FINAL REPORT - Keele University · There were several short talks by members of the 3ME Initiative on their areas of expertise, and Marius Kronje from CERAM Research in Stoke-on-Trent

FINAL REPORT

KEELE UNIVERSITY

K E E L E , S T A F F O R D S H I R E , S T 5 5 B G

h t t p : / / w w w . k e e l e . a c . u k / 3 m e /

http://www.keele.ac.uk/3me/


INTRODUCTION

The 3ME Initiative has been an inter-disciplinary project which aimed to develop collaborative research in Modeling Methods for Medical Engineering.

The 3ME Initiative was conceived in 2006 as a result of a successful grant application to the Biotechnology & Biological Sciences Research Council the previous year, involving biomedical engineers and mathematicians working together on a stem cell manipulation project. Crucial to its success is the numerical simulation and mathematical modeling of the solid and fluid mechanics problems that arise in the laboratory experiments.

Looking around in Keele it was apparent that there were state-of-the-art modeling and imaging techniques being developed in other fields that were very valuable to current medical engineering projects. The application of these techniques to real biomedical problems would also be of tremendous value to the modelers and there were many parallels to be explored in using imaging in diverse applications. As a result, members from the recently formed Keele Research Institutes, Science & Technology in Medicine (ISTM), and Environment, Physical Sciences and Applied Mathematics (EPSAM), came together to propose to propose and unusual collaborative partnership, spanning biomedicine, mathematics and geophysics.

The 3ME Initiative brings together three well established Keele research groups:

1. The Institute for Science & Technology in Medicine (ISTM), including the Bioengineering and Therapeutics group led by Prof Alicia El Haj and the Imaging & Diagnostics group led by Prof Jon Dobson, other members include Prof Sally Roberts, Dr Isaac Liu, Dr Sarah Cartmell, and Dr Jan-Herman Kuiper.

2. The Mathematical Modelling Group in EPSAM comprises Prof Graham Rogerson, Prof Yibin Fu, Dr Shailesh Naire and associated research staff who employ mathematical modelling including asymptotic and numerical techniques to solve problems related to industrial processes, biology and human physiology. This group enjoys an RAE 5 rating and an international profile, having become increasingly interested in emerging areas such as stem cells and cell engineering.

3. The Applied and Environmental Geophysics Research Group, also in EPSAM, includes Professor Peter Styles, Dr Ian Stimpson, Dr Nigel Cassidy Dr Jamie Pringle, Dr Sam Toon, and a range of research staff who offer ultra-high resolution geophysical techniques and numerical modeling in Environmental, Geodynamic, Hydrocarbon and Archaeological areas. Expertise covers fuel cells, clean energy, biomass utilisation, pollution control, waste management, green chemistry, clean and innovative utilisation of coal, involving academic and commercial links throughout the world. They have extensive expertise in the imaging of a parameter space, using techniques that transcend disciplines and can equally well be applied from geological to human bodies.


OBJECTIVES

The 3ME Initiative Objectives were to:

1. Create an interdisciplinary environment and culture that enables Keele researchers to work together in small groups on new common interest areas

2. Host international senior research visitors to enhance the research skills of Keele and the UK's capability in medical engineering

3. Invest to start up new key collaborative medical engineering projects

BENEFICIARIES

The 3ME Initiative has successfully generated a range of new interdisciplinary grant applications as well as publications. Among others, the beneficiaries of this initiative were:

1. Clinicians

2. Patients involved in new clinical trials

3. Industrial partners, such as Astra Zeneca

4. Engineering researcher.

5. Mathematics researchers.

6. Geophysics researchers.

COLLABORATIVE SUPPORT

The Initiative offered a range of support to build collaboration between disciplines such as:

3ME “Speed Dating” in which all staff interested in taking part in the 3ME Initiative match up expertise and explore potential collaboration.

3ME Problem Scoping Workshops

The “Researcher in Residence” scheme, in which staff swapped roles to immerse themselves in the research culture of the other‟s laboratory and discipline.

3ME “Sandpits” which were carefully designed to generate preferred paths to the solution of their focal problem or theme.

“Back-to-Back” and subsequently “Front-to-Front” Seminars, which provided a regular physical meeting space, with opportunity for informal discussions too.

3ME Themed “Research Retreat”


STEERING GROUP COMMITTEE

Professor Alicia J. El Haj Chair in Cell Engineering and Theme Lead in Bioengineering and Therapeutics

Professor Peter Styles Professor in Applied and Environmental Geophysics

Prof Jon Dobson Professor of Biophysics and Biomedical Engineering

Professor Graham Rogerson Head of School of Computing and Mathematics


Mr Mark Smith Research Institute Manager ,Institute for Science and Technology in Medicine

Dr Nigel Cassidy Senior Lecturer in Applied Geophysics

Ms Pauline Weston Research Institute Manager, EPSAM


EVENTS

OPENING MEETING

The opening meeting for the 3ME Initiative took place at the North Staffordshire Medical Institute on the afternoon of Friday 18 April 2008. 27 members took part.

The programme covered an introduction1 from the scientific perspectives that the project aims to bring together. Mark Smith gave a summary of how to apply for the resources on offer. All the participants then enjoyed a “Meet and Eat” event in which they had a chance to meet many others and discuss ideas for collaboration one-to-one in a 5 minute “speed dating” format.

Participants then formed into four groups to brainstorm ideas for activities, seminars, visitors, external collaboration, etc. These ideas were then presented to the whole meeting.

1 Please see slides in Appendix 1


SANDPITS

Just in case anyone wasn‟t sure, a “Sandpit” in this case does not involve buckets and spades, it‟s a term used by research funders for a scientific discussion intended to generate new collaborative ideas that are then judged and supported at the end of the meeting to explore the idea further.

First Sandpit Event, 2008

By the shore of Lake Ullswater, twenty members of Keele‟s 3ME Initiative enjoyed two days in a Sandpit, from 10 to 12 September 20082.

Left to right: Alicia El Haj, Mark Smith, James Richardson, Hu Zhang, David Meredith (STFC Daresbury), Srabasti Chakravorty, Sarah Cartmell, Ying Yang, Helen Wright, Araida Hildago, Jonathan Healey, Peter Styles, Tajeshwar Aulakh, Shailesh Naire, Sergei Annenkov, Graham Rogerson, Darren Clement, Robert Emery, KP Lam. Also taking part but not on the photograph: Andrew Curtis (Edinburgh), Jon Dobson and Yibin Fu.

Participants came from the Keele Research Institutes of Engineering Physical Sciences & Mathematics (EPSAM) and Science & Technology in Medicine (ISTM), and were joined by two key speakers:

Dr David Meredith from the National Grid Service supercomputing section of Daresbury Laboratories, and

Dr Andrew Curtis, Director of Edinburgh Seismic Research at Edinburgh University.

Focus of the Sandpit meeting was on two themes to enhance Keele‟s cross RI capability in Modelling Methods for Medical Engineering. The first was data visualisation and “data mining” covering the technical possibilities using Keele and Daresbury‟s supercomputing resources, and clinical needs such as knee cartilage monitoring. The second theme was wave propagation, which spanned techniques such as seismic interferometry used to study the earth, to biomedical applications in cardiovascular systems and tissue engineering.

Participants then discussed ideas at the boundaries of these topics and formed into small groups to develop concrete proposals for collaboration. On day two, the 3ME Initiative ran its own version of the BBC2 television programme “Dragons Den”3. Seven small teams of ISTM and EPSAM

2 For the First Sandpit Programme please see Appendix 2 3 For details of the proceedings please go to Appendix 3


members were told “I‟m in” and offered support of student project placements, researcher or facility time and a cash total of approximately £25,000 from the EPSRC “Bridging the Gaps” grant and ISTM‟s Doctoral Training Centre.

Second Sandpit Event 2009

Our second successful Sandpit meeting was held at the Isle of Anglesey on 13 and 14 July. This was another key event in Keele‟s “Bridging the Gap” project funded by the Engineering & Physical Sciences Research Council (EPSRC).

Left to right: Frank Rutten, Jon Dobson, Mark Davidson (Microfabritech), David Smith, Monica Spiteri, Graham Rogerson, Josep Sule-Suso, Alastair Channon, Dave Collins, Paula Marsh, Michael Lutiyanov, Nick Forsyth, Simon Pearce, Jan-Herman Kuiper, Joanna Collingwood, Michael Evans, Chris Brazel, Eustace Johnson, Shailesh Naire, Sally Roberts. Also taking part but not on the photograph: Marius Cronje (CERAM Research), Alicia El Haj, Mark Smith.

