研究领域
1 Synthetic Biology
Kitney has been undertaking research in the field of Synthetic Biology over the last eight years and is one of the international leaders. Synthetic Biology can be defined as aiming to design and engineer biologically based parts, devices and systems, as well as redesigning existing natural biological systems. The research has comprised the development of biologically based oscillators; biological logic gates and inverters; and biosensors. In addition, he has worked with his colleague Paul Freemont (a structural biologist) over the last few years to establish the Centre for Synthetic Biology and Innovation (CSynBI) at Imperial College (the Centre is now generally recognised as one of the leading international centres in the field and was the subject of a major EPSRC/BBSRC Science and Innovation Award).
The strategy for synthetic biology research comprises two components: (a) the development of platform (or foundational technology) which can be applied across a range of application areas, and (b) application projects. The sections below describe this approach in more detail; however, an even more detailed overview can be found in Kitney's IET Kelvin Lecture given earlier this year at The Royal institution http://tv.theiet.org/channels/news/19888.cfm
(a) Platform technology for synthetic biology
The development of platform technology is an important aspect of Kitney's work in synthetic biology. As described in the definition of synthetic biology we are creating synthetic biology devices and systems that are built from parts (BioParts) which reside in a Registry of Parts. Kitney has worked on the development of an information system for synthetic biology, as well as an extension of the DICOM standard (DICOM-SB). Both areas are described in subsequent sections.
(i) The web-based information system.
We have developed a web-based information system for synthetic biology - SynBIS. This comprises a four layer design (the interface or HTML layer, the communication layer - based on XML, the application layer, and the database layer - comprising a commercial SQL database). The system stores and displays information relating to BioParts (the Parts Registry); as well as chassis (cellular hosts) and the associated metadata. The information system also contains a repository of computer models for synthetic biology (from a range of sources). In addition, the system is also designed to incorporate a range of BioCAD software, which enables the high level design of gene circuits. The information system is being made available to members of the synthetic biology community via the CSynBI collaboration with the universities of Stanford and Berkeley in the US and Cambridge, Edinburgh and Newcastle.
(ii) DICOM-SB
DICOM-SB is an extension of the DICOM standard to synthetic biology. Kitney's research related to the DICOM standard is being extended to incorporate the data and metadata associated with different types of BioParts (e.g. promoters), as well as their associated chassis (hosts). The development of DICOM-SB is important because synthetic biology (and particularly the associated platform technology) is seen as having major industrial applications. As DICOM is widely used in biomedicine (industry, academia and healthcare), its extension to synthetic biology and its acceptance by international industry should be relatively straightforward.
(iii) Workflow
An important aspect of the work on synthetic biology over the last two years has been the development of workflow based on automation. This comprises the extensive use of laboratory robots for the characterisation of bioparts and gene circuits. The workflow is based upon SynBIS (described above) and comprises a number of stages which are illustrated in the figure below. The righthand side of the figure comprises a small diagram of a web page. Click on the image to see a larger version. As part of the workflow for bioparts we have developed web based datasheets which comprise a wide range of information relating to a particular part (particularly information relating to characterisation data and metadata).
(b) Application Project Areas
(i) Bio-logic gates
Kitney's work on bio-logic gates and inverters has been based on the pseudomonas syringae hrp regulatory system. In nature the regulatory system is based on a twin channel system which comprises a single inducer that acts simultaneously on two promoters. The system has been modified to separate the two channels so that an output is only obtained when both inputs are high (i.e. a logic state of 1). A synthetic biology based design has been successfully built and implemented to produce a stable AND gate. The work has also been extended to produce a NAND gate by incorporating a biological inverter. The ability to produce bio-logic gates is significant because these are the direct equivalents to electronic logic gates, which form the basis of all digital devices. The work is seen as highly significant because such gates could form the basis of a range of bio-logic devices; including, in the future, intracellular control devices.
The work on biological digital devices has now been successfully extended to a wider range of modular logical devices. For example, the development of a biologically based half-adder. Work is now ongoing to produce a full-adder. These devices together with the range of logic gates which we have developed will form the basis of more sophisticated biological digital control devices, eg, in relation to the development of more advanced biosensors.
