Current PhD Opportunities

Oralbiology 515x198

The following projects are research topics proposed for potential self-funded candidates. To find out more please contact Julie McDermott.

Atomic force microscopy studies of bacterial interactions involved in dental caries

Lead Supervisor: Dr Neil Thomson
Co-Supervisor: Professor Deirdre Devine

Project Summary

Dental caries is caused by processes occurring within the biofilm (plaque) that builds up on teeth and which is not always removed during routine brushing. While there are a wide variety of bacterial species within plaque, tooth decay is thought to be caused principally by species which produce high levels of lactic acid during processing of dietary sugars, such as Streptococcus mutans and lactobacilli. Not only does the ability to ferment sugars to produce acid result in acidic environments that promote enamel dissolution, but they promote extracellular polysaccharide production and increased bacterial adhesion to surfaces and to each other.

Aims and Objectives

Atomic force microscopy (AFM) has the ability to image bacterial cell surfaces at high resolution and measure forces between surfaces. This project will involve a combination of in situ AFM imaging and force measurements on these species in controlled environments including those with sugar present and at varied pH to gain greater insight into the bacterial interactions triggering caries. Data will be acquired on cellular mechanics, cell surface morphology and adhesion forces with enamel surfaces to see how the bacteria respond to their environment.

Atomic force microscopy studies of the molecular mechanisms of nested genes related to tooth formation

Lead Supervisor: Dr Neil Thomson
Co-Supervisors: Dr William Bonass; Dr Georg Feichtinger

Project Summary

Transcription is the molecular process in the cell whereby the genetic information from DNA is copied into messenger RNA by the molecular motor RNA polymerase (RNAP) which catalyses the polymerisation of ribonucleotides. Since DNA is a helical molecule, the RNAP needs to rotate relative to the DNA template to undergo transcription. On a torsionally constrained template, the RNAP will therefore cause over-winding of the DNA in front of it and under-wound DNA behind, as it translocates along the DNA. This effect is known as the twin supercoiling domain hypothesis and it is expected that build-up of localised supercoiling within the DNA will affect the ability of the RNAP to copy the gene in question: it is therefore a fundamental physical mechanism that modulates gene expression.

Aims and Objectives

We investigate this question through constructed systems in vitro using high resolution imaging of individual molecular complexes using atomic force microscopy (AFM). The translocation of DNA through RNAP as transcription occurs in vitro was first followed using atomic force microscopy (AFM) at the single molecule level and more recently, we have been investigating the interactions of more than one RNAP on a single DNA template. Interestingly, we find that the position of one RNAP during transcription is influenced by another RNAP operating at the same time. Currently, it seems that this effect occurs regardless of whether these RNAPs are travelling towards each other or in the same direction. This project will continue our investigations into the fundamental mechanisms involved in spatial regulation of the RNAPs. Our working hypothesis is that local supercoiling of the DNA between RNAPs causes them to stall or pause when they get too close to one another. This may be one fundamental way that the cell controls gene expression through the physical properties of the DNA, but more work is needed to prove the hypothesis and understand the details.

It is being increasingly discovered that many genes lie in a nested formation, such that the promoters are convergently aligned on opposite DNA strands in the double helix. The implications for simultaneous expression of these genes are obvious and lead one to ask what would occur if two RNAP encounter each other on a single template. We propose to investigate a nested gene system involved in tooth enamel development where the expression of the biomineralising amelogenin protein may be compromised. The outcomes of this project will help to inform us about fundamental aspects of developmental biology and have long term impact on the treatment of diseased states associated with altered gene expression.

Digital manufacturing of complete dentures

Lead Supervisor: Professor David Wood
Co-Supervisors: Dr Andrew Keeling; Dr Paul Hyde

Project Summary

The method by which dentures are constructed has remained largely unchanged for many decades. It is known that inaccuracies occur during manufacture, leading to a reduction in the quality of ‘fit', which can impact on comfort, retention and function for the denture wearer.

This project would investigate the application of modern 3D printing techniques, to manufacture part, or all, of the denture. The potential benefit would be improved accuracy of manufacture leading to better comfort and function for the denture wearer. The cost should also be minimal and processing times could be reduced.

Aims and Objectives

1. Review the current state of the art and determine the most appropriate potential 3D printing method (i.e. print whole denture or a hybrid technique)
2. Identification, or development, of a suitable biocompatible 3D printing material, having good mechanical and aesthetic properties
3. Robust assessment of the material; Mechanical, Biocompatibility; Aesthetics; Accuracy
4. Development of a suitable design/scan and print protocol for cost effective manufacture whilst maximizing the control the dentist and patient have over the form and appearance of the denture

This project would be suitable for a candidate with an Engineering or Material Science background, who is also IT-literate and comfortable with, (or willing to learn) 3D CAD techniques and 3D printing.