Although a “Sandpit” in North Wales sounds like a beach holiday, in fact the 24 participants took part in an intensive two day scientific meeting4, to generate new collaborative ideas that were then judged and supported to explore them further. Members of the 3ME Initiative were joined by key speaker Dr Mark Davidson from Microfabritech at the University of Florida, USA. He opened the meeting with a presentation on studies of iron biominerals associated with neurodegenerative diseases and the application of recent laboratory research to the clinic. There were several short talks by members of the 3ME Initiative on their areas of expertise, and Marius Kronje from CERAM Research in Stoke-on-Trent closed the meeting with a summary of computer modelling capability.

Overall focus of the Sandpit was allocate £25,000 of EPSRC funding to new project ideas through a version of the BBC2 television programme “Dragons Den”. Three teams of 3ME Initiative members convinced the “Dragons”, and received a total of £20,000 to develop their collaborations up to the stage of initial joint publications and major grant applications.

Held at the Trearddur Bay Hotel near Holyhead, the participants experienced the full extremes of Welsh summer weather but did find time during the meeting to walk along the sand to discuss their ideas.

4 The program can be found in Appendix 4


WORKSHOPS

Project Progress Workshops

The first Project Progress report was held on the 30 of April 2009 with great feedback from participants who found the results to date from the projects very fascinating. The second Project progress report was held on the 24 November 2010 where members of the Modelling Methods for Medical Engineering (3ME) initiative gathered at the Keele Management Centre to share the first results of some of the projects supported at its "sandpit" meetings.

Six of the speakers are pictured above, from the left: Dr Josep Sule-Suso, Mr Michael Lutiyanov, Dr Nigel Cassidy, Dr Sarah Griffiths, Dr Frank Rutten and Dr Shailesh Naire.

Speakers included the 3ME Researchers in Residence, who presented the results of mathematical and computer-based modelling and imaging work relevant to the study of cells and tissue engineering.

Creativity@Home Workshop, 4 March 2010

Keele University through Professor Alicia El Haj has been selected to take part in an EPSRC pilot programme called “Creativity@ Home”. As part of the program, the Regenerative Medicine group held a workshop on March 4, 2010 which spanned from Cell therapies, Bioengineering to Ageing.

The objective of this workshop was to facilitate an opportunity for academics in regenerative medicine to take a fresh look at their research and consider potential links to many allied research areas at Keele such as Primary care, Ageing, Geophysics and Applied Mathematics. The EPSRC funded Tim Morley from the Innovation Lab to facilitate the event and he will be providing further facilitator training to one of the Researchers in Residence, Dr Sarah Griffiths as part of the EPSRC funded 3ME programme at Keele.


RESEARCH RETREAT

3ME Research Retreat and Grant Writing Workshop

Sitting on the western shore of Coniston Water in the Lake District is the University of Birmingham‟s Raymond Priestley Centre, the venue for the 3ME Research Retreat and PhD symposium on the 22nd, 23rd and 24th of March 2011. This was the final Key event in Keele‟s Bridging the Gap” project which is funded the Engineering & Physical Sciences Research Council (EPSRC).

Although the name of this event gives the impression that this was a holiday in the Lake District, in fact the 28 participants took part in an intensive three day scientific meeting, to look back at the ideas born by the 3ME Initiative and map their course for generating new collaborative ideas that could make the basis for further grant applications.

The Research Retreat began with several short talks by new members of the 3ME Initiative on their areas of expertise, followed by a Cross Disciplinary grant opportunities workshop, a Tutorial for PhD student in Paper Writing as well as poster presentations. The meeting came to an end following presentation of new collaborative grant ideas developed during the meeting.

The Lake and surrounding area provided a fantastic setting for kayaking, canoeing, high rope, biking and hiking and the delegates were treated to two sessions of activities in between their meeting this proved to be a great opportunity to increase team building between students and academics from both the research institutes of ISTM & EPSAM. The members also enjoyed some fine food at the Church House Inn & the Wilson Arms Country Inn in the Village of Torve.

Group discussions on day 2

Retreat Group Photograph

Left to right: Ying Yang, Dhaya Perumal, Will Smith, Hareklea Markides, Khondoker Akram, Folashade Kuforiji, Alex Lomas, Neil Telling, Zanzhe Yu, Alan Harper ,Catriona Kelly, Nigel Cassidy, Paul Roach, Alicia El Haj, Sarah Griffiths, Nick Forsyth, Maria Kyriacou, Sammy Wilson, William Webb, Deepak Kumar, Frank Rutten, Ka Wai-Wan, Mark Smith and Ian Wimpenny Also taking part in this event but not in the photo were Graham Rogerson, Michael Lutiyanov, Shailesh Naire & Angeliki Fouriki.


Future Directions Research Retreat,

A future Directions Research Retreat was held on Monday, 4th of July and Tuesday 5th of July at Wychwood Park golf centre near Crewe. During the retreat there were presentations by Professor Pauline Ong (Institute for Primary Care) on translation to clinical practice and Professor Andrew Dobson (Institute for Law, Politics and Justice) on his Interdisciplinary ERSC programme commenced the efforts to explore links to other disciplines on campus.

In addition, the pilot research projects, a product of our previous “sandpits”, presented posters on their progress so far. The standard was very high, and two winners were declared by the judges, and in the photograph ISTM student Miss Angeliki Fouriki and ISTM Senior Lecturer Dr Ying Yang are seen with their posters, holding the certificates they received on behalf of their co-authors. Each winning poster received a prize of £250, contributed to the event by ISTM.

ISTM student Miss Angeliki Fouriki and Senior Lecturer Dr Ying Yang with their posters, showing the certificates for their co-authors and £250 prizes.


BACK-TO-BACK SEMINARS

The 3ME Initiative supported collaboration via a series of two 40 minute seminars one after the other, on the same topic from contrasting perspectives, ie mathematical and bioengineering.

Over the four years, six seminars were planned which provided the members of the Initiative with the opportunity to have informal discussions.

The first Back-to-Back Seminar was delivered to an audience of 25 researchers and included three well received talks entitled “Challenges of stem cell therapy” by Professor Alicia El Haj; “ Nano-Optical-Mechanical Manipulation of stem cells in physiological flows: Design principles for delivering stem cell therapy” by Dr Isaac Liu and finally “ On Continuum-mechanical modeling of aneurysm formation” by Professor Yibin Fu.5

A second Back-to-Back Seminar was organized on the 2nd of February 2009 at the Guy Hilton Research Centre. Two speakers gave different approaches to related topics:

5 Programme can be found in Appendix 5

Dr Federico Sabina, visiting from the National Autonomous University of Mexico in Mexico City, spoke first on "Modelling microstructures through the homogenisation method"

Dr Ying Yang, a member of ISTM at Keele, then spoke on "The implication of scaffold architecture in the growth of engineered tissues".

On the 15th of October 2009, the 3ME Initiative was delighted to announce the Back-to-Back Seminar by Prof Euan Nisbet and Professor Patrik Spanel which took place at the Keele Medical School on Wednesday 15 October 2009. Professor Nisbet and Professor Spanel gave different approaches to the subject of methane gas on vastly different scales, in the global atmosphere, and in the human body.

Prof Euan Nisbet, visiting from Royal Holloway, University of London, spoke first on "Atmospheric methane - the quiet giant", a fully illustrated talk on methane and its potential role in climate change, drawing on results from monitoring stations thoughout the world.


Prof Patrik Spanel, who holds a dual appointment with Keele's Research Institute for Science & Technology in Medicine (ISTM) and the J. Heyrovský Institute of Physical Chemistry in Prague then spoke on "Methane and other trace gases in exhaled breath; their role in medical diagnostics". One of several trace gases under investigation with world-leading specialist equipment at Keele, Prof Spanel included research results achieved only a few days prior to giving the talk. 6

A large audience representing many discipline backgrounds in the ISTM and EPSAM Research Institutes raised many questions for the speakers, and highlighted at least four areas of potential new research collaboration, making it one of the most successful Back-to-Back Seminars held so far.

On the 11th of October 2011, the 3ME Initiative, welcomed Professor John King from the University of Nottingham, to give a seminar on mathematical modelling of biological tissue growth. Over 20 members of the 3ME Initiative, drawn from the Research Institutes of Science and Technology in Medicine and the Environment, Physical Sciences and Applied Mathematics, attended the event at the School of Pharmacy.7

6 An Abstract of Prof Spanel‟s talk is in Appendix 5 7 Seminar Program can be seen in Appendix 5

Professor John King, pictured, is Professor of Theoretical Mechanics and Deputy Head of the School of Mathematical Sciences at the University of Nottingham, UK and has expertise in mathematical modelling, mathematical medicine, industrial mathematics, nonlinear mathematics, systems biology and computational toxicology.

A Second Front-to-Front Seminar was organized on the 3rd of November 2010, when Dr Gregory Vilensky from the University College London presented his work in a well received talk entitled “Modelling of Unltrasound absorption in biological fluids and tissue.

