supervisor: Alice Rothnie

    Email

     

    Project Title: Investigating how neurons repair DNA damage

    Project Overview:

    Each day the DNA in our cells is under constant attack from a multitude of DNA-damaging agents from both endogenous and environmental sources. If left unrepaired, this DNA damage would lead to genome instability and ultimately cell death. To combat this and maintain genome integrity, DNA repair factors operate within overlapping cellular DNA repair pathways to detect, signal and repair DNA damage as it arises. The importance of these pathways is highlighted by the fact that inherited mutations in many DNA repair proteins cause human disease. Neurodegeneration or defects in neurodevelopment is a common clinical symptom of these diseases. However, despite many decades of research many important questions remain unanswered. It is still poorly understood why neurons are particularly sensitive to the loss of DNA repair pathways, and it is unclear what types of DNA damage are so genotoxic to neurons.

    The aim of this project is to use a neuronal model system to investigate which DNA repair pathways are essential to maintain healthy neuronal function in the presence of DNA damage. This will be achieved by using specific small molecule inhibitors of essential DNA repair proteins on differentiated neuroblastoma cells. Additionally, different DNA damaging agents will be used to investigate how detrimental different types of DNA lesions are to neuronal health.

    Project Aims:

    • Grow and differentiate SH-SY5Y neuroblastoma cells
    • Test the sensitivities to various DNA damaging agents of differentiated SH- SY5Y neuroblastoma cells treated with DNA repair inhibitors.
    • Investigate the cellular consequences of unrepaired DNA damage on differentiated SH-SY5Y neuroblastoma cells, by measuring levels of genome instability, apoptotic cell death and transcription.

    Core Techniques:

    • Tissue culture and treatment of neurons with specific compounds/inhibitors
    • Immunofluorescence and brightfield microscopy imaging
    • Western blotting
    • Assays to analyse levels of DNA damage, such as comet assay

    Supervisor: John J Reynolds

    Email

    Project Title: DNA damage and trophoblasts: An undiscovered story

    Project Overview:
    Our lab has, over the years, been interested in learning more about the process of placental development, and in particular the role of the progenitor cells, known as trophoblasts. Trophoblast cells are the first cells emerging from the early embryo and they function to migrate and invade into the mother tissues, promoting attachment and embedding and thereby establishing the first steps towards placental development during the implantation stage.

    The placenta is one of the largest organs during embryogenesis and is formed in a very limited amount of time, leading to significant replicative pressures due to the extreme amount of cell proliferation needed to generate the placental cell mass. Trophoblasts are the main cell type which will make up the bulk of the placenta, and it is not clear how these cells regulate and repair the DNA damage that can arise under the huge levels of replicative stress caused by extensive cell proliferation.

    In this project, we propose to study whether there are differences in the presence of markers of DNA damage and replication stress between different trophoblast cells. We will compare different trophoblast cell lines, and also trophoblast cells at different passage numbers, allowing us to determine whether cells that have been allowed to proliferate for long periods of time accumulate DNA damage. We also would like to assess how trophoblasts manage to detect and repair different types of DNA lesion following differential treatments with DNA damaging agents. Ultimately, we propose to determine if specific DNA repair mechanisms and/or the expression of specific DNA repair factors are found to correlate with the ability of trophoblast cells to repair DNA damage. Our current work aims to characterise further at the cellular levels, the molecular changes which are being regulated.

    Project Aims:

    • Grow and manipulate trophoblast cells
    • Analyse levels of spontaneous DNA damage in different trophoblast cell lines
    • Compare high vs low cell passages and analyse for changes in levels of DNA damage
    • Use DNA damaging agents to induce different types of DNA damage in order to determine how trophoblast repair them
    • Study changes in motility markers by fluorescent microscopy including focal adhesion, filopodia, lamellipodia.


    Core Techniques:

    • Tissue culture
    • Gene expression manipulation of trophoblast cells
    • Treatment of cells with specific compounds/inhibitors
    • Immunofluorescence and microscopy imaging
    • Western blotting
    • Assays to analyse levels of DNA damage

    Supervisor: Stephane Gross and John J Reynolds
    Email


    Project Title: Developing a method to isolate nuclei from mammalian cells.

    Project Overview:
    The nucleus of the cell is responsible for storing hereditary information and controlling growth. Many ageing-related diseases are caused by abnormalities in the structure/functioning of the nucleus and the integrity of the nuclear membrane is also known to deteriorate during ageing.

    My previous research has shown that inhibition of the p97/VCP unfoldase, which is responsible for protein quality control in cells, causes alterations to the morphology of nuclei, with nuclei being significantly smaller. DNA replication is also perturbed in such cells, but it isn’t clear whether the two phenotypes are connected. Potential explanations for these smaller nuclei include more compacted chromatin structure or perturbations in the growth/structure of the nuclear envelope. Notably, either of these changes could disrupt DNA replication.

    The aim of this project will be to establish a method of isolating nuclei from model tissue culture cell lines. If this is successful, then we can start to determine the explanation for smaller nuclei upon treatment with the p97 inhibitor (CB-5083). Firstly, by analysing chromatin organisation/structure with the MNase assay and secondly, by analysing nuclear membrane composition and morphology by microscopy.

    Project Aims: 

    • Develop a method to isolate nuclei from model cell lines and confirm the efficiency.
    • Perform MNase assays to analyse nuclei for chromatin structure.
    • Perform microscopy analyses to examine the nuclear envelope.

    Core Techniques: 

    • Cell culture
    • Sucrose gradient centrifugation
    • Genomic DNA purification and MNase treatment
    • Agarose gel electrophoresis
    • Fluorescence and brightfield microscopy

    Supervisor: Rebecca Jones
    Email

     

    Project Title: Senescent Cells and Metabolic Dysfunction: Exploring the Link Between Aging, Type 2 Diabetes, and Glucose Homeostasis

    Project Overview:

    A distinctive feature of ageing is the accumulation of senescent cells, defined as cells that have undergone irreversible loss of proliferative capacity. The characteristic of senescent cells is the senescence-associated secretory phenotype (SASP) involving the production of pro-inflammatory factors which reinforce senescence arrest in neighbouring tissue environments and have been documented to be vital contributors in disrupting insulin receptor signalling. Type 2 diabetic (T2D) patients have been reported to exhibit an increased susceptibility to accumulate senescent cells, thereby providing a potential mechanistic link between T2D and ageing. Data from previous experiments reveal that SASP produced by senescent Human Dermal Fibroblasts (HDFs) induces the senescent phenotype in non-senescent C2C12 skeletal muscle cells, consequently, impairing glucose metabolism, glycogen storage, enhancing reactive species production and dysregulating mitochondrial membrane potential. Moreover, preliminary studies reveal a reversal of previously mentioned effects, by blocking NF-κβ. Therefore, the interplay between cellular senescence and glucose homeostasis suggests that senescent cells may contribute to the development and progression of metabolic disorders by disrupting the normal regulation of glucose levels in the body. Understanding the molecular mechanisms underlying this relationship is an area which warrants further investigation. Senescence research in diabetes is crucial for translational science as it provides insights into cellular ageing processes that can lead to innovative therapies and preventative strategies which target NF-κβ, reverse cellular senescence and improve metabolic health.

    Project Aims:

    • Induce cellular senescence into HDF’s and co-culture with C2C12 mature myotubes.
    • Characterise fibroblast-generated SASP, identifying key pro-inflammatory cytokines present
    • Confirm cellular senescence in C2C12 cells by observing the formation of senescence-associated heterochromatin foci
    • Measure cytosolic ROS and determine changes in mitochondrial membrane potential by quantifying the expression of mitophagy markers.

    Core Techniques:

    • Cell culture/co-culture
    • ELISA
    • Fluorescent microscopy
    • qPCR
    • Western Blot

    Supervisor: Dr Karan Singh Rana
    Email 


    Project Title: The functions of histone methyltransferase and cancer driver MLL2 in colorectal cancer cells.

    Project Overview:
    The histone 3 lysine 4 (H3K4) methyltransferase MLL2 emerged in the last 10 years as one of the most mutated genes in cancer genomes. It is responsible for the mono-, di- and tri-methylation of H3K4. We have previously reported the mechanism by which MLL2 mutations can contribute to disease by deregulating RNA polymerase II transcription and resulting in transcriptional stress, DNA damage and mutations.

    In this project we aim to investigate the role of the MLL2 in HCT116 colorectal cancer cells by employing a variety of molecular, cellular, biochemical and computational methods. We will take advantage of two established MLL2 knock-out (KO) cell lines, as well as the parental HCT116 cells, to study the role of MLL2 in gene expression, histone methylation and cell sensitivity to DNA damage.


    Project Aims:

    • Gene expression differences between wild-type and MLL2 KO cells
    • Changes on global and gene-specific histone methylation after MLL2 deletion
    • Effect of X-Ray irradiation and chemotherapeutic agents on cells with or without MLL2.


    Core Techniques:

    • Cell biology: cell culture, fluorescence microscopy, cell-based assays
    • Molecular biology: gDNA and RNA isolation, PCR/RT-qPCR
    • Biochemistry: fractionation and protein isolation, Western blotting, chromatin immunoprecipitation (ChIP)
    • Computational techniques: RNA-Seq analysis

    Supervisor: Theo Kantidakis
    Email


    Project Title: Analysing connections between the nuclear envelope and DNA replication.