IGF axis regulation of matrix mineralisation of dental stem cell populations

Lead Supervisor: Dr James Beattie
Co-Supervisor: Dr Reem El-Gendy; Dr Josie Meade

Project Summary

The insulin-like growth factor (IGF) axis is comprises two polypeptide growth factors (IGF-1 and IGF-2), two cell surface receptors (IGF-1R and IGF-2R) and six high affinity, soluble binding proteins (IGFBP-1, IGFBP-2, IGFBP-3, IGFBP-4, IGFBP-5 and IGFBP-6) The IGF axis is known to play a role in the differentiation of stem and progenitor cells into skeletal and dental mineralized tissue. This molecular axis is also involved in induction of enamel bio-mineralization, differentiation of dental pulp cells and reparative dentinogenesis. IGF-1 is important for osteogenesis, and when delivered by liposomes into the tooth socket it enhanced deposition of osteodentin-like matrix around dental implants in combination with calcium hydroxide IGF-1 in combination with platelet derived growth factor (PDGF) and calcium hydroxide, improve healing of apical tooth perforations in a canine model Further evidence suggested that IGF-1 regulates the balance between odontogenesis and osteogenesis in apical papilla stem cells IGF-1 is expressed by dental pulp cells and enhances odontogenic differentiation and deposition of extracellular matrix IGF-2 is also expressed by dental pulp cells at both gene and protein levels, although its function in this tissue is still largely unknown IGF-1R showed higher expression in teeth with incomplete root development, suggesting the role of IGF-1 in root development IGFBP-1, -3, -5, and -6 have also been detected in DPSCs isolated from healthy premolars and third molars. .Despite the presence of IGFBPs in dental pulp cells the role of these proteins in the regulation of phenotype during differentiation of these cells is largely unknown. This project aims to examine both the IGF-dependant and IGF independent functions of IGFBP species in this tissue culture model with a special emphasis on the intracellular signalling mechanisms which may be involved in such actions.

Immunological complicity in evolution of potentially malignant oral lesions

Lead Supervisor: Dr Alasdair McKechnie
Co-Supervisor: Dr Josie Meade

Project Summary

Despite a number of innovative improvements in management of other cancers, survival rates of patients with oral cancer remain poor and unchanged in the last 4 decades. The majority of oral cancers arise in areas of long-standing epithelial dysplasia, yet an accurate means of predicting which dysplastic lesions will progress to malignancy remains elusive. Elucidation of the factors that determine whether dysplastic oral lesions will regress, persist or progress to malignant transformation may help guide clinical management strategies and allow development of chemo-preventive therapy.

The PD-1/B7 pathway plays a key role in regulation of immune responses. Variations in expression of the components of the pathway are implicated in T cell mediated immune disorders such as oral lichen planus, and also in the immunological anergy which characterises cancer. The pathway has been successfully manipulated in the clinical setting in order to stimulate effective anti-tumour immune responses, but the involvement of such pathways in oral premalignancy has not been investigated.

Immunological and inflammatory mechanisms have a complex relationship with carcinogenesis which is well illustrated by recent reports on immunotherapy of cancer. While PD-1 blockade was demonstrated to improve survival of patients with recurrent head and neck cancer, a potential side effect of PD-1 blockade for management of melanoma is a chronic oral graft-versus-host type reaction in which development of oral squamous cell carcinoma has been reported.

Aims and Objectives

This study will answer three questions:

1. Can alterations in immune checkpoint expression, such as the PD-1 pathway be demonstrated in lesions which are at risk of developing into oral cancer?
2. Can the alterations be used to predict the degree of epithelial dysplasia (mild, moderate or severe) and risk of progression to malignancy?
3. What are the effects of manipulation of the pathways in vitro?

Investigating the genetic association between systemic disease and oral health through genome-wide association study

Lead Supervisor: Dr Jianhua Wu
Co-Supervisors: Dr Alan Mighell; Professor Sue Pavitt

Project Summary

Oral health genetics has been an area of active research for several decades, with evidence from twin and family studies overwhelmingly demonstrating the heritability of dental caries, periodontal disease, tooth loss and other dental traits. More recently, candidate gene studies have investigated the association between a limited number of genetic variants in and around candidate genes (chosen a priori based on known biological functions with plausible impact on disease) and many oral outcomes. The genomic era of biomedical research has given rise to the genome-wide association study (GWAS) approach, which attempts to discover novel genes affecting an outcome by testing a large number (i.e., hundreds of thousands to millions) of genetic variants for association. The GWAS design is now being widely applied to the study of many common human disorders, including oral health outcomes.