His work looked into the physics of propagation of nonlinear ultrasound waves in soft biological tissue. And showed that t he central result of the study was the set of macroscopic evolutionary equations which describe the dynamics of the nonlinear sound fields for a very wide range of types of lousy media.

An extra year of the 3ME Initiative was made possible by the new sponsorship offered to Keele University and which gave rise to an additional front-to-front seminar “Computational Modelling and Computational Neuroscience” by Dr Theocharis Kyriacou which was based on two themes. The Seminar was a great success with various one-to-one meetings being organized between the researchers at ISTM and the speaker. For the program and a copy of the talk‟s abstract, please see appendix 3.


VISITING ACADEMICS

The 3ME Initiative provided support for two visiting Senior Researchers to spend a period of at Keele, delivering lectures and one-to-one sessions.

Our first International visitor was Professor Yitong Zhang, Tainjin University, China with along with Prof Graham Rogerson and Prof Yibin Fu from Keele University were provided with approximately £5,000.00 to facilitate Professor Zhang‟s visit and work on a new project entitled “Continuous Mechanical Modelling of Aneurysm”. During Professor Zhang‟s visit he had met with various clinicians based in the North Staffordshire University Hospital and ended his visit by presenting the work conducted during his visit. His talk8 on “A viscoelastic model for pathological abdominal aortas and its application to aneurysm modeling” was well received by the 30 participants including students, clinicians and academics from both EPSAM & ISTM.

The 3ME Initiative was also pleased to welcome Professor Kannan Krishnan, from the University of Washington, USA in June 2009.

Professor Krishnan came to Keele as part of his Distinguished Lecturer Series supported by the IEEE, the world leading technology advancement association, and was hosted by the Keele biomagnetics group led by Professor Jon Dobson. His seminar9, held in Keele Medical School, was entitled "Biomedical nanomagnetics: A spin through new possiblities".

Professor Krishnan has been Campbell Chair Professor of Materials Science and Adjunct Professor of Physics at Washington since 2001 and has a range of international awards for his cross-disciplinary research and work in the public understanding of science.

8 Please see Appendix 6 for details of his talk 9 Details in Appendix 7

He first gave an overview of state-of-the-art nanotechnology, size-dependent magnetic behavior and the emerging field of biomedical nanomagnetics. He then explored his group's current work in these areas highlighting the fundamental principles behind research in the context of several emerging technological and clinical opportunities.

On the 15th of March 2011, the 3ME Initiative, welcomed Professor Ralph Müller who is a Professor of Biomechanics & Director of the Institute for Biomechanics at ETH Zurich in Switzerland to give a Seminar on Bone Imaging.


Over 50 members of the 3ME Initiative drawn from two Keele Research Institutes, ISTM and EPSAM, as well as NHS consultants and nurses heard the seminar which was held at the Guy Hilton Research Centre10.

10 Details of the Seminar in Appendix 8

Professor Ralph Müller‟s research employs state-of-the-art biomechanical testing and simulation techniques as well as novel bio-imaging and visualization strategies for biological tissues. His approaches are now often used for precise phenotypic characterization of tissue response in mammalian genetics, stem cell-based tissue engineering and mechanobiology.

He is an author of 360 refereed original journal and proceeding articles, 2 books, 58 chapters and reviews, and over 410 peer-reviewed abstracts. He has received a number of awards, including the Inaugural John Haddad Young Investigator Award (1998) from the American Society for Bone and Mineral Research (ASBMR) and Advances in Mineral Metabolism (AIMM) as well as the Promising Young Scientist Award (1999) from the International Society of Biomechanics (ISB). In 2004, he was named Young Leader by the American-Swiss Foundation and in 2007; he received the Publication Group Award from the German Academy of Osteological and Rheumatological Sciences.

SEED CORN PROJECTS

The 3ME Initiative has spent £50,000 on a series of projects to nurture new ideas and collaborations between members of Keele's research institutes of Science and Technology in Medicine and Environment, Physical Sciences and Applied Mathematics.

Sandpit Title PI Collaborators Awarded

2008 Mathematical Modelling and Evaluation of an Osteo-chondral Co-culture Dr Shailesh Naire

Dr Halil Aydin, Dr Ying, Yang, Dr Sarah Cartmell, Dr Sarah Griffiths, Dr Sergei Semenov £ 5,000.00

2008 Stem Cell Deformation under Different Flow Rates Prof Peter Styles.

Dr Hu Zhang and the EPSAM High Performance Computing Group £ 4,000.00

2008 Computational Services for Feature Extraction in Cell Engineering (FACE) Dr KP Lam,

Prof James Richardson, Mr Robert Emery and Dr David Meredith (STFC Daresbury Supercomputing) £ 5,500.00

2008 Continuous Mechanical Modelling of Aneurysm Prof G Rogerson Prof Yibin Fu £ 6,500.00

2009

Fourier Transform Infrared Spectroscopy of Single Cells: towards a clinical application in pathology Dr Nick Forsyth

Dr Josep Sule-Suso and Dr David Collins £ 10,000.00

2009 Modelling Stem Cell Regneration of Knee Cartlidge

Dr Jan-Herman Kuiper

Dr Michael Lutiyanov, Dr Shailesh Naire, Dr Simon Pearce, Prof Sally Roberts £ 5,000.00

2009 PADI-MS to Characterise the Metatastic Profile of Cancer Cells Frank Rutten

Dr Nick Forsyth and Dr Josep Sule-Suso £ 3,500.00

Jan-11

Modelling & Design of Omptimal Flow Perfusion Bioreactors for Tissue Engineering Applications: Follow-up Funding Request Shailesh Naire £ 1,000.00


Jan-11 Mathematical modelling of functional tissue-engineered annulus fibrosus Ying Yang,

Michael Lutiyanov, Jan Herman Kuiper, Sally Roberts £ 1,700.00

Jan-11 Modelling regeneration of osteochondral defects in the knee after cell therapy.

Jan-Herman Kuiper

Michael Lutiyanov, Shailesh Naire, Sally Roberts £ 3,300.00

Jan-11 Chemical Characterisation of Functionalised Nanomagnetic Therapy Materials Paul Roach Frank Rutten £ 4,500.00

Jan-11

Voltage operated calcium channel agonist/antagonists for mechanotranduction and bone remodelling Ying Yang Dhaya Perumal, Alicia El Haj £ 5,000.00

Jan-11 Alice:Autofocusing Live Cells KP Lam K Wright, DJ Collins, JH Kuiper, S Roberts, J Richardson £ 5,143.73

Jun-11 Develpment of a human 3D cell-culture model for the study of atherosclerosis Ying Yang

Alan Harper, Michael Lutiyanov, Shailesh Naire & Ying Yang £ 3,000.00

Jul-11

Using NARMAX (Nonlinear Auto-regressive, moving average models with exogenous inputs) to create quantitative models of human platelet Ca2+ signalling.

Dr Alan Harper (ISTM)

Dr Theocharis Kyriacou (EPSAM - School of Computing and Mathematics) £ 3,467.90

Jul-11

Testing the anti-inflammatory and therapeutic potential of GIBBERELLIN

Catriona Kelly Dhaya Perumal, Angeliki Fouriki, Oksana Kehoe and Jon Dobson £ 3,000.00

Jul-11

Rapid Monitoring In Pharmaceutical Discovery And Production Using PADI Mass Spectrometry

Frank Rutten*, Paul Roach§,

Paul Davey†, Tony Bristow† and Andrew Ray† £2,450.00

Jul-11

The application of Artificial Neural Networks to identify differentiated human embryonic stem cells with vibrational spectroscopy

Kumar D., Butchers J., Day C., Yang Y., Forsyth N. R., and Sulé-Suso J. £3,500.00

MATHEMATICAL MODELLING AND EVALUATION OF AN OSTEO-CHONDRAL CO-CULTURE

Investigators: Dr Shailesh Naire (EPSAM), Dr Sarah Griffiths (ISTM), Dr Araida Hidalgo (ISTM- now at

Manchester University), Dr Sarah Cartmell (ISTM- now at Manchester University)

For a project overview and outcomes, please see the entry for Dr Sarah Griffiths and Dr Shailesh Naire under Researcher in Residence as well as follow up funding below.

COMPUTATIONAL SERVICES FOR FEATURE EXTRACTION IN CELL ENGINEERING (FACE)

Investigators: Dr KP Lam (ISTM), Prof James Richardson (ISTM)

Project Overview:

This project utilised computerised image analysis in conjuction with digital microscopy to quantify several aspects of cell growth and differentiation. This was accomplished by applying the contemporary branch of computational geometry/mathematics concerning Fractals to such biological systems, with the principal goal of providing an objective description of morphological and biochemical complexity. A primary focus of our work thus concerned a detailed investigation of how colonies of cells are organised and described from a spatial viewpoint. To achieve this, the role of positional information at the microscopic level was examined empirically with the goal of understanding how it might regulate pattern formation at the macroscopic level using a pattern recognition (and mining) approach. Based on geometry, this project sought to develop advanced image analysis techniques, coupled with data and rules mining principles, to describe and characterise such complexity of cell/tissue structures in an objective way.