    Project Overview: 
    Many ageing-related diseases are caused by abnormalities in the structure of the nucleus. Progeria syndrome, for example, is caused by disruptions in the lamina meshwork, which lines the inside of the nucleus. Ageing phenotypes associated with these diseases are likely caused by genomic instability, which in turn arises because of faulty DNA replication. Indeed, evidence suggests that lamin proteins regulate DNA replication but the mechanism as to how they do this is currently unclear.

    The aim of this project will be to deplete lamin proteins from standard model cell lines and analyse the effects on DNA replication using a range of cell biology techniques.

    Project Aims:

    • Deplete lamin A/C from cells using siRNA and analyse
      • (1) DNA replication kinetics in cells with DNA fibre analyses and immunofluorescence microscopy
      • (2) nuclei morphology using microscopy.
    • Generate a lamin-degron cell line using CRISPR-Cas9 – this will enable rapid degradation of the protein, allowing us to analyse more immediate effects upon DNA replication.

    Core Techniques: 

    • Cell culture
    • Microscopy
    • SDS-PAGE and Western blotting
    • PCR and Agarose gel electrophoresis • Molecular cloning

    Supervisor: Rebecca Jones
    Email

    Ageing and Age-Related Diseases

    Project Title: Stress granule dynamics in C. elegans neurodegeneration models

    Project Overview: Stress granules (SGs) are dense aggregations of proteins and mRNAs appearing in the cytosol under stress conditions. They are transient and dynamic structures and play a critical role in mRNA metabolism and translational control by modulating the stress response. RNA-binding proteins control the sequestration of mRNA within SGs upon induction of stress. SG formation represents a physiological response to stress, however chronic stresses associated with ageing and neurodegenerative diseases lead to formation of persistent SGs that contribute to the aggregation of disease-related proteins. SGs dynamics have been mainly studied in yeast or human cell lines and not enough information is available on stress granules in multicellular organisms. C. elegans represents a powerful model to study ageing and neurodegeneration and dissect molecular mechanisms and signalling pathways contributing to pathology. An array of established C. elegans mutants can give insight into different aspects of neurodegenerative disease pathogenesis. Similarly, several tools are now available to study the role of cytoplasmic stress granules in stress response in C. elegans. The aim of this project is to use C. elegans models for neurodegenerative diseases (Alzheimer’s Disease (AD) and Parkinson’s Disease (PD)) to investigate SG dynamics and role in neurodegeneration.

    Project Aims:

    Analyse SG dynamics in C. elegans AD and PD models using fluorescently labelled SG marker. For this objective GFP-tagged SG marker GTBP-1 will be crossed into AD and PD mutant worms and SG dynamics will be analysed using fluorescence microscopy for day 1 and day 8 old adult worms. Investigate whether modulation of SG formation affects AD and PD disease phenotypes. This objective will be achieved by crossing loss-of-function mutations of SG key proteins TIAR-1 and GTPB-1 into mutant AD and PD worms and analysing the resulting phenotypes. Together these objectives will allow us to understand whether SGs play a crucial role in AD and PD pathogenesis and potentially suggest novel therapeutics for neurodegeneration.

    Core techniques: 

    • Genotyping (PCR, agarose gel electrophoresis)
    • Light and fluorescent microscopy
    • SDS-PAGE and Western Blotting
    • C. elegans maintenance and genetic crosses

    Supervisor: Zita Balklav

     Email

     

    Project Title: Unravelling the role of Parkinson’s disease associated protein DJ-1.

    Project overview: DJ-1 is a small, highly conserved protein of 189 amino acids, which is ubiquitously expressed and dimeric under physiological conditions. In humans, DJ-1 is encoded by the PARK7 gene, which was first linked to early onset, familial forms of Parkinson’s disease in 2003. DJ-1 is involved in protection from oxidative stress, although the molecular mechanisms underlying these effects are not entirely clear: its overexpression blocks oxidative damage, while oxidative stress-induced cell death increases in the absence of DJ-1 in cell culture and animal models. We have recently shown that DJ-1 is associated with cytoplasmic RNA granules arising during stress and neurodegeneration, providing a possible link between DJ-1 and RNA dynamics. This work will provide important insight into the biological function of DJ-1, which may be relevant for PD pathogenesis.

    Project aims:                           

    • Further characterize the interaction between DJ-1 and RNA in human cells.
    • Explore whether oxidative stress condition (oxidative stress, parkinsonian neurotoxins) can have any effect on DJ-1 / RNA interaction.

    Core techniques: Tissue culture for growing U2OS cells expressing a fluorescent stress granule marker (U2OS GFP-G3BP1/dG3BP1), biochemical approaches to purify stress granule cores and DJ-1 interacting RNA, immunofluorescence and in situ hybridization.

    Supervisor: Mariaelena Repici

    Email

     

    Project Title: Investigating how the stiffness of the extracellular matrix impacts upon the efficiency of DNA repair and replication pathways

    Project Overview:

    Cells in our bodes do not exist in isolation as they are surrounded by a highly complex assembly of structural and functional proteins in a network called the Extracellular Matrix (ECM). Cells actively probe their environment and signals from the ECM serve as critical regulators of fundamental cellular processes. One important characteristic of the environment that surrounds cells that can have a significant impact on cellular function is the rigidity or elasticity of the ECM. However, the exact mechanisms underlying this mechanosensing are still unclear.

    Understanding the effect of the rigidity of the ECM on fundamental cellular process is critical as it has particular relevance to human disease. In a healthy human liver, the tissue is relatively soft, the ECM is quite elastic and it functions to provide scaffold for the cells of the liver. In ageing and chronic disease, more ECM is made, making the tissue stiffer, which can drive disease progression. Furthermore, as the liver has a unique capacity to regenerate after damage, it is important to understand how the rigidity of the ECM impacts upon DNA replication pathways during cell division. The aim of this project is to investigate how liver cells replicate in the presence of matricies with increasing stiffness, from a soft ECM (0.2kPa) to a stiff ECM (32kPa). As liver disease is the 3rd leading cause of death in the UK, gaining a better understanding of how mechanosensing regulates DNA replication will be crucial in developing new therapeutic strategies to promote healthy liver regeneration.

    Project Aims:

    • Culture liver cells in 3D cultures within matracies of increasing stiffness using hydrogel technology Evaluate the effect of stiffness on cell health and expression of liver growth factors
    • Measure the ability of replicating liver cells within environments of increasing stiffness to efficiently repair DNA damage
    • Measure DNA replication dynamics of dividing liver cells within environments of increasing stiffness

    Core Techniques:

    • Hydrogel preparation and characterisation of 2D and 3D cell culture
    • Western blotting Immunofluorescence and brightfield microscopy imaging
    • Assays to analyse DNA replication dynamics, such as DNA fibre assay

    Supervisor: John J Reynolds and Emma L Shepherd

    Email


    Project title: Organelle crosstalk in neuroinflammation.

    Project overview:

    Cellular homeostasis is maintained by organelle cooperation and contact, which enables rapid material and information exchange and execution of various biological processes under different conditions. The endoplasmic reticulum (ER), is the hub for protein synthesis, folding, modification and transport as well as for phospholipid and cholesterol biosynthesis while the mitochondria is the cell’s powerhouse, producing necessary energy (ATP) to support cellular functions. Increasing evidence suggests that neuroinflammation contributes to mitochondrial dysfunction and ER stress while defects in mitochondria and ER communication are emerging as hallmarks of neurodegeneration.

    Although the mitochondria and ER seem to interact to promote healthy cellular functions, neuroinflammation appears to cause dysfunction in both organelles. It is not known whether neuroinflammation affects ER and mitochondria coordination, interaction and communication.

    Because neuroinflammation is associated with the onset of neurodegenerative diseases such as Parkinson’s and Alzheimer’s disease, it is imperative to better understand molecular events mediating communication between these organelles. This way we can effectively recognise targets of therapeutic intervention to address neurodegeneration early.

    Project aims:

    • To establish and characterise a neuroinflammatory environment using brain cells (e.g. neurons and astrocytes) in co-culture.
    • Explore changes in the structure and function of mitochondria and ER under an inflammatory environment.
    • Study changes in structural dynamics using molecular biology approaches.
    • Investigate signalling events (e.g. mTOR activation/inhibition) implicated in changes I'm ER and mitochondrial dynamics.


    Core techniques:
    • Cell culture,
    • immunohistochemistry,
    • western blotting,
    • calcium metabolism (ER function)
    • XFe24 Extracellular Analyser (mitochondrial function).

    Supervisor: Lissette Sanchez-Aranguren
    Email


    Project title: Understanding the links between vascular ageing and mitochondria.

    Project overview:

    Ageing of the vasculature is a contributing factor to the onset of age-related vascular diseases, including chronic kidney disease, atherosclerosis and vascular dementia. Throughout the lifespan, and to sustain vascular functions, endothelial cells undergo energy-expensive biological processes, including neovascularisation and angiogenesis. The energetic requirements to support these processes are supported by the mitochondria. However, during ageing, a decline in mitochondrial bioenergetics, particularly in endothelial cells, has been recognised as a crucial factor leading to adverse cardiovascular outcomes.

    In health and disease, gaseous transmitters such as hydrogen sulphide, have been observed to improve mitochondrial bioenergetics and angiogenesis of the vasculature. Nonetheless, the association between vascular ageing, mitochondrial dysfunction and hydrogen sulphide has not been established before.