Oral health outcomes, such as periodontal disease and tooth loss, have been widely linked to other systemic diseases such as cardiovascular disease and rheumatoid arthritis. However, very little research has been done for such association at genetic level. The recent development of GWAS approach and the availability of large health resource (i.e., UK Biobank) have made it possible to study such association at genetic level for very large sample sizes. This PhD project is to utilise the GWAS approach to investigate the association between oral health outcomes and systemic disease and single out the underlying common genetic variants that could affect both diseases. The project will also adapt the GWAS approach and develop new analytical methodology to deal with such large scale individual and genetic data.

This is a multidisciplinary PhD project combining oral public health, genetics, epidemiology and biostatistics. The result of this PhD research will contribute to the understanding of the underlying genetic relationship between systemic diseases and oral disease, and provide important research direction and insight into oral genetic research.

Investigating joint effects of alcohol drinking and tobacco smoking on oral health in the UK

Lead Supervisor: Dr Jing Kang
Co-Supervisors: Professor Gail Douglas; Dr Julia Csikar

Project Summary

The project involves viewing the joint effects of tobacco smoking and alcohol drinking in the UK. The key risk factors of oral health include tobacco smoking and alcohol drinking. Smoking and drinking can cause oral cancer/precancer, periodontal disease, caries, tooth loss, gingival recession implant failure and other benign mucosal disorders. However, even though abundant studies have shown the negative effects of smoking and alcohol drinking on oral health independently, they overestimate the independent effects4 but ignored the joint effects of smoking and alcohol drinking in the analyses. So far, studies on joint effects of smoking and drinking on oral health are still very scarce.

Aims and Objectives

This PhD project proposes to view the joint effects of tobacco smoking and alcohol drinking in the UK population, starting from assessing the relative importance of independent and joint effects of alcohol drinking and tobacco smoking on oral health, after controlling demographic features and environmental factors, using Adult Dental Health Survey data and Health Survey data ofEngland, Wales and Northern Ireland, and Scottish Health Survey. Multivariate analysis will be performed in terms of various oral health outcomes, including self-reported oral health status, dental caries, periodontal disease, and edentulousness. At the second stage we will focus on linking the discovery from oral health survey data to administrative data with cross-validation. Finally, the last stage of the project will focus on subgroup analysis by comparing discoveries among England, Wales and Northern Ireland and Scotland. If time permits, comparisons between UK and USA will also be performed on the joint and independent deteriorate effects of alcohol drinking and tobacco smoking, as USA’s NHANES datasets is public accessible with valid information.

This PhD project is inter- disciplinary and combines the fields of dental public health, epidemiology, and biostatistics. Future investigation of cessation effects of smoking and alcohol drinking can also be performed, including cessation of smoking only, cessation of drinking only, and the joint effect of cessation of both smoking and drinking. The result of this PHD research will benefit people’s understanding on those substance use abuse, its consequences, (how and when to intervene), and its relation to quality of life.

Investigation of association between oral diseases and cardiovascular disease

Lead Supervisor: Dr Jing Kang
Co-Supervisors: Professor Gail Douglas; Dr Jianhua Wu

Project Summary

Many studies have investigated the associations between oral diseases, particularly dental caries and periodontal diseases, and cardiovascular disease (CVD). However, due to the variations in study designs, population selection, and the statistical analyses used in the plethora of reported studies, results of different studies have been contradictory. To date, there is a lack of consensus among experts on the nature of these associations, and difficulties in understanding the causative link between oral disease and CVD.

Aims and Objectives

This project aims to uncover the relationships between oral diseases and CVD, and their corresponding risk factors. Additionally, prediction models will be built based on the existing information extracted from the well-established health survey data in the UK (Adult Dental Health Survey, Health Survey England, Scottish Health Survey) and USA (National Health and Nutrition Examination Survey, NHANES) to predict the chance of one developing CVD in a certain time, based on his/her oral health record and the demographic background.

This PhD project is interdisciplinary and combines the fields of public health, epidemiology and biostatistics. So far no dental public health research has linked the UK dental survey databases and US oral health survey data to investigate the association between oral health and general health to build statistical models to predict the risk of CVD for individuals. New methodology will be developed to suit the analysis for linked national survey datasets with huge sample size.

This project will lead to high quality academic and socioeconomic impact. The results of this research will benefit our understanding of the association between oral diseases and CVD, the risk factors that contribute to the development of CVD, and the prediction and prevention of CVD. This project will provide updated guidance for general practice and practicing dentists. High impact publications will be produced and through public engagement activities, we will ensure the general public will obtain a better understanding of linkage between oral diseases and CVD.