CONTINUOUS MECHANICAL MODELLING OF ANEURYSM

Investigators: Professor Graham A. Rogerson (10%, 3 months): EPSAM, Keele University, Professor

Yibin Fu (20%, 3 months): EPSAM, Keele University.

Staff employed: Professor Yitong Zhang (100%, 3 months): Department of Mechanics, Tianjin

University, China

Project Overview:

The title of our proposed project is Continuum-mechanical modeling of aneurysm formation. An aneurysm is a bulge (dilation) in the wall of an artery, usually the aorta. An aneurysm that grows and becomes large enough can burst, causing dangerous, often fatal, bleeding inside the body. Information from mathematical modelling of aneurysm formation can help doctors make the difficult decision about which course of action to take once an aneurysm has been diagnosed (whether to carry out a surgery, to prescribe appropriate drugs to reduce the risk of aneurysm bursting or to simply put the patient under observation). It can also help in preventing an aneurysm from recurring after a repair operation. Previous studies have focused on modelling the evolution of aneurysms numerically once they have already formed.

The proposed research focusses on how an aneurysm is initiated. Our research was motivated by a recent discovery for a geometrically similar problem, namely that the initial onset of localized bulging in an inflated membrane rubber tube is a bifurcation phenomenon. We show that despite the


constitutive differences between a membrane rubber tube and a human artery, the initial onset of aneurysm formation can also be modelled as a bifurcation phenomenon. This bifurcation interpretation provides a theoretical framework under which different mechanisms leading to, or reducing the risk of, aneurysm formation can be assessed in a systematic manner. In particular, this could potentially help in assessing the integrity of aneurysm repairs.

FOURIER TRANSFORM INFRARED SPECTROSCOPY OF SINGLE CELLS: TOWARDS A CLINICAL APPLICATION IN PATHOLOGY

Investigators: Josep Sulé-Suso, Nick Forsyth, Dave Collins

Project Overview:

The resistance of cancer cells to different treatments has always been difficult to understand. Recently, it has been suggested that cancer stem cells present in tumors could be responsible for such resistance. Therefore, the identification and localization of such cells in different tumours would help clinicians to better understand how cancer behaves in front of a given treatment, and more importantly, to tailor treatment to each individual patient. However, it has been difficult up to know to detect the presence of stem cancer cells in the vast majority of tumours.

On this basis, we decided to use Fourier Transform Infrared (FTIR) Spectroscopy as a prospective tool for detection of these elusive cells. This technique uses an infrared beam that, after interacting with the sample, gives highly informative molecular information. Also, spatially resolved biochemical information from cells and tissue samples can be obtained by mapping or imaging techniques. In IR spectroscopy, the frequency of light that is absorbed by a sample depends upon the nature of the bond between the atoms, the atoms involved in the bond, and the type of vibration. The amount of light absorbed by a vibrating bond is linearly related to concentration. Therefore, the IR spectrum of a sample is a direct indicator of its chemical composition. Several studies have shown that FTIR spectroscopy can detect differences between cancer cells and their normal counterparts [1]. Our previous work was aimed at separating physical and chemical properties of cells measured with FTIR spectroscopy [2, 3]. Furthermore, we were the first to carry out FTIR spectral analysis of single cells either in cytology or tissue samples that had been previously stained with either H&E or Pap [4, 5], two staining procedures widely used in pathology. This has important implications in this project as we intend to study the presence of cancer stem cells in already stained tissue samples.

Based on our expertise using synchrotron-based Fourier Transform Infrared (S-FTIR) spectroscopy, we first obtained FTIR spectra of single human Embryonic Stem Cells (hESC) and human Mesenchymal Stem Cells (hMSC) at Soleil synchrotron, France. This preliminary work showed that there are differences between the spectra of hESCs and hMSCs (Figure 1). In fact, hESCs had increased peaks at 2920, 2850, 1740, and 1450 cm-1. These peaks are caused by lipids which would suggest that hESCs have a higher amount of lipids than hMSCs. We are now carrying out histological staining of these cells at the Pathology department, UHNS in order to confirm this finding. We are presently writing a manuscript focused on the interpretation of these novel findings.

Our future work will be as follows. First, we will carry FTIR spectroscopy of hESCs and MSCs at different stages of differentiation in order to assess how the biochemical make up of these cells varies with the stage of differentiation. Second, we will obtain FTIR spectra of lung cancer cells present in lung tissues (ethical approval already obtained) and compare spectra of stem cells with spectra of lung cancer cells in tissues in order to identify common markers. These two experiments


will be carried out at both Soleil and Diamond synchrotron (U. K.) in 2010 as we have already obtained beamtime at both synchrotrons. We believe that during these two periods, we‟ll be able to obtain the S-FTIR spectra of at least 3000 cancer cells giving us a good insight on whether it is possible to identify spectral markers similar to spectral markers of stem cells. This will be carried out using PCA analysis comparing the whole spectra and areas within spectra. Third, we are going to study these stem cells with Raman spectroscopy at the University of Reims, France. This technique uses a laser beam giving biochemical information of cells similar to FTIR spectroscopy. However, both techniques complement each other and therefore, this combination increases the chances of characterizing spectral markers of cancer stem cells. The work at Reims University will be carried out in March 2010 as part of our research collaborations with Dr Sockalingum through the Franco-British Partnership Programme (Alliance).

MODELLING STEM CELL REGNERATION OF KNEE CARTLIDGE

Investigators: Dr Michael Lutianov (ISTM, Keele University, 50%), Dr Shailesh Naire (School of

Computing and Mathematics, 20%), Dr Jan Herman Kuiper (10%), Prof. Sally Roberts (5%)

Staff Employed: Research in Residence - Dr Michael Lutianov (postdoc, 6 weeks full time)

Collaborating Partners: OsCell, Oswestry (UK), data on cell densities

Project Overview:

The aim of the project was to develop a mathematical model of cartilage regeneration in a chondral defect after autologous cell implantation (ACI) therapy. The specific objectives were (1) To quantify how certain parameters influence cartilage growth, in particular Initial cell density, nutrient supply and initial availability and mechanical loading (2) To give insight into the optimal initial number of cells required for „effective‟ repair of the defect. (3) Use this information to guide clinicians. (4) Bridge the gap between modellers and clinicians. (5) Allow new researchers to gain skills and experience in modelling. (6) Build a platform for future studies.

The project has finished and delivered all objectives except the investigation of mechanical loading. Briefly, cell implantation density and nutritional supply were predicted to have only a small influence on the overall regeneration process. Cell type was predicted to influence the pattern of regeneration.

This information has a direct impact on our clinical cell therapy service, because it explains many of our clinical findings, such as the small importance of cell implantation density. It has been a true interdisciplinary project, with direct involvement of biologists, engineers and mathematicians, and has given a young researcher the opportunity to expand his modelling skills.


PADI-MS TO CHARACTERISE THE METATASTIC PROFILE OF CANCER CELLS

Investigators : Frank Rutten, Josep Sulé-Suso and Nick Forsyth,

Project Overview:

Lung cancer can manifest itself in 2 different types: small cell and non-small cell cancer. The patterns of metastases for each type of cancer are somewhat different. In fact, while both can metastasize to brain, liver and bone amongst other, small cell lung cancer has a higher tendency to metastasize to brain. For this reason, radiotherapy to brain as a prophylactic measure is standard in the management of small cell lung cancer. Furthermore, it is not possible at present to predict where the primary tumour will metastasize.

Therefore, advances in healthcare require targeted treatment to ensure maximum effectiveness and patient survival. As cells of both cancer types are understood / known to circulate through the body in a similar manner, a logical hypothesis is that the molecules expressed at the cell surface differ and that this makes the cells “stickier” to specific parts of the body.

A novel mass spectrometry technique, PADI-MS, has shown very promising results when used for the analysis of solid surfaces. Compared to more established surface analytical techniques, it has the distinct advantage that no vacuum is required and that at the same time highly specific molecular level information can be obtained. Whereas the technique has thus far not been applied to cells, experiments on plant leaves and cast polymer (both natural and man-made) layers have been extremely promising and have yielded highly sample-specific mass spectra.

The aims of this proposal were twofold:

(1) For optimum treatment, rapid and reliable identification of the specific type of cancer at an early stage are required to target treatment and thus greatly reduce morbidity. It was hoped that PADI-MS could be applied to cancer cells to obtain surface-specific mass spectra which could in turn be used to distinguish different cancer cell types.

