Dr Helen Chappell

Profile

*** PhD Projects Available for Self-Financing Students. See projects below!!!***

I was appointed as a University Lecturer in September 2017, and Associate Professor in 2025. With a background in chemistry, materials modelling and molecular biology I obtained a PhD in 2006 from the University of Cambridge (Churchill College; Department of Materials Science & Metallurgy), focussed on the computational modelling of novel bone graft materials. I have since held several research posts, including a Career Development Fellowship (2013-2016) at the Medical Research Council Human Nutrition Research unit (Cambridge), focussing on the modelling of inorganic-organic interfaces of endogenous calcium phosphate nanoparticles found in the human gut. During this period I also held a College Research Associate position at Wolfson College, Cambridge. Prior to joining the MRC I spent 4.5 years employed as a Scientific Advisor at English Heritage where I was involved in, amongst other things, the protection of the Must Farm Bronze Age Settlement, the archaeological assessment of the new Sizewell C Nuclear Power Station, and the scientific assessment of offshore archaeology for several large wind-farm arrays off the East Anglian coast. I also acted as English Heritage scientific advisor for several episodes of the popular Channel 4 archaeological series Time Team.

Responsibilities

• Deputy Director of Postgraduate Researchers, School of Food Science & Nutrition
• Module Leader - Food1010 Food: Origins and Form
• Module Leader - Food3140 Appraisal of Scientific Literature

Research interests

My research is focused on the computational modelling of organic-inorganic interfaces in biological, medical and environmental materials linked to health and disease. With particular emphasis on bacterial biofilms and biomaterials, I am interested in the formation of biological composities and the way material properties (both natural and synthetic) influence disease pathologies.

In particular, my group is interested in:

• Molecular and atomic interactions at the interface of bacterial biofilms, particulalry within the cystic fibrosis lung.
• Acid demineralization of human teeth, and strategies for remineraliztion.
• Structure, formation and treatment of kidney stones.
• The development and effects of bacterial biofilms in contact with medical equipment.
• Causes and treatment of canine and human herniated spinal discs.
• Structure-function relationships of novel iron supplements composed of both inorganic and organic phases.
• Interactions of antiobiotic molecules with agricultural soil minerals and how these interactions affect retension and uptake by plants and lower animals.

!!!!PhD Projects Available for Self-Financing Students!!!! Please contact me if you are interested in the following projects. Unfortunately, no funding is in place for these projects and I can only consider students who are self-financing, or who are willing to apply for a scholarship (e.g. governmental) to fund the PhD.

Project One: Intervertebral Disc Degeneration in Short-legged Dogs – Understanding Chemical and Structural Changes using Computational Methods.

Supervisors: Dr Helen Chappell, Dr James Smith (Leeds), Professor Paul Freeman (external, University of Cambridge).

Details:

Intervertebral disc herniation (IVDH) has been recognised in chondrodystrophic dogs (short-legged dogs such as Dachshunds, Welsh Corgis and West Highland Terriers) since at least the 1880s, but only in recent years has the genetic basis of this predisposition been confirmed. In these animals, their intervertebral discs, usually spongey, high water-content structures providing cushioning and shock absorbance during normal movement, gradually become stiffer, dehydrated and increasingly solidified until, ultimately, this calcified central part of the disc (nucleus pulposus) can rupture through a tear in the outer, fibrous rim (annulus fibrosus) with potentially catastrophic and often fatal consequences. The herniation causes compression and contusion of the spinal cord, which can cause severe pain and, in some cases, irreversible paralysis. This is an extremely distressing disease for dogs and owners alike, but it is also expensive to treat, with some animals requiring surgery and, unfortunately, it has a relatively high recurrence rate of up to 20%.

In this project we aim to understand the fundamental chemical and microstructural changes in the disc as the disease progresses, and ultimately use these data as a starting point for the development of new treatments to retard or reverse crystallization of the disc. We will use molecular dynamic simulations at (canine) body temperature to understand the molecular interactions that occur in the centre of the intervertebral disc, between the growing mineral phase and the native organic molecules (proteoglycans, collagen). To make the models as realistic as possible, we will integrate data obtained from samples of disc material removed during life-saving surgery on canines carried out at The Queen’s Veterinary School Hospital (University of Cambridge), which have been analysed to pinpoint the composition, levels of crystallization present, stiffness and density. This integration of, and comparison with, experimental data obtained directly from diseased animal tissue, will provide increased interpretability.

The project will be based at the University of Leeds, and will be entirely computational. However, there will be close collaboration with Professor Paul Freeman, Principal Clinical Neurologist, at the Department of Veterinary Medicine (University of Cambridge) and there will be opportunities for visiting the Queen’s Veterinary School Hospital throughout the project.

Project Two: Understanding the structural chemistry of millet – a high-nutrient crop for the climate change era.