Investigation of matrix-mineral interactions of enamel formation in Amelogenesis Imperfecta

Lead Supervisor: Dr Neil Thomson
Co-Supervisor: Professor Jennifer Kirkham

Project Summary

Amelogenesis imperfecta (AI), an inherited enamel biomineralisation defect in quality and quantity of dental enamel, is associated with mutations in genes encoding enamel extracellular matrix proteins (EMP). Amelogenin is the main EMP (90% of all matrix protein) in developing enamel and self-organizes in to polymeric nanospheres that associate with the apatite mineral surfaces and are thought to orientate the growth of enamel crystals. This project will study the interactions between amelogenin and the primary mineral structure of enamel, apatite nano-rods. It will test the hypothesis that mutated amelogenin has a higher affinity for mineral surfaces compared with wild-type protein, resulting in crystal growth inhibition leading to AI. Using recombinant amelogenins, including a known mutation that causes AI in mice, the student will use a combination of physical techniques to explain the effects of the mutation on amelogenin-mineral interactions. Atomic force microscopy (AFM) will be employed to visualise organization of nanospheres with mineral crystals and determine the binding-unbinding forces of the protein on the crystal surfaces. TEM experiments will permit identification of the specific crystallographic faces at which these interactions occur. Data generated will give entirely novel information relevant to AI pathology and the fundamental mechanisms of biomineralisation.

Aims and Objectives

This project will use atomic force microscopy (AFM) to study interactions between wild-type and mutant amelogenins and the enamel crystals themselves. It will test the hypothesis that amelogenin mutations in AI perturb protein-protein and protein-mineral interactions during enamel formation resulting in biomineralisation defects. AFM will be used in imaging and force modes to study amelogenin self assembly ± mutations and to characterise interactions between these proteins and apatite crystals to explain the effects of the mutation on AI pathobiology.

Metabolic labelling approach for the incorporation of functional groups in therapeutic DNA enabling advanced payload delivery strategies in peptide-based gene delivery

Lead Supervisor: Dr Georg Feichtinger
Co-Supervisor: Dr Robert Davies

Project Summary

Non-viral gene delivery strategies have the potential to provide advanced regenerative solutions for cost-effective approaches to improve treatment and restore function of tissues for patient benefit. Effective delivery of therapeutic nucleic acids in a safe and targeted manner using biomaterials in conjunction with defined peptide agents for assembly and delivery could potentially accelerate the translation of non-viral gene therapeutics. This would address significant clinical challenges in dental and musculoskeletal research aiming at the restoration of tissue defects. Research aimed at generating pilot data for such technologies have potential to generate new intellectual property, facilitate interdisciplinary collaboration, lead to the generation of high impact publications and provide valuable data for subsequent larger grant applications.

Aims and Objectives

The current project proposes the incorporation of functional groups into therapeutic plasmid DNA via a novel metabolic labelling strategy during amplification in E. coli using thiophosphate as a phosphate analogue. As the DNA is amplified in E. coli, thiophosphate is incorporated in the plasmid DNA, introducing accessible functional thiol-groups that enable the conjugation of the produced DNA payload to biomaterial surfaces and delivery agents for enhanced delivery. The advantage of using a thiol-based system lies in the compatibility of said system with currently available novel biomaterial systems (as part of a collaboration with Dr. Tronci using collagen and gelatine biomaterial systems developed at Leeds) and advanced peptide systems for gene delivery (provided as part of an ongoing collaboration with Imperial College, London) thus facilitating interdisciplinary collaboration within the University of Leeds and beyond. Furthermore, it has been shown that incorporation of thiophosphate into DNA improves its resistance to nuclease attack, further improving its stability in vivo and the compatibility of the thiol-group approach for attachment opens further avenues for combination of gene therapy approaches with currently investigated self-assembling peptide technologies at the department. Disulphide linkage of payload and delivery agent/material finally allows automatic payload release upon cellular uptake as disulphide groups are reduced in the cytoplasm.

Initial experiments demonstrated the feasibility of the metabolic labelling strategy to introduce thiol-groups into expression capable therapeutic DNA. Furthermore, there is a plethora of synthetic pathways that would facilitate cross linkage between the introduced thiophosphate to the biomaterial surfaces and delivery agents, including (but not limited to) thiol Michael-type reactions or by simply controlling the local redox environment. All synthetic strategies considered will be mild and involve non-toxic catalysts. This project aims at providing the pilot data for application of the principle within biomaterial and peptide-based delivery systems for enhance non-viral DNA delivery in vitro. This pilot data will feed into further grant applications, aimed at translating the most promising delivery strategy in in vivo models of musculoskeletal tissue regeneration via follow-up projects.