(2) It would be of great benefit to the development of cancer treatments to gain more insight into the processes of tumour invasion and metastasis. It was hoped that PADI-MS would help to better understand the surface chemistry on these lung cancer cells and hence contribute to a fuller understanding of the “stickiness” of these cells.


MODELLING & DESIGN OF OMPTIMAL FLOW PERFUSION BIOREACTORS FOR TISSUE ENGINEERING APPLICATIONS: FOLLOW-UP FUNDING

REQUEST

Investigators: Sarah Griffiths (Postdoctoral Researcher, ISTM), Shailesh Naire (Mathematics Lecturer,

Keele), Sarah Cartmell (Biomedical Engineering Lecturer, ISTM), Araida Hidalgo-Bastida (Postdoctoral

Researcher, ISTM), Paul Roach (Biomedical Engineering Lecturer, ISTM), Halil Aydin (Postoctoral Researcher,

ISTM), Sundaramoorthy Thirunavukkarasu (Masters Student, Keele), Sergei Annenkov (Mathematics, Keele)

Tim Spencer (Sheffield Hallam)

Staff Employed: Sarah Griffiths (Researcher in Researcher, ISTM) full time, 6months.

Project Overview:

Bioreactors provide a unique 3D platform with which to manipulate cell growth under „near‟ biological conditions, including fluid (nutrient) flow and its resulting mechanical forces (shear). These bioreactors therefore are of great use in the field of tissue engineering to develop biological substitutes to restore or replace damaged or diseased tissue. However there are many types of bioreactor and an optimised system is still in development.

This short study focuses on the application of a simple, single-layered, homogenous porous scaffold geometry, computer modelled system within a basic perfusion bioreactor system, for comparison with a laboratory experiment to test the validity and suitability of the computer model for purpose.

The mathematical analysis revealed that a circular bioreactor design favoured in tissue engineering to match clinical need (drill shape) produced hotspots and shear stress that would be potentially damaging to cell viability. A square bioreactor was designed to provide a laminar flow and remove these negative shear effects of fluid flow. A new „in-house‟ method for creating PLGA scaffolds using supercritical CO2 was developed to produce scaffolds with a more homogenous internal structure to match the mathematical model more closely. Laboratory analysis was then performed using both circular and square bioreactors containing the equivalently shaped PLGA, PLLA (polymer) and agar scaffolds, to perfuse them with media containing Lugol‟s Iodine solution. This made the fluid visible to real-time analysis with the Xtreme-CT device (Scanco) in an attempt to validate the computer model of lower shear stresses in the square system. Our results whilst showing that the square bioreactor was possible, that further optimisation is required to ensure optimised fluid flow within the chamber and that a distinction needs to be made between true fluid flow and diffusion within the porous materials. The computer model would also need to be modified to account for the difference in behaviour/fluidic properties of the „iodine laced media‟ compared to media alone. However potential exists for creating computer „real‟ versions of the scaffolds that could be modelled to replace the simplified version giving a higher level of accuracy and predictability within the bioreactor chamber.


MATHEMATICAL MODELLING OF FUNCTIONAL TISSUE-ENGINEERED ANNULUS FIBROSUS

Investigators: Jan Herman Kuiper, Robert Jones and Agnes Hunt Orthopaedic Hospital NHS

Foundation Trust, 20%, Michael Lutiyanov, Mathematical Department, 50%, Ian Wimpenny, ISTM, 100% (for

three months), Sally Roberts, Robert Jones and Agnes Hunt Orthopaedic Hospital NHS Foundation Trust

10%, Ying Yang, ISTM, 40%

Staff Employed: Researcher in ResidenceMichael Lutiyanov, postdoctoral, research residence, 50% of his

time on this project; Ian Wimpenny, PhD student, 100% of his time on this project

Collaborating Partners: Prof JB Richardson, Robert Jones and Agnes Hunt Orthopaedic Hospital

NHS Foundation Trust

Project Overview: The aim of the project is to generate tissue-engineered annulus fibrosus (AF) patches through a layer-by-layer method by stacking aligned nanofiber layers, with precisely arranged angles as in native AF tissue, which are embedded in a native ECM hydrogel. The AF patches have been produced and characterized by histological and mechanical analysis. The mathematical personnel working on the project have undertaken a modelling study to predict the effect of hydrogel concentration, nanofiber angle and number of nanofiber layers on the general mechanical properties of the patches. The modelling results are consistent with the experimental data, implying a reliable technique to predict accurately parameter changes in complex AF patch so reducing the number of experiments required.

MODELLING REGENERATION OF OSTEOCHONDRAL DEFECTS IN THE KNEE AFTER CELL THERAPY.

Investigators: Dr Michael Lutianov (ISTM, Keele University, 50%), Dr Shailesh Naire (School of

Computing and Mathematics, 15%), Dr Jan Herman Kuiper (15%), Prof. Sally Roberts (5%)

Staff Employed: Dr Michael Lutianov (postdoc, 50% FTE, 1 March to 31 May 2011)

Collaborating Partners: OsCell (UK), data on cell densities

Project Overview:

The aim of the project was to develop a mathematical model of cartilage regeneration in an osteochondral defect after autologous cell implantation (ACI) therapy. This project would built upon the results of an earlier 3ME project, “Modelling Stem Cell Regeneration of Knee Cartilage“. The specific deliverables were (1) To formulate a set of equations to predict the evolution in time of stem cell/chondrocyte/osteoblast densities and cartilage/bone matrix densities inside an osteochondral defect as a function of nutrient supply and critical stem cell densities. (2) To mathematically simulate the repair of osteochondral defects (3) To Investigate the influence of initial conditions (e.g. cell density, ratio of chondrocyte to stem cell density) and boundary conditions (nutrient supply, defect depth) on the repair process.

The project is ongoing and has so far achieved the first two deliverables. We are now in the process of investigating the influence of the various variables, which is the final deliverable. When that has been achieved, the information will have a direct impact on our clinical cell therapy service, because the majority of defects we currently treat are osteochondral defects. This project extended a


multidisciplinary collaboration between biologists, mathematicians and engineers. Together with the earlier 3ME project, this project forms the basis of further grant applications.

CHEMICAL CHARACTERISATION OF FUNCTIONALISED NANOMAGNETIC THERAPY MATERIALS

Investigators: P. Roach (ISTM) and F. Rutten (EPSAM)

Project Overview:

Advances in biomaterials over the past decades have led to the development of materials with excellent bulk properties required for implantation at their host site. Interest has now turned to surface properties as it has become apparent that the outermost layer of materials interacting with biological systems dictates the immediate biological response. This has been particularly relevant in the development of nanomagnetic therapies in tissue engineering. Nanoparticles comprising a core of iron oxides and outer coatings of specific functionalities, e.g. the well-known RGD motif, can be used to stimulate cell receptors to display desired cellular responses. This technique relies entirely on the chemical groups presented and detailed physico-chemical surface characterisation of manufactured particles is clearly essential. Plasma assisted desorption ionisation (PADI) offers distinct advantages over current analytical techniques allowing confirmation of nanomagnectic particle surface modifications. Development of this instrumentation and associated methodology will enable rapid sample characterisation without the need for sample preparation.

Set up and optimised electronics to sustain an atmospheric pressure helium plasma, with the extension to other gases progressing in the near future. As shown in Figure 1 the plasma pen encompasses an inner aluminium oxide ceramic tube coaxially positioned within a glass outer tube. A central tungsten filament ignites the plasma. The electronics are optimised such that a very stable plasma can be rapidly ignited at the press of a button, being sustained indefinitely. This, being aimed at a target sample allows ions to be ejected, collected in the inlet of a mass spectrometer.

The MS has been donated from AZ, having also been optimised to rapidly, and in real-time, collect sample data. This is currently being optimised through the physical modification of the front end of the mass spectrometer inlet allowing direction of the sample ions into the MS.


Figure 1: PADI set-up showing, left) the plasma pen, middle) plasma in relation to sample and MS inlet and right) schematic of coaxial gas flow.

Construction and optimisation of instrumentation is progressing well, via the use of standardised polymer matrices, such as paraffin, poly(lactic acid) and poly(tetrafluoro ethylene), as shown in Figure 2. Magnetic nanoparticle characterisation using PADI will follow on from water contact angle infrared and Raman spectroscopic analysis - currently in progress. This will give confidence of sampling data achieved by PADI. Subsequent analysis by the former techniques will give insight into any plasma induced changes.

Figure 2: PADI MS of paraffin film. Coloured dots indicate series of peaks of repeating monomer units.

Summary :

The plasma pen and associated electronics and gas feeds have been designed, custom built and optimised in order to sustain a stable atmospheric helium plasma.