(ii) Biosensors
The research on biosensors has, to date, focussed on the development of a biosensor for urinary tract infection (a common problem in the elderly who are singly incontinent and have indwelling catheters). The biosensor exploits the quorum sensing mechanism, in which a bacterial infection is based on a colony of cells (pseudomonas). The cells release a small signalling molecule called AHL which brings the colony together. The biosensor which Kitney and his colleagues have developed comprises a three stage biological device, designed on synthetic biology principles. The first stage comprises a detector which detects the AHL molecules. This triggers a response which is amplified (via the second stage, a biological amplifier) and the third stage comprises an indicator or reporter (green fluorescent protein). When the biosensor is applied to the area of the infection it fluoresces green. The work is now being extended to the detection of MRSA, using a modified version of the design. An additional development of the research on biosensors now comprises the creation of combined biosensors and delivery mechanisms based on protein nano-cages.
(iii) Bio-oscillators
The problem is to design and build stable molecular-based oscillators which can be controlled in terms of both amplitude and frequency. (This is important because such oscillators act as the clock for digital devices based on logic gates.) A study of previous molecular oscillators showed that they are inherently unstable. To overcome this problem a design was chosen which is based on Lotka-Voltera dynamics. An important aspect of the work was the use of what is called the synthetic biology design cycle; i.e., the cycle of device/system specification, design, modelling, implementation, and testing and validation. The Lotka-Voltera dynamic, in the context of a predation oscillator, amounts to a predator-prey approach this was used as the basis of oscillator designs. Oscillators were designed and detailed modelling undertaken to establish the modes of the dynamic; how they could be tuned for stability; and how to control their amplitude and frequency.
2 Biomedical Information Systems
An important theme of Kitney's research over the last 20 years has been the development of medical information systems capable of handling the complete range of medical information: text, numbers, physiological waveforms, still and moving images etc. Coupled to this has been extensive work on the development of a DICOM library. DICOM (Digital Imaging and Communications in Medicine) is the international standard for all medical images. Kitney's group has worked with the DICOM Committee in Washington on the development of the standard over many years. The standard http://medical.nema.org/ comprises over 3000 pages. Kitney's research group wrote a full implementation of the standard (i.e. a DICOM Library) -the software currently is around 450,000 lines of code. The DICOM standard now forms the basis of all medical scanners and other medical equipment throughout the world and the operation and integration of such equipment is achieved via the DICOM library. Over a number of years, Kitney's group has developed information systems which allow the integrated, storage and display of data and images from a wide range of medical devices. Part of this research was the subject of an Imperial College spinout company (www.visbion.com) which is now commercially successful with 400 systems in 10 countries. The company received a ComputerWorld Smithsonian Award in the USA. The research on medical information systems is currently continuing via an EPSRC-MRC funded Grand Challenge Project (in which Kitney is PI) under their Information Driven Health Initiative.
Kitney's research on medical information systems, MR and optical imaging has been extended to applications in multilevel imaging using OA in the human knee as an exemplar. In OA it is necessary to understand the progression of cartilage loss and study the effectiveness of therapeutic interventions. Hence, it is important to have accurate, fast diagnosis of the disease. Kitney's team has achieved this by developing a web-based system which includes a user interface that enables the direct viewing of 2-D and 3-D image data from the visceral and tissue levels - whilst preserving geometric integrity. This is achieved despite the fact that the data are from different modalities (i.e. MR and light microscopy). The interface allows the clinician to view both MR and light microscopy images in an integrated manner - with the information linked geometrically.
3. Analysis and modelling of cardio-respiratory and thermoregulatory activity
This work, which originally began when Kitney was a research student, involves the mathematical modelling and analysis of cardio-respiratory and thermoregulatory activity in humans. His paper, in Nature was one of the first to describe the importance of nonlinear oscillations in physiological systems. Kitney was one of the, half-dozen, international pioneers of the field of heart rate variability - now an important research field, with wide application in medicine and basic medical science. Over a number of years he worked on the development of new methods for the analysis of short-term variations in physiological signals, e.g., heart rate, blood pressure, respiration and thermoregulation and computer models of cardio-respiratory and thermoregulatory activity. In addition to the research on adults, Kitney undertook significant research on cardio-respiratory activity in babies and infants using and developing advanced signal processing methods. This resulted, for example, in a non-invasive test for potential sudden infant death (SIDS) - based on the relative response of the sympathetic and parasympathetic divisions of the autonomic nervous system - and the discovery of a very low frequency respiratory component in heart rate variability in infants. Much of this work has had significant clinical impact. In collaboration with clinical colleagues, Kitney developed a new type of cardio-respiratory baby monitor, which was produced by Space Labs Inc (a major American physiological monitoring company).