Mimicking microenvironment for controlling stem cell behaviour to enhance tissue engineering efficacy

Lead Supervisor: Dr Xuebin Yang
Co-Supervisors: Dr Lin-Hua Jiang (Faculty of Biological Sciences); Michiya Matsusaki (Osaka University)

Project Summary

It has been generally accepted that tissue engineering requires three basic elements: cells, growth factors and biomaterial scaffolds. However, only these three basic elements may be not sufficient enough for functional tissue engineering. Therefore, there are increasing research efforts looking at how the biological, chemical and/or mechanical microenvironments influence stem cell/progenitor behaviour.

In natural conditions, bone is formed by two processes – intramembranous and endochondral ossification. Intramembranous ossification is that osteoblast directly lays down type I collagen extra cellular matrix (ECM) into the primitive connective tissue (mesenchyme). These ECMs can then become mineralised to form bone. While endochondral ossification involves cartilage as a precursor and osteoblast lay done bone matrix to replace the cartilage precursor. But in both processes, osteoblasts will be trapped within the newly formed bone matrix and either change to osteocytes or undergo apoptosis. During this cascade event of bone formation, the microenvironments surrounding the stem cells, osteoprogenitor, osteoblast and osteocytes are dynamically changed. Therefore, how to mimic the microenvironmental surroundings may play a key role in controlling cell function, which in turn controls tissue regeneration strategy.

We have recently shown the possibility of fabricating hydroxyapatite nanocrystal composites on the surface of individual stem cells (Saha et al, Chemistry Letters, 2015). The overall aim of this project is to use similar approaches and/or develop novel approaches to mimic the microenvironment of targeting cells for controlling cell behaviour and function to enhance tissue engineering efficacy.

This is a collaborative project between Dr Xuebin Yang (Clinician and bioengineer with expertise in clinical orthopaedics and tissue engineering), Dr Lin-Hua Jiang (Biologist with expertise in ionic signalling) and Dr Michiya Matsusaki (Material scientist with expertise in functional polymers and biomaterials for biomedical applications) at Osaka University (Japan).

Aims and Objectives

The objectives include but are not limited to:

1. Isolation of stem cells from human tissues (such as bone marrow or dental pulp tissue);
2. In vitro expansion and characterisation of these stem cells;
3. Using layer-by layer coating methods or 3D printing methods to create nano-films on individual cells or 3D in vitro models;
4. Using alternate soaking method to fabricate Hap nanocrystals on the individual cell or cell pelleted to create a hard shell on individual cell or pellet;
5. Assessment of the effect of this microenvironment change on the cell cycle, signalling pathway and functionality;
6. Assessment of stem cell surface marker expression before and after the change of the microenvironment;
7. assessment of the cell functionality after removing the shell;
8. Use elected/optimised approaches to test their potential for enhancing bone tissue engineering strategy in vitro and/or in vivo.

Osteochondral tissue engineering using novel epigenetic approaches and multi-layered cell sheet technology

Lead Supervisor: Dr Xuebin Yang
Co-Supervisors: Dr Lin-Hua Jiang; Dr Xiaodong Jia

Project Summary

Osteochondral tissue damage or loss is one of the most common diseases due to traumatic injuries, natural degradation of cartilaginous tissue with aging, arthritis or surgery. These clinical situations encompass serious damage to not only articular cartilage but also the underlying calcified subchondral bone. The conventional therapeutic approaches include autografts, allografts, stimulation of bone marrow and debridement. Autografts have limited stock and allografts are associated with the risk of immune rejection or disease transmission, while bone marrow stimulation treatments are only palliative and not completely curative. Therefore, the ability to treat osteochondral defects is a major clinical need. Over the last decades, tissue engineering approaches have been utilised for regenerating articular cartilage. However the output of these is still not satisfactory. In this project, a multidisciplinary approach will be utilised to combine material science and mechanical engineering with stem cell biology for engineering functional osteochondral tissue for clinical translation.

Previously we have showed the potential of using epigenetic approaches to control stem cell function without change the genome. A novel histone deacetylase inhibitors (HDACi), MI192 pre-treatment enhanced the osteogenic differentiation of human adipose derived stem cells. In close collaboration with Tokyo Women’s Medical University, we have established the multi-layered cell sheet (MLCS) technology platform at Leeds, which allows us to harvest intact cell sheet with minimum damage to the cells and maximum retention of cell-cell junctions, extracellular matrix and growth factors embedded in the matrix.

Aims and Objectives

The aim of this project is to combine epigenetic approaches with multi-layered cell sheet technology for osteochondral tissue engineering in vitro and in vivo.