    This project aims to elucidate the role of a mitochondrial-specific hydrogen sulphide-producing enzyme, 3-mercaptopyruvate sulphurtransferase (3-MST), in mediating vascular dysfunction in ageing. To accomplish this aim, we will employ a robust cellular model of ageing and 3-MST attenuation using endothelial cells.


    Project aims:

    • To establish and characterise a senescent model of vascular dysfunction in endothelial cells
    • To attenuate 3-MST expression using siRNA silencing approaches.
    • Explore the effects of senescence and 3-MST attenuation in endothelial function.
    • To attest the effects of senescence and 3-MST attenuation in wound healing, proliferation and angiogenesis.

    Core techniques:

    • Cell culture,
    • immunohistochemistry,
    • Western blotting,
    • siRNA silencing,
    • cell viability,
    • senescence assays,
    • angiogenesis (tube-like formation).

    Supervisor: Lissette Sanchez-Aranguren

    Email


    Title: Investigating the role of Platelet Endothelial Aggregation Receptor 1-activation in vascular remodelling

    Project Overview: 

    Pathological vascular remodelling is a key component in the development of cardiovascular disease. It has previously been shown that PEAR1 is associated with Single nucleotide variants of PEAR1 are significantly associated with increased risks during cardiovascular disease. Interestingly, data which is publicly searchable in the GEO2 database shows that PEAR1 is significantly downregulated in abdominal aortic aneurysms and intracranial aneurysms (GSE75436, GSE15629). This is a strong indicator that PEAR1 is involved in the vascular remodelling of the vessel wall during aneurysm formation.

    Most studies investigating the function of PEAR1 in vascularisation have used methods of Pear1 knockdown rather than PEAR1 activation.

    Therefore, the aim of the present project is to use unique PEAR1 agonists to evaluate changes to extracellular matrix deposition, proliferation, and migration of primary human aortic fibroblasts.

    Project Aims:

    • Measure phosphorylation of Akt by Western blot to confirm cellular activation and optimal concentrations of agonists.
    • Induction of extracellular matrix deposition using TGFβ in the presence and absence of PEAR1 agonists followed by imaging and quantification of extracellular matrix deposition by microscopy.
    • Quantification of changes to cell migration and proliferation upon PEAR1-stimulation. Upon early successful completion of the primary aims and objectives of the project, there is potential scope for performing additional immunohistochemical staining of vascular tissue to investigate PEAR1 expression levels and collagen deposition.

    Core Techniques:
    • Western Blotting
    • Cell Culture
    • Microscopy and immunostaining
    • Viability Assays

    Supervisor: Caroline Kardeby
    Email

    Project Title: Investigating the role of Platelet Endothelial Aggregation Receptor 1-activation in
    extracellular matrix deposition by primary human lung fibroblasts


    Project Overview:

    Extracellular matrix remodelling is an important mechanism underlying the pathophysiology of disease, especially in incurable and deadly diseases like Idiopathic Pulmonary Fibrosis (IPF). In IPF, patients experience increased levels of inflammation and scarring in the lungs leading to difficulties to breath. Recent publications have shown that Platelet Endothelial Aggregation Receptor 1 (PEAR1) deficiency is associated with fibrosis formation in the lungs of mice. However, the role of PEAR1 in human lung fibrosis has not been explored yet.

    The project aims to use unique PEAR1 agonists to evaluate changes to extracellular matrix deposition, proliferation, and migration of primary human lung fibroblasts.

    Project Aims:

    • Measure phosphorylation of Akt by Western blot to confirm cellular activation and optimal concentrations of agonists.
    • Induction of extracellular matrix deposition using TGFβ in the presence and absence of PEAR1 agonists followed by imaging and quantification of extracellular matrix deposition by microscopy.
    • Quantification of changes to cell migration and proliferation upon PEAR1-stimulation. Upon early successful completion of the primary aims and objectives of the project, there is potential scope for performing additional immunohistochemical staining of lung tissue to investigate PEAR1 expression levels and collagen deposition.

    Core Techniques:

    • Western Blotting
    • Cell Culture
    • Microscopy and immunostaining
    • Viability Assays

    Supervisor: Caroline Kardeby
    Email

     

    Project Title: Senescent Cells and Metabolic Dysfunction: Exploring the Link Between Aging, Type 2 Diabetes, and Glucose Homeostasis

    Project Overview:

    A distinctive feature of ageing is the accumulation of senescent cells, defined as cells that have undergone irreversible loss of proliferative capacity. The characteristic of senescent cells is the senescence-associated secretory phenotype (SASP) involving the production of pro-inflammatory factors which reinforce senescence arrest in neighbouring tissue environments and have been documented to be vital contributors in disrupting insulin receptor signalling. Type 2 diabetic (T2D) patients have been reported to exhibit an increased susceptibility to accumulate senescent cells, thereby providing a potential mechanistic link between T2D and ageing. Data from previous experiments reveal that SASP produced by senescent Human Dermal Fibroblasts (HDFs) induces the senescent phenotype in non-senescent C2C12 skeletal muscle cells, consequently, impairing glucose metabolism, glycogen storage, enhancing reactive species production and dysregulating mitochondrial membrane potential. Moreover, preliminary studies reveal a reversal of previously mentioned effects, by blocking NF-κβ. Therefore, the interplay between cellular senescence and glucose homeostasis suggests that senescent cells may contribute to the development and progression of metabolic disorders by disrupting the normal regulation of glucose levels in the body. Understanding the molecular mechanisms underlying this relationship is an area which warrants further investigation. Senescence research in diabetes is crucial for translational science as it provides insights into cellular ageing processes that can lead to innovative therapies and preventative strategies which target NF-κβ, reverse cellular senescence and improve metabolic health.

    Project Aims:

    • Induce cellular senescence into HDF’s and co-culture with C2C12 mature myotubes.
    • Characterise fibroblast generated SASP, identifying key pro-inflammatory cytokines present
    • Confirm cellular senescence in C2C12 cells by observing the formation of senescence-associated heterochromatin foci
    • Measure cytosolic ROS and determine changes in mitochondrial membrane potential by quantifying the expression of mitophagy markers.

    Core Techniques:

    • Cell culture/co-culture
    • ELISA
    • Fluorescent microscopy
    • qPCR
    • Western Blot

    Supervisor: Dr Karan Singh Rana
    Email


    Project Title: Investigating the effects of anti-senolytics on Mesenchymal Stromal Cell expansion and immuno-modulatory properties

    Project Overview: 

    Mesenchymal Stromal Cells (MSCs) are a key cell for cell based therapies. Their ability to modulate the function of immune cells as well as regenerate damaged tissues, restoring function has made them a new clinical treatment that does not have the side effects of conventional drug-based therapies. However, as we age, MSCs in the body gradually become more senescent, with reduced proliferative capacity and less able to direct immune responses. This ageing phenotype is also observed when we expand MSCs in the laboratory – forcing cells to expand to the numbers required for effective clinical therapy often results in a similar increase in senescence and reduced therapeutic potential. Therefore, finding new growth conditions that allow the efficient expansion of younger donor MSCs without inducing this ageing phenotype will allow more patients to be treated with this cell based therapy. In addition this may inform us as to how we can expand older donor MSCs more effectively and rejuvenate their immune-modulatory properties as we culture them, making this cell based therapy more available to patients.

    Senescent MSCs secrete higher quantities of TGF-B which converts healthy cells in laboratory culture conditions to senescent cells, thus reducing the quality of the cell product. Anti-senolytics are a class of drugs which specifically target and kill senescent cells. This project will evaluate and compare how treating cultures of young and older donor MSCs with anti-senolytics affects the quality of the expanded MSCs and if this can improve the proliferation and functionality of these progenitors.

    Project Aims:

    • Evaluate the actions of anti-senolytics on MSC physiology (growth, differentiation and apoptosis).
    • Examine any impact on the immuno-modulatory activities of MSCs in co-culture with immune cells (macrophages and T cells)
    •  Measure changes in the cell secretome after anti-senolytic treatment
       

    Core Techniques:

    • Culture of human primary MSCs and peripheral blood immune cells
    • Flow cytometry
    • qPCR
    • Immunofluorescent staining and microscopy
    • Measurement of soluble factors by ELISA

    Supervisor: Ewan Ross
    Email

    Immunology

    Project Title: Extracellular vesicles - towards defining the functional surface of EV from cells of the neurovascular unit.

    Project Overview: Cell communication is central to the development of multicellular organisms and their effective physiological functioning. One novel mechanism is mediated by extracellular vesicles (EV). These EV are released from cells when viable, stressed or undergoing cell death and they are taken up by recipient cells where they mediate a broad range of effects including the induction of cell death, cell survival and inflammatory responses. Consequently, these EV are now established as contributing to a range of pathological conditions, including those associated with traumatic brain injury, dementia and diseases of the central nervous system (CNS). It is therefore essential that we understand the composition of these EV released from different cells under different conditions. This will enable us to define how these EV are taken up and how they exert their effects (both desirable and undesirable).
     
    This project will characterise EV release from cells of the neurovascular unit and subsequently identify and characterise key factors associated with EVs that mediate their inflammation-controlling function.  Using flow cytometry we will define molecules present on the surface of EV as these are the surface molecules that will facilitate EV uptake by recipient cells and may propagate pathology, as seen in dementia. By defining these molecules, it will be possible to modulate EV uptake for therapeutic gain (e.g. via antibody or small molecule inhibition) and will also highlight potential biomarkers for disease.  