A single quadrupole mass spectrometer has been modified and interfaced with the plasma source.

Mass spectrometric data analysis is progressing using standardised polymer samples to ensure reproducibility and accuracy of the method.

Supplementary analysis of the magnetic nanoparticles is continuing to act as a reference for PADI MS characterisation.

Continuing Work:

• A directional MS sampling orifice has been designed and is currently being constructed. This will significantly improve signal to noise ratio and enhance sensitivity.

• Plasma source: establish optimum parameters (power, coaxial gas flow, plasma orientation and position with respect to sample).


• Sample mount: precise position for optimal signal. Moving stage for continuous fresh surface and potentially imaging.

• A further grant awarded will allow us to carry out a survey of a wide range of sample types, phases and concentrations, and establish what can readily be detected under what conditions.

VOLTAGE OPERATED CALCIUM CHANNEL AGONIST/ANTAGONISTS FOR MECHANOTRANDUCTION AND BONE REMODELLING

Investigators: Dhaya Perumal, Pharmacy, 50%, Alicia El-Haj, ISTM, 10%, Ying Yang, ISTM, 40% (for

three months), Asha Rupani, ISTM, 100% (for two months)

Staff Employed: Asha Rupani, MSc student, 100% of her time on this project

Collaborating Partners: Steve Allen, Chemistry Dept.

Project Overview:

This proposed project has conducted a series studies aiming to further define the gene pathway of a voltage operated calcium channel agonist (FPL-64176) for mechanotransduction and bone remodelling. The ultimate goal is to define the gene path including early and late expressed genes in response to mechanical stimulation at different culture/stimulation time.

Rat osteoblast cells were isolated from tibia and femur bones and following outgrowth, were used below passage 2-3.

Two sets of experiments have been carried out with different mechanical stimulation conditions:

1. The application of a tensile force to cells seeded on coverslips or porous PLA scaffold using a 4-point bending bioreactor and

2. Cells subjected to stretching force via nanomagnetic RGD-coated particles (final concentration 12.5ug/ml in serum free media) bound onto the cell membranes under external magnetic field. Cells on 6 well plates were subjected to various timed and loading conditions as follows:

a. 1 hour cyclic loading for 7 days and post-culture for 24 hour, then termination of experiment.

b. 1 hour cyclic loading for 3 days and post-culture for 24 hour, then termination of experiment

c. 1 hour cyclic loading for 1 day and post-culture for 24 hour, then termination of experiment


d. 1 hour cyclic loading for 1 day and post-culture for 2 hour, then termination of experiment

Each of the four scenarios above were performed in triplicate for four different experiments: a) Static + FPL; b) Static – FPL; c) Magnetic stimulation + FPL and d) Magnetic stimulation – FPL

As reported previously, the 4-point bending experiments revealed stretched and networking cell morphology in specimens under loading and FPL in the culture media compared to the normal spinal shape in static cultured specimens. Also, higher alizarin red staining was observed in FPL incorporated constructs than on the no FPL counterparts.

Magnetic loading was easier to operate with no concern of contamination. All experiments, under the four timed and loading scenarios above have been completed. The extracted RNA from lysed cells has now been used in cDNA synthesis.

The initial work on designed PCR arrays has commenced. The customised Quality Control plates have been assessed and we are currently liaising with the manufacturer to optimise the PCR array system before commencement of the sample cDNA analysis from the various specimens above.

DEVELOPMENT OF A HUMAN 3D CELL-CULTURE MODEL FOR THE STUDY OF ATHEROSCLEROSIS

Investigators: Institute for Science and Technology in Medicine - Dr Alan Harper (30%) and Dr Ying

Yang (30%). Department of Mathematics - Dr Michael Lutiyanov (10%) and Dr Shailesh Naire (10%).

Staff Employed: MSc students – Wanjiku Njoroge (100%), Anthony Deegan (100%) and Aleksandra

Szczepanska (100%)

Project Overview:

Atherosclerosis is an unwanted thickening of the wall of blood vessels, which in some conditions can lead to obstruction of bloodflow to downstream tissues. This can result in heart attacks and strokes which cause the greatest numbers of premature death in the United Kingdom each year. However we currently lack an accurate model of human atherosclerosis formation and progression. Therefore In this project we aimed to develop a cell culture system to model the natural development of atherosclerosis in a realistic blood vessel construct cultured under blood flow conditions found at atherosclerosis-prone regions of the vasculature.

We have managed to generate a 3D construct of a blood vessel with intima and media layers. Initial testing suggests that this construct behaves like a normal blood vessel and can be moulded to form a tubular structure with a patent lumen. In consultation with Dr Naire and Dr Lutiyanov, we have designed and constructed a perfusion system capable of generating pathological blood flow conditions found inside an atherosclerotic-prone region of the vasculature. This collaboration between mathematicians and biologists has been vital to ensure that the generated model will be able to replicate the change in the physical environment which is known to be a key factor in this pathology. Further work will be required to attempt to generate pathological lesions in the 3D construct by attempting to alter the conditions of blood flow as well as changing the composition of the blood that the construct is exposed to.


We believe that this model has a number of experimental benefits over other models which will help facilitate our understanding of the biological processes underlying atherosclerosis formation. Our model also offers an alternative to the use of animal models for studying atherosclerosis as well as for preclinical testing of drugs aimed at preventing the progression of atherosclerosis in patients at risk of heart attack or stroke.

USING NARMAX (NONLINEAR AUTO-REGRESSIVE, MOVING AVERAGE MODELS WITH EXOGENOUS INPUTS) TO CREATE QUANTITATIVE

MODELS OF HUMAN PLATELET CA2+ SIGNALLING.

Investigators: Dr Alan Harper (Institute for Science and Technology in Medicine) and Dr Theocharis

Kyriacou (School of Computing and Mathematics)

Collaborating Partners: Dr Stewart Sage (Department of Physiology, Development and Neuroscience,

University of Cambridge)

Project Overview: The aim of this project was to investigate the feasibility of developing a mathematical model of platelet cytosolic calcium signals using a Nonlinear Auto-Regressive Moving Average models with eXogenous inputs (NARMAX) methodology. Our initial experiments have confirmed our ability to utilise experimental measurements of the component fluxes of calcium ions from the extracellular space, pericellular region and intracellular stores to recreate the changes in the calcium concentration caused by platelet activation with thrombin. These results confirmed that the signal is driven by the intracellular stores but extracellular calcium signal may also play a significant secondary role in shaping the cytosolic calcium signal. We also compared the model generated from data obtained from a type II diabetic against that obtained from a healthy volunteer. This set of results suggested that there may be a significant difference in the models obtained from these individuals, with diabetic losing the dependence on the extracellular Ca2+ signals. This is intriguing given the hypercoagulable phenotype known to be possessed by diabetic patients, and suggest the possibility that this model can help us analyse the known differences in Ca2+ signals generated from patient groups who have enhanced platelet Ca2+ signals. Further experiments are planned at the end of the month to investigate the reproducibility of these findings. If this work is successful we hope to apply for external funding in the near-future to help progress this work. The award of this grant has helped facilitate an ongoing collaboration between Dr Harper and Dr Kyriacou. We believe the use of this modelling technique will allow us to investigate the non-linearities of this system and therefore gain a deeper understanding of how calcium signals are generated beyond what can be predicted by experiment alone.

TESTING THE ANTI-INFLAMMATORY AND THERAPEUTIC POTENTIAL OF GIBBERELLIN

Investigators: Institute for Science and Technology in Medicine - Dr Catriona Kelly (30%), Dr Jon

Dobson (10%), Angeliki Fouriki (10%). Department of Mathematics - Dr Shailesh Naire (5%). School of

Pharmacy – Dr. Frank Rutten (5%).

Collaborating Partners: Dr. Dhaya Perumal, Dept. of Pharmacy, Kingston University


Project Overview:

A20 is a gene that reduces inflammation in response to bacteria or viruses. A20 is reduced in lung disorders such as Cystic Fibrosis and asthma where chronic inflammation is a problem. At present a drug capable of inducing A20 is not available. Gibberellin (GA) is a plant extract that is known to increase the presence of A20 in rice crops. GA has previously been shown to have anti-inflammatory properties in diabetic mice although the mechanism of action was not explored. We hypothesise that the anti-inflammatory effect of GA results from its ability to induce A20.

Aim: To investigate the anti-inflammatory and therapeutic potential of the plant extract GA in the lung.

To date, we have established a safe concentration of GA which is well tolerated by cells from the lung. In addition, we have found that treating lung cells with GA prior to exposing them to bacterial products, results in a significant reduction in the inflammatory response.