The objectives include but not limited to:

1. Establishment of an epigenetic modified stem cell bank.

2. Fabricate cartilage phase in vitro using epigenetic modified stem cell, MLCS technology and novel collagen scaffolds.

3. Fabricate bone phase in vitro using epigenetic modified stem cell, MLCS technology and 3D printed porous polymer scaffold.

4. Osteochondral tissue engineering in vitro and in vivo.

Peptide-based matrix gene delivery for tissue regeneration and anti-microbial therapy targeting periodontal disease

Lead Supervisor: Dr Georg Feichtinger
Co-Supervisors: Dr Robert Davies

Project Summary

Periodontitis is the sixth most prevalent disease in the world, mostly (but not exclusively) affecting adults in their thirties and forties with a peak incidence at around 38 years of age 1. Periodontitis is a polymicrobial infection caused by co-operating consortia of organisms, predominantly growing as biofilms2. Periodontal pockets may harbour up to 108 diverse bacteria 3. The same bacteria are also associated with systemic effects through gaining access to the blood and the chronic infection/inflammation associated with periodontitis can underlie pathology at non-oral sites. P. gingivalis, a key periodontal pathogen, has been shown to invade human aortic endothelial cells and induced the production of pro-inflammatory molecules. It has been recovered from distant sites including atherosclerotic plaques, inflamed joints and brain tissue 4,5 Chronic periodontitis, advanced inflammatory periodontal disease, is a major cause of tooth loss significantly affecting the quality of life of patients with diverse chronic disease backgrounds. Current clinical treatment strategies, conservative and surgical, lack solutions effectively offering simultaneous and sustained periodontal tissue regeneration and anti-microbial action6. This relevant high-impact oral health challenge affecting up to 1/3rd of the population therefore requires advanced multi-modal treatment strategies to effectively combat infection, inflammation whilst supporting tissue regeneration.

Self-assembly peptides (SAPs) are self-assembling injectable molecules that can respond to environmental triggers forming a biomimetic hydrogel scaffold, with multiple capabilities to support enamel regeneration and mineralisation9,10. Rational design and optimisation of these system could potentially deliver a wide range of additional therapeutics depending on sequence, concentration, charge and hierarchical structures present. The properties of the hydrogel can be tailored to specific oral environments. Incorporating advanced drug payloads such as non-viral gene therapeutics into injectable SAP biomaterials could cost-effectively offer the potential to provide targeted advanced regenerative cues and anti-microbial action by delivering growth factor and antimicrobial genes directly to target cells at the defect whilst simultaneously providing a regenerative matrix. Such an approach would therefore minimally invasively address significant clinical challenges in dental and musculoskeletal research.

The present project is aimed at developing SAP-gene therapeutic combination treatments through peptide-chemistry, biomaterial sciences as well as molecular and cell biological approaches in vitro. The project has the potential to generate new intellectual property, preclinical research data and facilitates interdisciplinary collaboration. SAP-gene therapeutics will be optimised and characterised with regard to the physico-chemical properties of the peptide sequence and release studies will be investigated via a number of analytical techniques (HPLC MS/ UV and FTIR spectroscopy). Biocompatibility and gene delivery efficacy testing in cell culture will be performed using clinically relevant mesenchymal dental pulp stem cells (DPSCs) extracted from teeth. Furthermore, a novel strategy incorporating functional groups for cross-linking therapeutic DNA with SAPs to improve payload delivery will be investigated.

Successively to delivery optimisation, this project will investigate osteoinductive, angiogenic and antimicrobial candidate genes and gene-activated matrix systems in 3D DPSC cultures to identify most promising delivery strategies for subsequent translation-geared preclinical development.

Sugar and tooth decay – is it ‘too much’ or ‘too often’?

Lead Supervisor: Professor Deirdre Devine
Co-Supervisors: Professor Philip Marsh; Dr David Head (School of Computing)

Project Summary

Understanding the relationship between sugar and health is a major Government priority. The link between sugar and caries is known, but it is not clear what is most important: the frequency of sugar intake or the total amount of sugar eaten. Existing advice favours the over-riding importance of frequency of sugar intake. This has been challenged recently by surveys of diet and decayed teeth in >1,500 participants, which suggest a stronger link exists between caries and the total amount of dietary sugar. This must be addressed if the best guidance is to be given to parents, carers and children. We aim to determine which is most important (frequency or total sugar) in enhancing the growth of acid-producing plaque bacteria, and what factors may mitigate the effects. This will lead into more focused, better designed clinical studies that will help shape dietary advice to minimise caries risk in children.