    Project Aims: 

    • To characterise EV release from cells of the neurovascular unit, in isolation or co-culture.
    • To identify key proteins, present on EV that mediate EV function in modulating the innate immune response. Lead proteins for study may be selected from our existing large dataset of mass-spectrometry results of the EV proteome. 
    • To define the function of selected proteins in EV activity. Using a variety of cell biological and molecular approaches, this will assess proteins as key ligands for EV binding, uptake or active function. 

    Core Techniques: Tissue culture for the harvesting of EV; single particle analyses to characterise EV (number and size); live cell imaging to identify the capacity of EV to recruit macrophages; flow cytometry to reveal the EV surface proteome and flow cytometry of macrophages to define their phenotype after treatment with EV. 

    Supervisor: Andrew Devitt

    Email

     

    Project Title: Extracellular vesicles – structure/function relationships in the control of inflammation.

    Project Overview: Inflammation is a key defense mechanism though its benefits are only realised when the response is turned off and tissue homeostasis restored. This process relies on intercellular communication mediated by extracellular vesicles (EV). These EV can attract macrophages, drive a change in macrophage phenotype and provide additional signals that drive the tissue repair. Relatively little is known about how these EV act or the key molecular factors that underpin their function. Our extensive preliminary work reveals that EV carry a large range of factors that may underpin their activity. 

    This project will identify and characterise key factors associated with EVs that mediate their function. The results from this project will therefore enable a better understanding of the molecular players and mechanisms involved in EV function providing important insight for the control of inflammation and regenerative medicine applications.

    Project Aims: 

    • To identify key proteins, present on EV that mediate EV function in modulating the innate immune response. Lead proteins for study will be selected from our existing large dataset of mass-spectrometry results of the EV proteome. 
    • To define the function of selected proteins in EV activity. Using a variety of cell biological and molecular approaches, this will assess proteins as key ligands for EV binding, uptake or active function. 

    Core Techniques: Tissue culture for the harvesting of EV; single particle analyses to characterise EV (number and size); live cell imaging to identify the capacity of EV to recruit macrophages; flow cytometry to reveal the EV surface proteome and flow cytometry of macrophages to define their phenotype after treatment with EV. 

    Supervisor: Andrew Devitt

    Email

    Project Title: Crosstalk between mesenchymal stem cells and immune cells.

    Project Overview: Mesenchymal stem cells are stromal/structural cells found in many adult tissues, including the bone marrow, but they are also found throughout the body, associated with capillaries (known as pericytes). These cells are an attractive progenitor cell source for the renewal of damaged tissues due to their ability to self-renew, their high proliferative capacity and their differentiation potential. Under certain circumstances, usually associated with chronic inflammation, MSCs/pericytes are capable of differentiating into another cell type known as myofibroblasts; these cells release excessive amounts of extracellular matrix proteins and ultimately lead to tissue destruction through the process of fibrosis. This is a normal bodily reaction to an injury (for example, skin scarring after an injury), but if left unresolved, it can also lead to the loss of organ function. As fibrosis has no currently available treatment, this loss of function has serious detrimental effects. 

    Project Aims: 

    • To determine the mechanisms by which MSCs/pericytes impact on the function of macrophages, an immune cell type closely associated with wound healing and fibrosis. 
    • To determine the role of cell-to-cell contact and soluble factors in modulating macrophage function. 
    • To specifically identify the mediators produced by healthy pericytes as well as pericytes that have been grown under pro-fibrotic or oxidative stress conditions, and the impact of these products on macrophage activation, polarization, and cytokine secretion.

    Core Techniques: Cell culture; ELISA; immunostaining; microscopic imaging and digital data analysis.

    Supervisor: Jill Johnson

    Email

     

    Project Title: Growing a better MSC: Investigating the immuno-modulatory properties of cultured MSCS.

    Project Overview: Cell-based therapies have become an increasingly effective clinical approach to promote tissue repair, wound healing or reduce inflammation. Mesenchymal stem cells (MSCs) are a key cell type in this approach as they can restore damaged tissues (fat, bone, muscle) and reduce inflammation through direct cell-cell contact or release of soluble mediators (proteins, extracellular vesicles (EVs)). Therefore, the ability to grow and maintain functional MSCs in the laboratory is a crucial research goal. 

    Producing MSCs for patients in the laboratory is difficult as they spontaneously differentiate in culture over time, losing their immuno-modulatory abilities. We have recently demonstrated growing MSCs on specialised surfaces or treating with certain compounds can maintain their therapeutic potential by modulating their metabolism. This results in turn maintains their ability to suppress lymphocyte proliferation. This project will further develop this work by investigating the mechanisms by which MSCs are educated by these surfaces or compounds to promote their immuno-modulatory effects. 

    Project Aims:

    • To investigate physiological changes to the MSC as it adheres to the immunized surface. Preliminary data on changes to the cytoskeleton and mitochondrial function will form the starting point of this study. 
    • Co-culture of MSCs grown on surfaces or treated with compounds with lymphocytes to monitor effects on immune-modulation. T cell proliferation and the development of regulatory T cells will be assessed.
    • MSCs EVs will be purified and their effects on macrophage and T cell function will be assessed.
    • Physiological and phenotypic changes to MSCs after treatment with compounds will be investigated to monitor their naïve, therapeutic potential.

    Core Techniques: Cell culture, immunohistochemistry and microscopy, flow cytometry, PCR, SDS-PAGE and western blotting. 

    Supervisor: Ewan Ross 

    Email


    Project Title: Development of an in vitro diabetic skin model to test novel therapeutics for enhanced wound healing

    Project Overview:


    Diabetic wounds, particularly those associated with pressure ulcers, represent a significant global health challenge, with 15-25% of diabetic patients developing a foot ulcer during their lifetime. These ulcers are notoriously difficult to heal due to prolonged inflammation and impaired angiogenesis, which are critical factors in tissue repair and regeneration. The primary objective of this project is to develop a robust 3D in-vitro diabetic skin model that accurately mimics the impaired healing environment observed in diabetic patients. This model will be used to test the efficacy of novel dermal treatments designed to enhance wound healing by reducing inflammation and promoting angiogenesis. The development process will involve culturing human endothelial cells and dermal fibroblasts to form the base layer of the skin model, with keratinocytes seeded on top to mimic the epidermal layer. The cells will be exposed to a hyperglycaemic environment and treated with inflammatory reagents. The novel treatments will be assessed for safety and for efficacy by measuring inflammatory markers such as IL-6, wound closure rates, and angiogenesis through tube formation rates. This project aims to create a reliable in-vitro diabetic wound model that can facilitate the preclinical testing of new treatments, ultimately leading to more effective therapies for diabetic wound healing and reducing the incidence of severe complications.


    Project Aims:

    • Establish a multilayered 3D in-vitro diabetic skin model
    • Characterise cellular responses to hyperglycaemic and inflammatory stimuli
    • Assess wound healing potential and angiogenesis in the diabetic skin model

    Core Techniques:

    • Cell culture and 3D skin model development
    • Hyperglycaemic and inflammatory conditioning
    • Assessment of inflammatory markers
    • Wound healing and angiogenesis assays
    • Treatment efficacy assessment

    Supervisor: Dr Mandeep Marwah

    Email

     

    Project Title: Investigating the effects of anti-senolytics on Mesenchymal Stromal Cell expansion and immuno-modulatory properties

    Project Overview:

    Mesenchymal Stromal Cells (MSCs) are a key cell for cell based therapies. Their ability to modulate the function of immune cells as well as regenerate damaged tissues, restoring function has made them a new clinical treatment that does not have the side effects of conventional drug-based therapies. However, as we age, MSCs in the body gradually become more senescent, with reduced proliferative capacity and less able to direct immune responses. This ageing phenotype is also observed when we expand MSCs in the laboratory – forcing cells to expand to the numbers required for effective clinical therapy often results in a similar increase in senescence and reduced therapeutic potential. Therefore, finding new growth conditions that allow the efficient expansion of younger donor MSCs without inducing this ageing phenotype will allow more patients to be treated with this cell based therapy. In addition this may inform us as to how we can expand older donor MSCs more effectively and rejuvenate their immune-modulatory properties as we culture them, making this cell based therapy more available to patients.

    Senescent MSCs secrete higher quantities of TGF-B which converts healthy cells in laboratory culture conditions to senescent cells, thus reducing the quality of the cell product. Anti-senolytics are a class of drugs which specifically target and kill senescent cells. This project will evaluate and compare how treating cultures of young and older donor MSCs with anti-senolytics affects the quality of the expanded MSCs and if this can improve the proliferation and functionality of these progenitors.


    Project Aims: 

    • Evaluate the actions of anti-senolytics on MSC physiology (growth, differentiation and apoptosis).
    • Examine any impact on the immuno-modulatory activities of MSCs in co-culture with immune cells (macrophages and T cells)
    • Measure changes in the cell secretome after anti-senolytic treatment

    Core Techniques:

    • Culture of human primary MSCs and peripheral blood immune cells
    • Flow cytometry
    • qPCR
    • Immunofluorescent staining and microscopy
    • Measurement of soluble factors by ELISA

    Supervisor: Ewan Ross
    Email


    Project Title: Optimising bioreactors to expand human mesenchymal stromal cells.