We will next focus on effective and accurate delivery of the drug to the lung using a novel magnetic drug delivery system. In addition, to optimise drug delivery to the cells, we will mathematically model (i) the magnetic-targeted drug delivery process by modelling the movement of the particles across the magnetic field, and (ii) the uptake of drug across the cell membrane. It is anticipated that these studies will be completed by the end of October 2011.

The absence of an A20-inducing drug has limited therapeutic targeting of this gene. The mechanism of A20 action is common to all cell types and the finding that GA induces A20 and downregulates inflammation will have implications beyond inflammatory lung disease.

THE APPLICATION OF ARTIFICIAL NEURAL NETWORKS TO IDENTIFY DIFFERENTIATED HUMAN EMBRYONIC STEM CELLS WITH

VIBRATIONAL SPECTROSCOPY

Investigators: Mr Deepak Kumar (Guy Hilton Research Centre, ISTM) (50%), Mr John Butchers

(School of Computing and Mathematics, Keele) (50%), Dr Jacek Pijanka (Diamond Synchrotron, Oxford)

(50%), Dr Ying Yang (Guy Hilton Research Centre, ISTM), Dr Charles Day (School of Computing and

Mathematics, Keele) (50%), Dr Nicholas R Forsyth (Guy Hilton Research Centre, ISTM), Dr Josep Sulé-Suso

(Guy Hilton Research Centre, ISTM)

Staff Employed: Mr Deepak Kumar (PhD student) (50%)

Collaborating Partners: Keele University, School of Computing and Mathematics and Guy Hilton

Research Centre (ISTM).

Project Overview:

The aim of this project was to establish an automated classification software system using Artificial Neural Networks (ANNs) which would be able to identify and differentiate between human mesenchymal stem cells (hMSCs) and human embryonic stem cells (hESCs) in different oxygen concentrations 2% O2 and 21% O2) and have the ability to distinguish between pluripotent hESCs and differentiated hESCs towards adipogenesis, chondrogenesis and osteogenesis.


Synchrotron based FTIR (S-FTIR) data had been previously obtained for hESCs and hMSCs cultured in both oxygen concentrations (2% O2 and 21% O2) Pijanka et al 2009. The FTIR data was preprocessed using PCA and averaged over batches of five cells of each sample type analysed using a Self Organising Map (SOM) artificial neural network (ANN). A SOM was trained using six examples of each class of stem cell; hESC and hMSC. After training was complete, the SOM was tested with five similarly pre-processed but previously unseen examples of each stem cell type.

Despite the small amount of training data, these results were highly promising as 75% of the test patterns were correctly classified. These promising initial novel results show the huge potential of ANNs in the automatic classification of stem cells to distinguish between stem cell types and the oxygen environment in which they have been cultivated. They could be utilised in the future in order to autonomously identify and recognise stem cells from heterogenous patient samples such as bone marrow. Other applications may also include, evaluating the „stemness‟ of populations – in order to confirm pluripotency/multipotency of stem cells quickly rather than using laborious techniques such as PCR.

Now that an ANN has been established, future work will include, producing an ANN for the FTIR data which has been obtained from hESCs differentiated towards skeletal lineages; adipogenesis, chondrogenesis, osteogenesis. Due to the small amount of training data used for the ANN produced so far, the next set of FTIR data contains larger training and testing datasets (i.e. more FTIR spectra for each sample type) and thus may further consolidate the findings shown so far. To confirm the differentiation of hESCs into each lineage, relevant histological stains have been performed.


RESEARCHERS IN RESIDENCE

The 3ME “Researcher in Residence” scheme has proved to be the key mechanism to deepen collaboration between ISTM and EPSAM. The scheme allows staff to swap roles and immerse themselves in the research culture of the other‟s laboratory and discipline.

During the duration of this initiative, four Researchers in Residence were drawn from Lecturers and Senior Lecturers involved in the 3ME Initiative:

DR SERGEI ANNENKOV

(Nov 2008 and May 2009) Project Overview:

The process of tissue engineering develops under controlled conditions inside a bioreactor, where a culture of cells builds up under conditions that support efficient nutrition of cells. It is well-known that the supply of oxygen and soluble nutrients is the crucial limiting factor for the in vitro culture of 3D tissues. In a perfusion bioreactor, this supply is provided by the flow of a given rate through an inlet pipe, which perfuses through pores of the cell-seeded 3D scaffold and exits through an outlet pipe (Figure 1). Direct perfusion is known to enhance cell growth, survival and function. However, the effects of direct perfusion can be highly dependent on the hydrodynamic properties of the flow. Optimizing a perfusion bioreactor for the engineering of a 3D tissue must address a careful balance between the mass transfer of nutrients and waste products, homogeneity of the flow, and the flow-induced shear stresses at the surfaces of the pores. In particular, low flow rates and flow inhomogeneity may lead to the development of hypoxic, necrotic areas within the scaffold. On the other hand, high flow rates generate high shear stress and cause cell damage. The optimal flow conditions of a bioreactor should not be determined through a trial-and-error approach, but rather supported by simulation methods. Computational fluid dynamics (CFD) simulation is crucial in understanding how changes of macroscopic bioreactor parameters lead to changes of microscopic characteristics of flow at the pore level, such as flow speed and wall shear stress. Geometric complexity of the bioreactor interior poses considerable challenges for a CFD simulation and requires the use of a parallel supercomputer to address them.

Project Conclusion:

A simple, but computationally demanding model of a perfusion bioreactor has been investigated in a supercomputer environment. Use of a computer cluster allowed us to go to much lower pore size and much finer meshes than it was possible on a single processor workstation.

Distribution of flow speed was found to be only weakly sensitive to the pore size, but much more sensitive to porosity, with more uniform flow for higher porosity. These effects have been statistically quantified. Wall shear stress was found to be very sensitive to pore size, but less sensitive to porosity, although higher porosity leads to a somewhat more uniform shear stress distribution. Pore sizes of 200–250 μm were found to provide optimal conditions for cell growth, while pore sizes of 150 μm lead to unifom shear stress at the scaffold centre, but dangerously high shear stress levels at the inlet. At even lower values of the pore size, comparable to gap width, the flow bypasses the scaffold, apparently leading to hypoxic conditions.


DR SARAH GRIFFITHS

(Mar to July 2010)

Project Overview:

There is a current need in the medical field for tissue engineering, a process that aims to develop biological substitutes that restore, maintain or improve tissue function to seriously diseased or damaged tissues or organs. This technique generally incorporates the use of living cells with some form of scaffold matrix, which acts to guide tissue development and more recently incorporates the use of an artificial 3D environment provided by a bioreactor, which aims to better mimic biological conditions for the developing tissue by creating a controlled biochemical and biomechanical environment. The process of tissue engineering is closely linked to a number of other disciplines, which all need to interact to produce the desired results (see Table 1.2 for a basic example of these interactions).

These studies can either be performed in vivo within the context of an intact organism or in vitro, which is under controlled artificial (laboratory) conditions either in 2D (static, cell culture wells) or in 3D (static or non-static scaffold constructs). In general it is the practice of combining these two methods for elucidating mechanisms and components of complex biochemical and cellular processes, such as bone wound healing, where tightly controlled in vitro work is often the forerunner to in vivo modelling.

Table 1.2: Interconnecting disciplines and approaches for tissue engineering

Physical and Electrical Stimulus

Chemical Stimulus

Cell Biology Scaffolds Bioreactors

Cell Differentiation

Cell Adhesion and Proliferation

Cell Signalling

Cell Networking

3D Design & Co-Tissues

Bioreactors provide a unique 3D platform with which to manipulate cell growth under „near‟ biological conditions, including fluid (nutrient) flow and its resulting mechanical forces (shear). Bioreactors work under closely monitored, tightly controlled environmental and operating conditions (e.g. pH, temperature, pressure, nutrient supply and waste removal), giving them a high degree of reproducibility, control, as well as increasing biomonitoring, storage and transportation options as well as the potential for automation (Martin et al. 2004; Visconti et al. 2006).

The type of bioreactor used for tissue engineering varies depending on cell type, loading form needed i.e. compressive or tensile, and whether or not a scaffold has been used, as certain scaffold materials cannot withstand direct force application. Generally however, the scaffolds are used to direct loading to the cells seeded within, without damaging the cells. Types of bioreactor include a spinner flask, rotating vessel, perfusion system, compression bioreactor, blood vessel bioreactor, magnetic force bioreactor and high-density culture flasks.


Project Conclusion:

Whilst the laboratory tests were able to determine proof of concept by utilising the microCT and XtremeCT scans to produce a 3D modelled version of the scaffolds that could potentially be used to determine fluid flow throughout the scaffold materials, further optimisation is required in both the model and practical procedures to make this a viable method. The model will need to incorporate the iodine as a unique substance with its own properties more accurately, which may vary with different scaffolds, as well as accommodating the effect this will have on scan clarity due to the metals artefact production. As such an alternative mechanism for dying the scaffolds for tracking via XtremeCT may be necessary, potentially for low density materials the media alone should be sufficient and would not require further alterations to the simplified computer model proposed here.