Aims and Objectives

We will use laboratory experiments and computational modelling to reveal the combinations of total sugar intake and frequency of intake that have the best and worst effects in promoting the growth of acid-producing or beneficial bacteria over many weeks. This will allow us to design the most effective clinical studies to confirm what really matters in terms of dietary sugars and childhood caries, speeding up the process from theory to practice.

Thus, we will:
• Grow communities of plaque bacteria and systemically vary the frequency and total amount of sugar supplied to them with and without fluoride. We will monitor the effects of these combinations on the bacterial community as well as the amount of acid generated and compare both against conditions known to initiate tooth decay. We will also determine if beneficial bacteria (probiotics) or other agents that affect the microbial ecology can influence the outcome.
• The limited parameter sampling and durations achievable in the experiments will be mitigated by the use of a computational plaque model being developed in collaboration with Dr Head (Computing), preliminary results for which suggest a comparable role for both frequency and total sugar intake. Once calibrated to the experiments, this in silico model will provide a unified, long-time picture of the dietary risk factors for childhood caries.

We will identify high risk factors that should be avoided, and provide bounds on the frequency and/or amount of sugar that we expect to reduce the risk of caries. This will be used to inform the design of pilot studies in children attending the Leeds Dental Institute, in collaboration with experts in Paediatric Dentistry and Dental Public Health. This will also be an important experimental project in an ongoing cross-Faculty collaboration that promises to deliver a powerful future technology for oral healthcare research.

Temporomandibular disorders (TMD) in adults consulting with Otalgia – a primary care prospective study

Lead Supervisor: Dr Vishal Aggarwal
Co-Supervisors: To be confirmed

Project Summary

Chronic pain affecting the face, mouth or jaws is common, distressing and disabling with a population prevalence of 7% (Aggarwal 2006). Like other chronic pain conditions, it is a diagnosis by exclusion. Early diagnosis is therefore rare and patients are often subjected to multiple consultations and investigations to identify an organic cause for reported symptoms. This places a huge burden on already stretched healthcare resources.

Of particular concern is the iatrogenic harm that can occur when chronic oro-facial pain is misdiagnosed. This can take the form of multiple tooth extractions, jaw joint surgery and / or ENT procedures (pffafenratth et al).

The most common type of chronic oro-facial pain is Temporomandibular disorder (TMD) which presents in the jaw joints and associated musculature.

The majority of chronic oro-facial pain including TMD often present initially to general medical practitioners (bell et al BDJ). This may be due to poor access to NHS dental services, costs of dental treatment and general fear of dentists. TMD pain should be relatively easy to diagnose and manage given the availability of clear Diagnostic Criteria for TMD (DC/TMD) that aids clinicians in assessing patients and eases communication regarding consultations, referrals and prognosis (Schiffman et al., 2014). However, it is a condition that is often misdiagnosed. Given the close proximity of the Temporomandibular joints to the ear, it is not surprising that TMD pain is often mistaken for Otalgia by general medical and dental practitioners (Jaber JJ et al., 2008; Kuttila SJ et al., 2001). Such misdiagnoses are associated with onward referral to ENT where more invasive management could ensue leading to iatrogenic harm.

In an attempt to understand the extent of the problem, an audit of 133 adult patients presenting with otalgia to a general medical practice was conducted. Of these, 130 (98%) had otalgia of undermined diagnosis and several had recurrent consultations for Otalgia with some patients seeing the GMP upto seven times. Despite this, none of the patients had their Temporomandibular joints examined nor was this included in the list of differential diagnoses. It is therefore likely that TMD were being misdiagnosed as otalgia in this population. Therefore the overall aim of the current project will be to determine the prevalence of TMD in patients presenting to primary care with Otalgias.

Aims and Objectives

1. Determine the association of secondary and referred Otalgias with TMDs
2. Develop and validate guidelines to allow GPs to make early diagnosis of TMD 3. Educate GPs how to clinically examine TMJs and to accurately ask patients for the related signs and symptoms during history taking.

The potential use of bioactive peptides from food and waste as anti-cariogenic agents

Lead Supervisor: Dr Joanne Maycock (Food Sciences)
Co-Supervisor: Dr Simon Wood

Project Summary

Bioactive peptides derived from plant protein sources have not yet been fully investigated with respect to their role in the prevention of dental caries and periodontal disease, two of the most common diseases in Man. This study is innovative in that it will identify bioactive peptides from plant waste material which will enable the development of cost-effective functional foods that can be used for the prevention of dental caries in a variety of settings. The work could then be further expanded to investigate other conditions such as periodontal disease.

Bioactive peptides produced from oil seed press cake will have anticariogenic effects and can be used to produce functional foods which will have a role in the prevention of dental caries.