    Project Overview:

    Mesenchymal Stromal Cells (MSCs) are key cells for cell based therapies due to their abilities to both reduce inflammation and promote repair of damaged tissues. Unfortunately, these are a rare population of tissue progenitor cells and require expanding in the laboratory to generate the large numbers of cells required for effective therapies. This forced growth often leads to the loss of their immuno-modulatory properties and can result in premature ageing. Therefore new methods to expand these cells whilst retaining their regenerative properties are required. At Aston, we have developed a stirred tank bioreactor protocol for growing MSCs using microcarriers as an adhesive substrate. This system allows us to efficiently grow large numbers of these cells in a relatively small amount of media. From these we can harvest functional, viable cells that retain their important clinical activities. This project will look to further refine this system, investigating the potential of hydrogel mediated release of soluble factors directly into the bioreactor, to further promote MSC expansion and immuno-modulatory properties. This project will provide training in both biomaterials as well as the growth of stem cells and analysing their functional potential.

    Project Aims: 

    • Develop gel based materials for the slow release of soluble factors to promote MSC expansion
    • Assess how changing the environment affects MSC stem like properties including differentiation
    • Upscaling optimal conditions from small (100ml) to large scale (1L) bioreactors to demonstrate the potential for large scale expansion.

    Core Techniques

    • Culturing of human MSCs and testing their immunomodulatory activities
    • Use of bioreactors for expanding MSCs
    • Formulation of materials for the release of soluble factors
    • Analysis techniques (flow cytometry, qPCR, microscopy)

    Supervisor: Ewan Ross
    Email

    Biotechnology

    Project Title: Novel antimicrobials for Pseudomonas aeruginosa

    Project Overview: Healthcare-acquired infections (HCAI) are a major problem in hospitals throughout the world, costing the NHS more than £1 billion per annum. A large proportion of these infections are due to an opportunistic bacterial pathogen, Pseudomonas aeruginosa. Whilst healthy individuals are usually unaffected or recover well, seriously ill patients or those whose immune systems are not fully functional are more susceptible. In these cases, the infection is usually very serious and mortality rates can be as great as 70%. P. aeruginosa is particularly important for cystic fibrosis (CF) patients who typically contract chronic infections which cause permanent lung damage and this is the principal cause of morbidity and mortality. P. aeruginosa infection is difficult to control because it tends to be resistant to many antimicrobial agents. There exists an urgent need for novel antimicrobials.

    A protein that is essential for the growth of P. aeruginosa has recently been identified. This protein is thought to be involved in cell wall production, which is a common target for existing antibiotics. This protein, TgpA, is an enzyme that has transglutaminase (TG) activity and can cross-link proteins together to create stable structures. It is likely that TgpA catalyses the modification of an existing cell wall component or stabilises the cell wall by cross-linking of proteins. This project will recombinantly express the TgpA protein to characterise its transglutaminase activity and screen for novel small molecule inhibitors. This could allow development of these inhibitors into effective antibiotics against P. aeruginosa. Identification of a novel class of antibiotics could also allow this strategy to be adopted in other microorganisms that use transglutaminases for growth or virulence.

    Project Aims:

    • Recombinant expression and affinity purification of P. aeruginosa TgpA.
    • Characterisation of the transglutaminase activity of TgpA to determine substrate specificity.
    • In silico and in vitro screening of transglutaminase inhibitors.
    • Determine effects of TgpA inhibition on growth of P. aeruginosa

    Core Techniques

    • Molecular biology techniques
    • Recombinant protein expression
    • Affinity purification
    • Transglutaminase enzyme assays
    • Molecular visualisation software and docking

    Supervisor: Russell Collighan

    Email

     

    Project Title: Characterisation of novel recombinant lipases for biodiesel production.

    Project Overview: Biodiesel represents an alternative to petrochemical fuels and can be produced for example by trans-esterification of vegetable oils using enzymes. Lipases (triacylglycerol acyl hydrolases EC 3.1.1.3) can be used to catalyse biodiesel synthesis and are produced by a variety of microorganisms. Therefore, lipases represent an attractive biotechnological product with great commercial potential and environmental benefits. However, the relative low yields, complex purification and relative low substrate specificity hinders their real application. This project builds on previous work in collaboration with colleagues at the Energy and Bioproducts Research Institute at Aston and the University of Nigeria in which have recently extracted a novel lipase from the fungus Aspergillus flavus and cloned into the yeast Pichia pastoris for recombinant expression.

    Project Aims: 

    • Produce recombinant lipases using inducible and constitutive expression systems in Pichia pastoris.
    • Compare lipase activity between crude and purified protein extracts.
    • Evaluate the substrate specificity for biodiesel (Fatty Acid Methyl Esters / FAME) production.
    • Evaluate reaction conditions to optimise lipase activity 

    Core techniques: Recombinant protein expression in yeast; protein purification and chromatography approaches; biochemical assays.

    Supervisors: Alan Goddard/ Alfred Fernandez Castane (EBRI) 

    Email

     

    Project Title: The role of redox balance in magnetotactic bacteria 

    Project Overview: Magnetotactic bacteria produce magnetosomes, structures that contain magnetite (Fe3O4) and allow the microbe to align in magnetic fields. Magnetosomes are of great interest as sources of magnetic nanoparticles for biotechnology applications, but knowledge of their synthesis, regulation and biochemical effects is still limited. Evidence is emerging that their production is redox-dependent, they may be redox-active in vivo and have protective effects against environmental stress. 

    Building on expertise in growth of magnetotactic bacteria at Aston, this project will investigate the properties of the magnetosome membrane under different growth and redox conditions to study how the bacteria avoid lethal oxidative damage from iron-dependent reactions and what antioxidant activities are present. 
     

    Project Aims: 

    Characterization of the magnetosome membrane to understand whether it is resistant to oxidation using spectrophotometric assays to determine low molecular weight antioxidant status and oxidative stress. 
    To determine which lipid oxidation products alter the balance of cell proliferation versus cell death by lipidomic analysis to characterize the magnetosome membrane. 

    Core techniques: Recombinant protein expression in yeast; protein purification and chromatography approaches; biochemical assays.

     Supervisors: Corinne M. Spickett/ Alfred Fernandez Castane (EBRI)

    Email

     

    Project Title: A 3D printing approach for drug discovery


    Project Overview: Drug Discovery has reached a significant bottleneck over the last decade, which has seen many promising compounds fail in pre-clinical trials. While these failures have several underlying causes, drug screens using traditional 2D cell culture have often led to misleading results. 3D printing combined with advances in cell culture have revolutionised how cells are studied and provide an opportunity to replace studies performed in vivo. While methods to develop these devices (popularly referred to as ‘Organs on a Chip’) are still in their infancy, many systems mimicking heart, lung and bone have been successfully developed. These systems are able to perform a range of functions and provide an excellent platform for exploring drug target-ligand interactions as well and studying diseases.  

    This project will provide training in biomaterials and cell biology to develop a 3D printed micro-physiological chamber (‘organ on a chip’; ‘pancreas on a chip’) containing encapsulated insulin secreting cells. This device will ultimately be used for drug discovery. 

    Project Aims: 

    • Explore methods to genetically manipulate hydrogel encapsulated cells to either express new proteins or to suppress existing ones to aid drug discovery.
    • Explore surface modifications for 3D printed components to provide extra functionality to the chamber e.g. cell trapping, ‘in device’ cell signalling assays.
    • Explore ways that the 3D printed device(s) can be modified for high throughput drug discovery.
    • Explore alternative hydrogel formulations and other environmental factors to develop a native like environment for cell signalling, and proliferation.

    Core Techniques: Computer Aided Design (CAD); FDM 3D printing; 3D cell culture; cell signalling assays; cell viability analysis; molecular biology and microscopy.

    Supervisor: John Simms 

    Email


    Project Title: Optimisation of 3D printed microneedles for targeted delivery of vitamin B12 to treat anaemia and protect against oxidative stress

    Project Overview:
    This project aims to optimise 3D printed microneedles for the targeted delivery of vitamin B12 to treat anaemia and protect against oxidative stress in human endothelial cells. Anaemia, often resulting from a vitamin B12 deficiency, affects millions globally, with current treatments like oral supplements and injections facing challenges in absorption and patient compliance. By leveraging advanced 3D printing techniques, this project will fabricate microneedles that encapsulate and release vitamin B12 in a controlled manner. The project will investigate the protective effects of vitamin B12 against oxidative stress-induced cell injury using endothelial cells exposed to various superoxide sources, mimicking inflammatory and oxidative conditions observed in vascular pathologies. Through a series of comprehensive in vitro studies, including cell viability assays, oxidative stress assessments, and wound healing assays, the efficacy of the microneedles will be evaluated within a controlled cellular environment. This innovative approach has the potential to significantly enhance treatment outcomes for anaemia by providing a minimally invasive and targeted delivery method, while also offering insights into the protective mechanisms of vitamin B12 in safeguarding vascular health.


    Project Aims:

    • To fabricate microneedles optimised for vitamin B12 encapsulation and release,
    • To evaluate the efficacy of vitamin B12 delivery in treating anaemia,
    • To assess the protective effects of vitamin B12 against oxidative stress in endothelial cells.

    Core Techniques:

    • Advanced 3D printing for precise microneedle fabrication,
    • In vitro release studies to evaluate the controlled release profile of vitamin B12,
    • Cell culture and oxidative stress assays to investigate the protective effects ofvitamin B12 in endothelial cells.
    • In vitro testing to assess microneedle efficiency, pharmacokinetics, and therapeutic efficacy.

    Supervisor: Dr Mandeep Marwah

    Email


    Project title: Targeting the mitochondria using novel biodegradable lipid carriers.