Supervisors: Dr Helen Chappell, Dr James Smith (Leeds)

Details:

Millet has long been touted as a nutritional powerhouse due to its high dietary fibre and trace element content. Because of its lean requirements in terms of environmental conditions (e.g. low-rainfall tolerance), the potential of this crop as a source of nutrients, particularly in areas of the world where the effects of climate change are being felt most readily, is now being closely examined. Several commercial varieties of millet are grown – e.g. foxtail, pearl and proso – but it is finger millet, which has high levels of calcium, potassium, and to a lesser extent zinc. Arabinoxylans are the main dietary fibres found in finger millet, and it is their association with trace elements that permit such high nutrient levels within the grain structure. However, until now, it was not known what these interactions looked like, or why some metal ions (e.g. potassium and calcium) are found in much higher concentrations than others (e.g. zinc). Using computational modelling, and with funding from the World Universities Network, we have shown in a pilot study, that the arabinoxylans bond calcium and potassium ions particularly efficiently, with the precise binding pockets identified. Zinc on the other hand is too small to find a stable binding pocket without large distortions of the fibre structure, causing a structural (and energetic) instability. These results pinpoint the chemistry of nutrient binding to the millet dietary fibre structure and help to explain why we detect such high levels of calcium (364 mg/100 g) and potassium (443 mg/100 g) in the grain, but much lower levels of zinc (2.5 mg/100 g).

In this proposed project we will look further at the structure of the millet polysaccharides, and the nutrients that are found in the millet grain. We aim to understand the structural chemistry of millet and to develop a detailed model of the critical structures and interactions. We may also be able to look more closely at how the polysaccharides are digested, which will be a key step in understanding millet’s trace element bioavailability.

The project will be based at the University of Leeds, and has the potential to be either fully computational, or split 50:50 with an experimental component. We will also work closely with Dr Apramita Devi, an expert in millet from India who has been working on this topic for many years at both the National Cheng Kung University (Taiwan) and at UC Davis (USA).

Project Three: Collaboration or competition? Modelling the roles and impacts of extracellular matrix composition in a mixed species bacterial biofilm.

Supervisors: Dr Helen Chappell, Dr James Smith (Leeds)

Details:

Bacterial biofilms are a clever strategy used by bacteria to protect themselves in large colonies. The biofilm, which is composed of an extracellular mixture of sugars, proteins, DNA, ions and lipids, acts as a sophisticated barrier, preventing therapeutic molecules, such as antibiotics, from reaching the bacterial cells. The major components of most bacterial biofilms are polysaccharides (sugars), and each bacterial species has a different type or range of polysaccharides that it employs for this purpose. In this project we will look at the polysaccharide extracellular matrices (glycocalyx) of multi-species biofilms, for example Pseudomonas aeruginosa and Staphylococcus aureus, which are two dangerous pathogens linked to poor human health and the rapid development of antimicrobial resistance (AMR). Previous work has revealed an ambiguity with these two bacteria, showing both that they work cooperatively and, alternatively, antagonistically. For this PhD we will model the polysaccharide structures of the multi-species biofilms, exploring the interactions and partitioning behaviour of the biofilm components. We will also examine how quorum sensing molecules (the messages sent between bacteria to ensure positive collective behaviour) move through these structures; for example, can the quorum sensing molecules of one species navigate their way through the extracellular matrix of another species?

The project, based at the University of Leeds, will be entirely computational in nature, using first principles and MD methods, and working on the University of Leeds’ new High-Performance Computer, Aire. It would suit a student with a chemistry, physics, materials or maths background, or equally someone with a background in biology or microbiology who is also interested in exploring computational methods.

Current Lab Members:

Palwinder Kaur – PGR Student

Isaac Noble – PGR Student

Former Lab Members

Dr Oliver Hills – now at Cresset.

Dr Rhiannon Morris – now at the Department of Work and Pensions

Dr Yunqing Wang

Dr Yuwei Li

Our research is highly interdisciplinary. We are connected with various experts who have complementary strengths and facilities, both within our School of Food Science and Nutrition and outside in other schools, universities and institutions:

• The Queen’s Veterinary School Hospital, University of Cambridge
• The Biomineralisation Group, School of Dentistry, University of Leeds
• The McDonald Institute of Archaeological Science, University of Cambridge
• Disordered Materials Group, ISIS Neutron and Muon Source, Harwell.

Qualifications

• Ph.D, Bone Graft Materials Modelling, (Cantab)
• M.Phil. Modelling of Materials, (Cantab)
• M.Res. Biomolecular Science, (York)
• B.Sc. (Hons), 1st Class, Chemistry, (Open)

Professional memberships

• Member, Royal Society of Chemistry
• Member, EPSRC Peer Review College
• Member, NERC Peer Review College
• Member, The Microbiology Society

Student education

• Deputy Director of Postgraduate Researcher Students, School of Food Science & Nutrition
• Lecturer on Food: Origins and Form
• Module Leader of Food Science and Nutrition Research: Recent Revelations and Disputes
• Lecturer in undergraduate organic chemistry
• Research supervisor for final year undergraduate and postgraduate projects, across all degree programmes
• Personal Academic Tutor

Current postgraduate researchers

• Isaac Noble