Project Summary

The aim of this study is to determine the potential use of oil seed press cake food waste as a source of proteins for the production of bioactive peptides which can then be used as antimicrobial/anticariogenic agents.

The objectives for the study are: 

• Buy commercially, be gifted or produce oil seed press cakes
• To purify proteins from the press cakes to enrich the source
• To produce bioactive peptides by hydrolysis of press cake proteins
• To identify and characterise the peptides
• To determine the antimicrobial effects of the proteins on bacteria associated with causing dental caries
• To analyse structural characteristics of the peptides

Transient arrest of cell ageing during amplification of human cells in culture

Lead Supervisor: Dr Xuebin Yang
Co-Supervisors: Dr Georg Feichtinger; Dr William Bonass

Project Summary

One of the strategies that we are currently using to investigate tissue replacement for dental pulps involves seeding cells into inert scaffolds made from biocompatible materials. However, amplification of dental pulp cells to provide a sufficient population size for establishing a synthetic pulp results in the propagation of an aged cell population that is unsuitable for use in dental pulp tissue replacement.

In our previous studies, we have confirmed that human dental pulp (hDPCs) cells undergo chromosomal attrition and usually reach cell senescence by cell passage 12. Analysis of the telomeres in such amplified populations suggests a telomere attrition rate of 0.4-0.5kb per generation. In order to overcome this problem we have used synthetic telomere linker oligonucleotides for rescuing human dental pulp cells (hDPCs) from ageing associated with the “end replication problem”. One such linker oligonucleotide, “telome 3”, was found to arrest ageing in hDPCs, as judged by cell viability and total cell numbers, in a reproducible manner. Since current methods for measuring telomere length are either clumsy, inaccurate or both, we are investigating novel approaches to measuring telomere length as a guide to determining rates of cell ageing.

Aims and Objectives

The aim of the proposed research is to investigate the potential of delivering optimum oligonucleotides such as “telome 3’ to arrest hDPSCs ageing and whether this effect is transient and controllable. Other cell types may also be used as the control to look at if this arrest is a general phenomenon or is restricted to hDPCs. Moreover, the mechanism of delivery method will also be investigated, which may provide insight into future strategies for gene delivery. The novel methods for measuring telomere length will be further optimised in order to measure the length of individual telomeres. This would open up a whole new avenue to investigate the possibility that ageing is controlled by the attrition of specific chromosomes.

Understanding the causes of developmental tooth defects using a high-throughput genomic screening approach

Lead Supervisor: Dr Alan Mighell
Co-Supervisor: Professor Chris Inglehearn

Project Summary

Dental enamel is the hardest tissue in the human body. The process of enamel formation is called amelogenesis, and Amelogenesis imperfecta (AI) is the name given to a set of severe defects of this process which are inherited as Mendelian conditions. AI occurs in up to 1:700 live births and presentation varies with the genetic mutation(s) involved. Over 20 genes have been implicated so far by genetic studies, including many by the Leeds AI group (eg Smith et al 2016, EJHG 11:1565; Parry et al 2016, AJHG 99:984 and many other published papers). Clinical care is complex, demanding on patients and the dental team and requires long-term specialist treatment. Patients have difficulty maintaining oral hygiene, suffer low self-esteem and report an inferior quality-of-life.

Molar Incisor Hypoplasia (MIH) is another type of enamel defect which is similar to AI but only involves some of the teeth in the adult dentition. Unlike AI it is not a Mendelian condition, but there is evidence of both genetic and environmental contributions to susceptibility. It is common, with frequency ranging from 2.4%-40.2% in different populations. At optimum levels fluoride protects teeth from dental decay. Fluorosis is a third category of dental development abnormality of variable severity. It is largely due to a single environmental cause (excessive fluoride in drinking water) during tooth development, but there is data that supports a genetic susceptibility that may influence the severity of the enamel defects.

Aims and Objectives

This project aims to develop a screen for the genetic regions most frequently mutated in AI patients using Multiple Inversion Probes (MIPS) technology, then test this as a pre-screen on all of the new samples being collected by the Leeds AI group, through their network of collaborators around the world. Those that prove negative will then be tested by whole exome or whole genome next generation sequencing and bioinformatics analysis to find new AI genes, which could then be characterised in cell or animal models. The pathology of new forms of AI will be studied by micro-CT scanning, electron microscopy, immunofluorescence and biochemical analysis. Meanwhile the MIPS pre-screen will be applied to sets of patients with MIH and fluorosis to determine whether the same genes contribute to risk of these much more common dental conditions as well. This project will give the successful applicant the opportunity to train in and use a wide range of molecular genetic, bioinformatic, cell biology and pathology techniques, to publish their work with this highly successful group and to begin a career in dental research.