    Project overview:

    Mitochondrial dysfunction is increasingly recognised as a contributing factor in the onset of age-related disorders including those of neurodegenerative nature such as Alzheimer’s and Parkinson’s disease. Mitochondria are the powerhouse of the cell, and they are essential to sustain cellular functions, especially in energy demanding cells such as neurons. In neurodegeneration, an impairment in the function of the mitochondria often leads to oxidative stress. Therapies based on antioxidants to counteract the oxidative stress seen in neurodegeneration have been proposed but unfortunately proven unsuccessful. In our lab, we believe this lack of effects may be explained by the inability of antioxidants to reach and accumulate in cellular compartments such as the mitochondria.

    Targeting and accumulating drugs of interest into the mitochondria is relatively difficult due to its negative charge and slightly alkaline matrix. Our laboratory has designed and characterised novel liposomes targeting the mitochondria aiming to successfully deliver and accumulate drugs (antioxidants) inside the mitochondria.

    We aim to validate the mitochondrial targeting properties of these novel liposomes using brain-relevant cell lines as proof-of-concept for their potential use as drug delivery systems in the treatment of neurological disorders.


    Project aims:

    • Attest the biocompatibility of mitochondrial-targeted liposomes using 3D cell models.
    • Explore encapsulation rates of a library of drugs (e.g. antioxidants) of interest in neurodegeneration.
    • Investigate mitochondrial-specific accumulation in cells and specific organelles.
    • Explore molecular mechanisms of liposomal uptake and targeting properties using
    • Confocal microscopy.

    Core techniques:

    • Polymer synthesis and liposomal formulations,
    • zeta plus instrument,
    • dynamic light scattering,
    • HPLC, 2D and 3D cell cultures,
    • cell viability assays,
    • confocal microscopy,
    • biochemical assays.

    Supervisor: Lissette Sanchez-Aranguren
    Email

    Project Title: Investigating the Effect of Lipid Bilayer Composition on the Structure and Dynamics of the β2-Adrenergic Receptor using Coarse-Grained Molecular Dynamics Simulations

    Project Overview:

    The β2-adrenergic receptor (β2AR) is a well-studied, model G protein-coupled receptor (GPCR) that plays a crucial role in various physiological processes, including cardiovascular and respiratory function. The lipid bilayer composition is known to influence the structure and function of membrane proteins, but the specific effects on β2AR remain to be elucidated. Coarse-grained molecular dynamics (CG-MD) simulations provide an efficient way to study the behaviour of membrane proteins in different lipid environments over longer timescales than atomistic simulations.

    This project will provide valuable insights into the role of lipid bilayer composition in modulating the structure and function of β2AR, which can have implications for understanding the behaviour of other GPCRs in different lipid environments. The results obtained from this study can guide the design of experimental studies and contribute to developing more effective drugs targeting GPCRs.

    Project Aims:

    • To investigate the effect of different lipid bilayer compositions on the structure and dynamics of β2AR using CG-MD simulations.
    • To analyse the interactions between β2AR and lipids in different bilayer compositions and their influence on receptor stability and conformational changes.
    • Gain a better understanding of how lipid bilayer composition affects the structure and dynamics of β2AR.  Identification of specific lipid-protein interactions that influence the stability and conformational changes of β2AR.
    • Validation of the CG-MD approach for studying the effects of lipid bilayer composition on membrane proteins, which can be extended to other GPCR systems.

    Core Techniques:

    • Ideally, an applicant would have previous experience with Linux, computational chemistry, or structure.
    • Interests in molecular modelling software and programming languages.

    Supervisor: John Simms
    Email

    Project Title: Using molecular modelling to explore the Solubilising Efficiencies and Magnesium Sensitivity of SMA2000 Derivatives.


    Project Overview:
    This MRes project focuses on unravelling the mechanisms behind the solubilising efficiencies and magnesium sensitivity of SMA2000 derivatives in lipid SMALP (Styrene Maleic Acid Lipid Particle) systems. By employing molecular modelling, the project aims to simulate and analyse the behaviour of these derivatives, providing valuable insights into their unique properties.

    SMALPs have revolutionised the study of membrane proteins by preserving their native lipid environment. However, the factors influencing the solubilising efficiency and magnesium sensitivity of SMA2000 derivatives remain poorly understood. This project will attempt to address these critical questions through molecular modelling and simulations.

    The project outcomes will have significant implications for the rational design of improved SMA derivatives and the optimisation of SMALP-based membrane protein studies. The insights gained from this project will contribute to advancing membrane protein research and potentially lead to novel applications in drug discovery and biotechnology.


    Project Aims:

    • Developing molecular models of SMA2000 derivatives and lipid SMALP systems.
    • Simulating the interactions between SMA2000 derivatives and lipid bilayers using molecular dynamics.
    • Analysing the simulation results to identify the structural and dynamic factors contributing to the solubilising efficiencies and magnesium sensitivity of SMA200 derivatives.
    • Correlating the modelling results with experimental data to validate the findings and comprehensively understand the system.

    Core Techniques:

    • Ideally, an applicant would have previous experience with Linux, computational chemistry, or structure.
    • Interests in molecular modelling software and programming languages.

    Supervisor: John Simms
    Email

    Project Title: Optimizing Cell-Free Expression of Growth Factors for the smart delivery of
    peptide-based drugs.


    Project Overview:
    Growth factors and peptides play crucial roles in regulating cellular processes, including proliferation, differentiation, and migration. However, their short half-lives and rapid diffusion limit their effectiveness in traditional delivery methods. Cell-free expression systems offer a promising alternative for producing these molecules, allowing for fast and flexible synthesis without living cells. By encapsulating cell-free expression systems in alginate particles, we aim to create a controlled microenvironment for the sustained and localized delivery of growth factors and peptides. Cutting-edge subcutaneous administration of insulin is performed using alginate spheres containing protein expression machinery.


    Project Aims: 

    • This project addresses the need for advanced delivery systems to provide controlled and localised growth factors and protein-based therapeutics.
    • By combining cell-free expression technology with alginate particle encapsulation, we aim to develop a versatile platform for producing and delivering bioactive molecules.
    • The successful optimisation of this system could have significant implications for various applications, including tissue engineering, regenerative medicine, and drug screening using organ-on-a-chip models.

    Core Techniques:

    • Expertise in cell-free expression systems and their optimisation for protein synthesis.
    • Knowledge of alginate biomaterials and particle fabrication techniques.
    • Experience characterising particle properties, including morphology, stability, and release kinetics.
    • Experience in cell culture techniques and assessing cellular responses to bioactive molecules.
    • Familiarity with organ-on-a-chip models and their drug screening and tissue engineering applications.
    • Expertise in assay development to determine the effectiveness of the CFE system.

    Supervisor: John Simms
    Email

    Project Title: Investigating Cell-Free Expression of Adapter Proteins in Liposomes for Biomaterial Applications

    Project Overview:
    This MRes project aims to explore the use of cell-free protein expression within liposomes to
    develop novel biomaterials. The research will focus on the expression of "adapter" proteins at
    the liposome bilayer surface, which can recognise partner proteins and form organised
    networks.


    Cell-free expression systems offer a unique platform for protein synthesis without the
    constraints of living cells. The expressed adapter proteins can be localised to the bilayer surface
    by encapsulating these systems within liposomes. The adapter proteins will be designed to
    recognise specific partner proteins, enabling the formation of protein networks that span
    multiple liposomes.


    The transformative potential of this technology is vast, with applications ranging from drug
    delivery and biosensing to tissue engineering and regenerative medicine. Liposomes containing
    therapeutic cargo could be precisely targeted to specific sites via the protein networks, while
    the networks themselves could serve as scaffolds for cell culture or tissue growth guidance.
     

    Project Aims:

    • Design and optimise adapter proteins for cell-free expression and surface localisation
    • Develop reliable cell-free expression protocols within liposomes of varying compositions
    • Characterize the assembly of adapter proteins into networks on liposome surfaces
    • Demonstrate proof-of-concept applications, such as controlled release of encapsulated cargo

    Core Techniques:

    • Expertise in biomaterials development and characterisation.
    • Hands-on experience with cell-free protein expression systems
    • Proficiency in protein design and engineering techniques
    • Liposome preparation and analysis methods
    • Exposure to interdisciplinary research at the interface of synthetic biology, materials science, and nanotechnology.

    Supervisor: John Simms
    Email

     

    Project Title: Effect of butanol on biological membranes.

    Project Overview:

    Increasing concerns over climate change have driven the move towards sustainable “green” biotechnological alternatives to traditional petrochemical processes. A key example of this is production of biobutanol from Clostridia from waste products. However, this process is inhibited by butanol itself as it damages the bacterial cell membrane and ultimately kills the cells. Our group, and others, have demonstrated that this damage can be reduced by tuning the lipid composition, or corresponding physical properties, of the cell membrane. However, nearly all model systems for studying such interactions rely on the use of lipid-only bilayers.

    Biological membranes are approximately 50% protein by mass and, as such, proteins represent a significant membrane component. The interaction of butanol with membranes appears to occur via intercalation between the individual lipids in the bilayer which is likely to be significantly altered by the presence of proteins. We wish to address this knowledge gap using defined in vitro systems.

    Project Aims:

    This project will generate physiologically relevant model biological membranes to allow the characterisation of solvent-membrane interactions. These will be compared to lipid-only liposomes to assess the contribution of proteins to membrane stability. Ultimately, this will feed into ongoing projects in the lab to generate Clostridial strains that are more resistant to butanol, increasing the uptake of green biotechnology.