DR SHAILESH NAIRE

(June to August 2010)

Project Overview: “Modeling and Design of Optimal Flow Perfusion Bioreactors for Tissue Engineering Applications”

Flow perfusion bioreactors have been used in a variety of tissue engineering applications due to

their consistent distribution of nutrients and flow-induced shear stress within the cell-seeded scaffold.

A widely used configuration in bone and cartilage tissue engineering uses a scaffold with a

circular cross-section enclosed within a cylindrical chamber. Inlet and outlet pipes are connected to the chamber on either side through which media is continuously circulated. However, fluid-flow experiments and simulations have shown that the majority of the flow perfuses through the center of the scaffold. This flow pattern results in stagnant zones in the peripheral regions of the scaffold as well as high flow rate ("hot-spots") near the scaffold inlet and outlet. This non-uniformity of flow and shear stress, owing to a circular design, results in limited cell proliferation and differentiation in these areas.

The focus of this work is to design an optimized flow perfusion system using Computational

Fluid Dynamics (CFD) as a mathematical tool to overcome the time-consuming trial-and-error experimental method. We compared the flow within a circular and a rectangular bioreactor system. Flow simulations within the rectangular bioreactor are shown to overcome the limitations in the circular design. This work challenges the circular cross-section bioreactor configuration paradigm and provides proof of the advantages of the new design over the existing one.

Forthcoming Publications: This work has been submitted as a "Communications to the editor" to the Biotechnology and

Bioengineering journal.


DR NIGEL CASSIDY

Dr Nigel Cassidy worked in collaboration with Professor Dobson and Prof El Haj on Modelling the interaction of magnetic-electromagnetic fields with biocompatible magnetic nanoparticles for cell, drug and gene targeting. He also collaborated with Dr Sarah Cartmell in the area of Modelling/investigating the use of induced, low-frequency electrical signals for the stimulation and targeting of cell growth in bio-reactors between Aug 2010 & January 2011

Key Research Outcome :

The numerical models and experiments demonstrate that particular gene expressions can be significantly up-regulated/increased when simulated with optimised electrical The models also show that the electrode/sensor system design of the stimulation has a major influence on the success of this up-regulation and must be specifically tailored to account for changes in the properties of the cell culture medium.

Publications:

Balint, R., Cassidy, N. J. and Cartmell, S., 2011. The Effect Of Electrical Stimulation On Human Mesenchymal Stem Cell Behaviour, Tissue Engineering & Regenerative Medicine International Society EU (TERMIS EU) General meeting, Spain.

Balint, R., Cassidy, N.J., and Cartmell, S. 2011. The Influence of Electrical Stimulation on Primary Human Mesenchymal Stem Cell Activity. Transactions of The 12th Annual Conference of the Tissue and Cell Engineering Society (TCES) University of Leeds.

Forthcoming publications:

Balint, R., Cassidy, N. J. and Cartmell, S. The Effect Of Electrical Stimulation : a tool for tissue engineering. Journal of Cell Science, (to be submitted end October 2011).

Follow-on Funding:

Funded EPSRC DTA PhD studentship with Sarah Cartmell, Cassidy as joint Supervisor.

Loan of £11,000 „Phyback‟ Impulse electrotherapy system, from Impulse Medical Systems Ltd, Glasgow (new collaborative partnership).

3ME RiR-related Follow-on Funding

EPSRC DTG / Keele Acorn PhD studentship : “Development of novel hydro-chemical tracing methods (PADI-MS) for environmental and applications”. Lead-PI with F. Rutten & P. Roach (ISTM Keele).

Follow-on Funding Applications (Current):

AO foundation - Start up Grant : “Use of electrical stimulating regimes for bone tissue engineering” Cassidy Co-PI with Cartmell (€106,000).


Follow-on Funding Applications (Unsuccessful)

MRC Industrial CASE studentship : “Optimisation of novel cell/biomaterial constructs using electrical stimulating regimes (CoPIs Cartmell & Cassidy).

EPSRC Standard : “Virtual Environments for Medical Engineering (Ve-4-Me)”, EP/H024832/1. Cassidy Lead PI with ISTM staff (£250,000).

EPSRC Standard : “Modeling, Prototyping and Testing Novel Magnet Arrays for Nanomagnetic Applications in Biomedicine”, EP/I01666X/1 Dobson Lead PI, Cassidy as CoPI and ISTM staff (£250,000).

Leverhulme Trust : “Electrical Stimulation and Conductive Polymers in Tissue Engineering”, Cassidy Co-I with Cartmell (£58,000).

DR MICHAEL LUTIYANOV

Dr Michael Lutiyanov worked on various projects both with researchers in ISTM as well as clinicians based at Robert Jones and Agnes Hunt hospital, Oswestry during Aug 2010 to October 2010 as well as January 2011 to July 2011. For full details please see individual seed corn projects.


STUDENT TRAINING

The 3ME Initiative partly funded the Bioreactor Course 2010 held at Keele Management Centre and gave the opportunity to 30 Academics, PhD & MSc students from both ISTM and EPSAM to attend this 3-day interactive training course. The course aimed to provide delegates with a comprehensive understanding of the use of Bioreactors in Tissue Engineering and focused on bioreactors and growth environments for tissue engineering, covering bone, cartilage and connective tissue engineering.


APPENDICES

APPENDIX 1: SLIDES FROM THE OPENING MEEING




APPENDIX 2: FIRST SANDPIT PROGRAM



APPENDIX 3: SANDPIT PROCEEDINGS




APPENDIX 4: SECOND SANDPIT PROGRAM

Trearddur Bay Hotel, Isle of Anglesey, Wales

Monday 13th July 2009 (Pen Nant Room)

9.30am Mini buses depart: 24 hour reception, Main campus and Hartshill campus

12.00pm Lunch / Check in

2.00pm Keynote Speaker:

Dr Mark Davidson, Associate in Bioengineering, Microfabritech,

University of Florida

'Multimodal Studies of Iron Biominerals associated with Neurodegenerative

Disease: Moving from Science towards the Clinic’

3.30pm Coffee

4.00pm Short talks: ISTM & EPSAM Members

Prof David Smith, Professor of Chemical Physics, ISTM

‘ Breath Analysis at Keele: past, present and future’

Dr Michael Evans, Lecturer in Neuroscience, ISTM

‘Intracellular calcium concentration viewed / followed using imaging and

non-imaging methods’

Dr Frank Rutten, Lecturer in Physical Chemistry, EPSAM

‘The power of superficiality - application of surface chemical

analysis’

Dr Alastair Channon, Lecturer in Computer Science, EPSAM

'Many-Core Computing: technology for a step change in medical imaging

and modelling'

5.00pm Group Workshop to discuss Sandpit proposals (Group photo first!)

7.30pm Dinner – Pen Ross room

Tuesday 14th July 2009 (Pen Nant Room)

8.00am Breakfast / Check out

9.00am Short talks:

Prof Monica Spiteri, Professor in Respiratory Medicine, ISTM

‘Making sense of clinical and biological metrics for Development of

novel COPD Diagnostics’

Dr Josep Sule-Suso, Associate Specialist and Senior Lecturer in

Oncology, ISTM

‘Fourier Transform Infrared Spectroscopy of single cells towards a

clinical application in Pathology’

Dr Jan-Herman Kuiper, Lecturer in Biomechanics, ISTM

‘Of cells and patients - the need to understand them both’

10.15am Coffee


10.30am Group Workshop to discuss Sandpit proposals

12.30pm Lunch

1.30pm Invited Speaker

Mr Marius Cronje, Computational Modeller, CERAM

Discussion about requirements of modelling in the medical industry:

Finite Element Modelling (FEM) for thermal and stress analysis and

Computational Fluid Dynamics (CFD) for fluid flow analysis

2.30pm Presentation of Sandpit proposals

3.30pm Coffee

3.45pm Presentation of Sandpit proposals

4.45pm Close

5.00pm Depart


APPENDIX 5: BACK-TO-BACK SEMINARS

17 July 2008


2 February 2009


15 October 2009


11 October 2010


9 August 2011


APPENDIX 6: SEMINAR BY PROFESSOR YITONG ZHANG


APPENDIX 7: SEMINAR BY PROFESSOR KANNAN KRISHNAN


APPENDIX 8: SEMINAR BY PROFESSOR RALPH MULLER

Documents

FINAL REPORT - Keele University · There were several short talks by members of the 3ME Initiative on their areas of expertise, and Marius Kronje from CERAM Research in Stoke-on-Trent