    1. Purification of 3 model bacterial membrane proteins of various sizes and architectures. This will use detergents and/or polymer-based approaches as relevant and proteins will be characterised by SDS- PAGE.
    2.  Reconstitution of these proteins into liposomes of various lipid compositions to generate biological membrane mimics.
    3. Biophysical characterisation of these proteoliposomes in the presence of butanol e.g. size, surface charge, porosity, lateral pressure and fluidity.

    Core techniques:

    • Membrane protein expression in bacteria.
    • Membrane protein purification and chromatography approaches.
    • Generation of model lipid membranes.
    • Biophysical assays including dynamic light scattering, membrane fluidity and membrane integrity assays

    Supervisor: Alan Goddard
    Email

    Stem Cells and Tissue Engineering  

    Project Title: Breaking scars: evaluating liver matrix remodelling in vitro.

    Project Overview:
    If a tissue or organ is damaged by injury or trauma, a sequence of repair mechanisms is initiated to fix the wound and repair tissue architecture. However, in the context of chronic diseases of organs such as the liver, heart, lungs, kidney and intestines the repair process becomes dysregulated and results in fibrosis, or scarring. Tissue fibrosis is the loss of the normal epithelial and parenchymal cells within an organ and their replacement with non- functional connective tissue and extracellular matrix molecules. It is currently estimated that this organ fibrosis process is responsible for up to 45% of deaths in industrialized countries.

    There is an urgent unmet need to develop new medicines that can target fibroblast activity and breakdown the fibrotic scar to promote restore tissue homeostasis. In the context of liver fibrosis, this has the potential to allow the liver to regenerate and improve patient outcomes. However, assay systems to evaluate matrix being broken down are not well established. The aim of this project is to incorporate matrix proteins that fluoresce when cleaved to evaluate the mechanisms that regulate matrix turnover in an assay system which will be able to screen potential therapeutic candidates for “scar breaking” potential. 


    This aim will be met by the following objectives:

    • Establish optimal coating concentrations for matrix components in vitro
    • Optimize cell seeding and profibrogenic stimuli conditions to promote matrix
    • deposition and production of matrix remodelling factors
    • Screen small molecule inhibitor toolkit to evaluate active matrix remodelling


    Core Techniques:

    • Tissue culture
    • Cell health and phenotype assays
    • Immunofluorescence and microscopy imaging
    • Image analysis and coding to automate scoring
    • Matrix turnover assay

    Supervisor: Emma Shepherd

    Email

    Project Title: Crosstalk between mesenchymal stem cells and immune cells.

    Project Overview: Mesenchymal stem cells are stromal/structural cells found in many adult tissues, including the bone marrow, but they are also found throughout the body, associated with capillaries (known as pericytes). These cells are an attractive progenitor cell source for the renewal of damaged tissues due to their ability to self-renew, their high proliferative capacity and their differentiation potential. Under certain circumstances, usually associated with chronic inflammation, MSCs/pericytes are capable of differentiating into another cell type known as myofibroblasts; these cells release excessive amounts of extracellular matrix proteins and ultimately lead to tissue destruction through the process of fibrosis. This is a normal bodily reaction to an injury (for example, skin scarring after an injury), but if left unresolved, it can also lead to the loss of organ function. As fibrosis has no currently available treatment, this loss of function has serious detrimental effects. 

    Project Aims: 

    • To determine the mechanisms by which MSCs/pericytes impact on the function of macrophages, an immune cell type closely associated with wound healing and fibrosis. 
    • To determine the role of cell-to-cell contact and soluble factors in modulating macrophage function. 
    • To specifically identify the mediators produced by healthy pericytes as well as pericytes that have been grown under pro-fibrotic or oxidative stress conditions, and the impact of these products on macrophage activation, polarization, and cytokine secretion.

    Core Techniques: Cell culture; ELISA; immunostaining; microscopic imaging and digital data analysis.

    Supervisor: Jill Johnson

    Email

    Project Title: Growing a better MSC: Investigating the immuno-modulatory properties of cultured MSCS.

    Project Overview: Cell based therapies have become an increasingly effective clinical approach to promote tissue repair, wound healing or reduce inflammation. Mesenchymal stem cells (MSCs) are a key cell type in this approach as they can restore damaged tissues (fat, bone, muscle) and reduce inflammation through direct cell-cell contact or release of soluble mediators (proteins, extracellular vesicles (EVs)). Therefore, the ability to grow and maintain functional MSCs in the laboratory is a crucial research goal. 

    Producing MSCs for patients in the laboratory is difficult as they spontaneously differentiate in culture over time, losing their immuno-modulatory abilities. We have recently demonstrated growing MSCs on specialised surfaces or treating with certain compounds can maintain their therapeutic potential by modulating their metabolism. This results in turn maintains their ability to suppress lymphocyte proliferation. This project will further develop this work by investigating the mechanisms by which MSCs are educated by these surfaces or compounds to promote their immuno-modulatory effects. 

    Project Aims:

    • To investigate physiological changes to the MSC as it adheres to the immunized surface. Preliminary data on changes to the cytoskeleton and mitochondrial function will form the starting point of this study. 
    • Co-culture of MSCs grown on surfaces or treated with compounds with lymphocytes to monitor effects on immune-modulation. T cell proliferation and the development of regulatory T cells will be assessed.
    • MSCs EVs will be purified and their effects on macrophage and T cell function will be assessed.
    • Physiological and phenotypic changes to MSCs after treatment with compounds will be investigated to monitor their naïve, therapeutic potential.

    Core Techniques: Cell culture, immunohistochemistry and microscopy, flow cytometry, PCR, SDS-PAGE and western blotting. 

    Supervisor: Ewan Ross

    Email

     

    Project Title: DNA damage and trophoblasts: An undiscovered story

    Project Overview:
    Our lab has, over the years, been interested in learning more about the process of placental development, and in particular the role of the progenitor cells, known as trophoblasts. Trophoblast cells are the first cells emerging from the early embryo and they function to migrate and invade into the mother tissues, promoting attachment and embedding and thereby establishing the first steps towards placental development during the implantation stage.

    The placenta is one of the largest organs during embryogenesis and is formed in a very limited amount of time, leading to significant replicative pressures due to the extreme amount of cell proliferation needed to generate the placental cell mass. Trophoblasts are the main cell type which will make up the bulk of the placenta, and it is not clear how these cells regulate and repair the DNA damage that can arise under the huge levels of replicative stress caused by extensive cell proliferation.

    In this project, we propose to study whether there are differences in the presence of markers of DNA damage and replication stress between different trophoblast cells. We will compare different trophoblast cell lines, and also trophoblast cells at different passage numbers, allowing us to determine whether cells that have been allowed to proliferate for long periods of time accumulate DNA damage. We also would like to assess how trophoblasts manage to detect and repair different types of DNA lesion following differential treatments with DNA damaging agents. Ultimately, we propose to determine if specific DNA repair mechanisms and/or the expression of specific DNA repair factors are found to correlate with the ability of trophoblast cells to repair DNA damage. Our current work aims to characterise further at the cellular levels, the molecular changes which are being regulated.

    Project Aims:

    • Grow and manipulate trophoblast cells
    • Analyse levels of spontaneous DNA damage in different trophoblast cell lines
    • Compare high vs low cell passages and analyse for changes in levels of DNA damage
    • Use DNA damaging agents to induce different types of DNA damage in order to determine how trophoblast repair them
    • Study changes in motility markers by fluorescent microscopy including focal adhesion, filopodia, lamellipodia.

    Core Techniques:

    • Tissue culture
    • Gene expression manipulation of trophoblast cells
    • Treatment of cells with specific compounds/inhibitors
    • Immunofluorescence and microscopy imaging
    • Western blotting
    • Assays to analyse levels of DNA damage


    Supervisor: Stephane Gross and John J Reynolds
    Email

     

    Title: Investigating the role of Platelet Endothelial Aggregation Receptor 1-activation in vascular remodelling

    Project Overview: 

    Pathological vascular remodelling is a key component in the development of cardiovascular disease. It has previously been shown that PEAR1 is associated with Single nucleotide variants of PEAR1 are significantly associated with increased risks during cardiovascular disease. Interestingly, data which is publicly searchable in the GEO2 database shows that PEAR1 is significantly downregulated in abdominal aortic aneurysms and intracranial aneurysms (GSE75436, GSE15629). This is a strong indicator that PEAR1 is involved in the vascular remodelling of the vessel wall during aneurysm formation.

    Most studies investigating the function of PEAR1 in vascularisation have used methods of Pear1 knockdown rather than PEAR1 activation.

    Therefore, the aim of the present project is to use unique PEAR1 agonists to evaluate changes to extracellular matrix deposition, proliferation, and migration of primary human aortic fibroblasts.

    Project Aims:

    Measure phosphorylation of Akt by Western blot to confirm cellular activation and optimal concentrations of agonists.
    Induction of extracellular matrix deposition using TGFβ in the presence and absence of PEAR1 agonists followed by imaging and quantification of extracellular matrix deposition by microscopy.
    Quantification of changes to cell migration and proliferation upon PEAR1-stimulation. Upon early successful completion of the primary aims and objectives of the project, there is potential scope for performing additional immunohistochemical staining of vascular tissue to investigate PEAR1 expression levels and collagen deposition.
     

    Core Techniques:

    • Western Blotting
    • Cell Culture
    • Microscopy and immunostaining
    • Viability Assays

    Supervisor: Caroline Kardeby
    Email

    Project title: Investigating the role of Platelet Endothelial Aggregation Receptor 1-activation in extracellular matrix deposition by primary human lung fibroblasts

    Project Overview:

    Extracellular matrix remodelling is an important mechanism underlying the pathophysiology of disease, especially in incurable and deadly diseases like Idiopathic Pulmonary Fibrosis (IPF). In IPF, patients experience increased levels of inflammation and scarring in the lungs leading to difficulties to breath. Recent publications have shown that Platelet Endothelial Aggregation Receptor 1 (PEAR1) deficiency is associated with fibrosis formation in the lungs of mice. However, the role of PEAR1 in human lung fibrosis has not been explored yet.

    The project aims to use unique PEAR1 agonists to evaluate changes to extracellular matrix deposition, proliferation, and migration of primary human lung fibroblasts.

    Project Aims:

    • Measure phosphorylation of Akt by Western blot to confirm cellular activation and optimal concentrations of agonists.
    • Induction of extracellular matrix deposition using TGFβ in the presence and absence of PEAR1 agonists followed by imaging and quantification of extracellular matrix deposition by microscopy.
    • Quantification of changes to cell migration and proliferation upon PEAR1-stimulation. Upon early successful completion of the primary aims and objectives of the project, there is potential scope for performing additional immunohistochemical staining of lung tissue to investigate PEAR1 expression levels and collagen deposition.
       

    Core Techniques:

    • Western Blotting
    • Cell Culture
    • Microscopy and immunostaining
    • Viability Assays


    Supervisor: Caroline Kardeby
    Email

     

    Project Title: Investigating the effects of anti-senolytics on Mesenchymal Stromal Cell expansion and immuno-modulatory properties

    Project Overview:

    Mesenchymal Stromal Cells (MSCs) are a key cell for cell based therapies. Their ability to modulate the function of immune cells as well as regenerate damaged tissues, restoring function has made them a new clinical treatment that does not have the side effects of conventional drug-based therapies. However, as we age, MSCs in the body gradually become more senescent, with reduced proliferative capacity and less able to direct immune responses. This ageing phenotype is also observed when we expand MSCs in the laboratory – forcing cells to expand to the numbers required for effective clinical therapy often results in a similar increase in senescence and reduced therapeutic potential. Therefore, finding new growth conditions that allow the efficient expansion of younger donor MSCs without inducing this ageing phenotype will allow more patients to be treated with this cell based therapy. In addition this may inform us as to how we can expand older donor MSCs more effectively and rejuvenate their immune-modulatory properties as we culture them, making this cell based therapy more available to patients.

    Senescent MSCs secrete higher quantities of TGF-B which converts healthy cells in laboratory culture conditions to senescent cells, thus reducing the quality of the cell product. Anti-senolytics are a class of drugs which specifically target and kill senescent cells. This project will evaluate and compare how treating cultures of young and older donor MSCs with anti-senolytics affects the quality of the expanded MSCs and if this can improve the proliferation and functionality of these progenitors.


    Project Aims: 

    • Evaluate the actions of anti-senolytics on MSC physiology (growth, differentiation and apoptosis).
    • Examine any impact on the immuno-modulatory activities of MSCs in co-culture with immune cells (macrophages and T cells)
    • Measure changes in the cell secretome after anti-senolytic treatment


    Core Techniques:

    • Culture of human primary MSCs and peripheral blood immune cells
    • Flow cytometry
    • qPCR
    • Immunofluorescent staining and microscopy
    • Measurement of soluble factors by ELISA

    Supervisor: Ewan Ross
    Email

     

    Project Title: Optimising bioreactors to expand human mesenchymal stromal cells.

    Project Overview:

    Mesenchymal Stromal Cells (MSCs) are key cells for cell based therapies due to their abilities to both reduce inflammation and promote repair of damaged tissues. Unfortunately, these are a rare population of tissue progenitor cells and require expanding in the laboratory to generate the large numbers of cells required for effective therapies. This forced growth often leads to loss of their immuno-modulatory properties and can result in premature ageing. Therefore new methods to expand these cells whilst retaining their regenerative properties are required. At Aston, we have developed a stirred tank bioreactor protocol for growing MSCs using microcarriers as an adhesive substrate. This system allows us to efficiently grow large numbers of these cells in a relatively small amount of media. From these we can harvest functional, viable cells that retain their important clinical activities. This project will look to further refine this system, investigating the potential of hydrogel mediated release of soluble factors directly into the bioreactor, to further promote MSC expansion and immuno-modulatory properties. This project will provide training in both biomaterials as well as the growth of stem cells and analysing their functional potential.

    Project Aims: 

    • Develop gel based materials for the slow release of soluble factors to promote MSC expansion
    • Assess how changing the environment affects MSC stem like properties including differentiation
    • Upscaling optimal conditions from small (100ml) to large scale (1L) bioreactors to demonstrate the potential for large scale expansion.

    Core Techniques

    • Culturing of human MSCs and testing their immunomodulatory activities
    • Use of bioreactors for expanding MSCs
    • Formulation of materials for the release of soluble factors
    • Analysis techniques (flow cytometry, qPCR, microscopy)

    Supervisor: Ewan Ross
    Email

    Microbiology

    Project Title: Novel antimicrobials for Pseudomonas aeruginosa

    Project Overview: Healthcare-acquired infections (HCAI) are a major problem in hospitals throughout the world, costing the NHS more than £1 billion per annum. A large proportion of these infections are due to an opportunistic bacterial pathogen, Pseudomonas aeruginosa. Whilst healthy individuals are usually unaffected or recover well, seriously ill patients or those whose immune systems are not fully functional are more susceptible. In these cases, the infection is usually very serious and mortality rates can be as great as 70%. P. aeruginosa is particularly important for cystic fibrosis (CF) patients who typically contract chronic infections which cause permanent lung damage and this is the principal cause of morbidity and mortality. P. aeruginosa infection is difficult to control because it tends to be resistant to many antimicrobial agents. There exists an urgent need for novel antimicrobials.

    A protein that is essential for the growth of P. aeruginosa has recently been identified. This protein is thought to be involved in cell wall production, which is a common target for existing antibiotics. This protein, TgpA, is an enzyme that has transglutaminase (TG) activity and can cross-link proteins together to create stable structures. It is likely that TgpA catalyses the modification of an existing cell wall component or stabilises the cell wall by cross-linking of proteins. This project will recombinantly express the TgpA protein to characterise its transglutaminase activity and screen for novel small molecule inhibitors. This could allow development of these inhibitors into effective antibiotics against P. aeruginosa. Identification of a novel class of antibiotics could also allow this strategy to be adopted in other microorganisms that use transglutaminases for growth or virulence.

    Project Aims:

    Recombinant expression and affinity purification of P. aeruginosa TgpA. Characterisation of the transglutaminase activity of TgpA to determine substrate specificity. In silico and in vitro screening of transglutaminase inhibitors. Determine effects of TgpA inhibition on growth of P. aeruginosa

    Supervisor: Russell Collighan

    Email

    Project Title: Antimicrobial resistance and gene regulation in Enteroaggregative Escherichia coli. 

    Project Overview: Enteroaggregative Escherichia coli (EAEC) is increasingly recognized as a major cause of diarrhoeal disease in industrialized and non-industrialized countries and has been shown to be the cause of travellers’ diarrhoea and persistent diarrhoea in children and HIV patients. EAEC strains cause disease by binding to the human gastric mucosa and establishing a thick mucoid biofilm, damaging tissue by secreting various protein toxins. In spite of the widespread occurrence of EAEC strains and their impact on human health little is known about how EAEC strains control the expression of genes required to establish infection and cause disease. Furthermore, EAEC strains are becoming increasingly resistant to many clinical antibiotics, decreasing the options available to treat infections.

    Recently, we have been working with EAEC strains isolated from Egyptian and Brazilian children with diarrhoea. As we have now had their genomes fully sequenced, the first part of this project will be to analyse the genomes of these isolates, determining each strains characteristics (e.g. antibiotic resistance gene profile, virulence determinants and plasmid replicons etc.) using the simple software at the Center for Genomic Epidemiology (http://www.genomicepidemiology.org/). Once key virulence and antibiotic resistance genes have been identified, the promoters which control their expression, will be amplified by PCR and cloned into reporter gene expression plasmids. The transcription regulation of these promoters will then be examined under different environmental conditions to determine how and when the expression of these important proteins is switched on. 

    Aims of the project: 

    • Examine the antibiotic resistance and virulence genes carried by various pathogenic EAEC strains.
    • Amplify and clone the promoters that control the expression of some of these important genes.
    • Examine the expression of these promoters to determine how and when these genes are switch on.  

    Core techniques: Molecular biology techniques including PCR, DNA cloning, site directed mutagenesis, DNA sequencing, bacterial strain manipulation and reporter gene enzyme assays.

    Supervisor: Doug Browning

    Email

    Please review the research themes/project titles via the link below and make a note of your preferred theme/title. You will then need to add this to your personal statement when submitting your application. Your personal statement should explain your interest in the research theme/project, along with any other supporting information. 

    Stage two: apply via the Aston University portal

    Once you have reviewed the project themes, please begin the application process. 

    Apply

    Stage three: informal interview

    With a successful application, you will have an informal interview with a supervisor to discuss the MRes and extended research project.