4. The study of arterial disease
(a) The analysis of blood flow
Arterial disease kills around 50% of the population of the western world; hence, accurate diagnosis is very important. Diseased tissue (plaque) progressively blocks arterial flow as it develops. Diagnosis of the disease largely relies on non-invasive ultrasound methods - where flow disturbance downstream of the disease site is measured and analysed. Over a number of years, Kitney and his group developed a suite of new methods for the analysis of blood flow and blood velocity waveforms, measured using different modalities - including ultrasound. These methods allow much more accurate delineation of the level of the disease by accurately determining the level of flow disturbance (which can be directly related back to degree of arterial occlusion). The methods are mainly (although not entirely) based on advanced spectral techniques. Kitney and his collaborators were amongst the very first to develop and apply these methods.
(b) Imaging and visualisation
Today arterial disease can also be studied by imaging the diseased tissue in 2D and 3D using ultrasound. In 3D this can be achieved by intravascular ultrasound systems (IVUS). Kitney and his group developed one of the first two IVUS (the first solid state IVUS ). He was responsible for leading the development - including miniature solid-state ultrasound probes on the end of arterial catheters (68 piezoelectric elements on a 0.9 mm tip), as well as the signal processing and the development of special user interfaces that allow the real-time manipulation of both voxel- and surface-rendered models. Kitney and his clinical collaborators developed the research through to a full commercial system by means of a spinout company. The system is marketed (primarily in the United States) by Volcano Inc.
5 Medical Imaging and Visualisation
Kitney's work on imaging and visualisation systems for the study of arterial disease was modified and developed for medical magnetic resonance (MR) imaging. The research under this category principally involves two areas: the imaging of osteoarthritis and the development of micro endoscopes - which can, for example, produce optical images of the inside of the spine.
(a) MR imaging of osteoarthritis
Osteoarthritis (OA) is a debilitating disease which affects a significant percentage of the population. In OA cartilage damage (due to wear and other causes) ultimately results in significant bone damage. This is a common problem in the human knee, and at this stage the general clinical solution is knee joint replacement. What is important is the ability to accurately assess cartilage and bone damage and to track the development of the disease. Traditionally this is done using x-rays; however, MR lends itself better to the assessment of cartilage and bone damage. Prior to the work of Kitney and his group the use of MR for this purpose had not been widely investigated. Over a number of years Kitney and his group developed novel methods related to the study of OA in the knee in three areas: the application of different MR sequences; the development of image processing methods for the study of cartilage and bone damage; and methods for the automatic reconstruction of 3D computer models of the knee from 2D MR data (using voxel techniques). One example of the results of the research was a collaborative project with Smith and Nephew plc. The company were developing cartilage implants grown from cells using tissue engineering techniques. The imaging and visualisation methods developed by Kitney's group allowed the tracking of the viability of implants in sheeps' knees over long periods.
(b) Micro endoscopes and MR tracking for spinal cord imaging
The work on the development of miniature ultrasonic probes for the IVUS system (described above) and the work on MR imaging and visualisation became important as a result of the commercial availability of a new type of MR scanner called an interventional MR scanner. This device enables real-time imaging during therapeutic intervention (i.e. with the patient in the scanner). The application which was proposed by clinical colleagues was optical imaging of spinal cord damage, under MR guidance, using micro endoscopes. (Spinal cord damage is relatively common, due to industrial and other accidents, and there is interest in the placement of stem cells to repair the spinal lesions.) The project was carried out in collaboration with radiologists in London and Los Angeles. Kitney and his group developed a micro endoscope which is MR compatible (i.e. the endoscope does not affect the MR image of the spine). The result of the project was the ability to track in real-time the micro endoscope using MRI and to obtain high quality, simultaneous images of the porcine spinal cord.
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Chambers S, Kitney R, Freemont P, 2016, The Foundry: the DNA synthesis and construction Foundry at Imperial College, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 44, Pages: 687-688, ISSN: 0300-5127
Coghlan A, Kitney R, 2016, Tiny but mighty, NEW SCIENTIST, Vol: 230, Pages: 7-7, ISSN: 0262-4079
Florea M, Hagemann H, Santosa G, Abbott J, Micklem CN, Spencer-Milnes X, Garcia LDA, Paschou D, Lazenbatt C, Kong D, Chughtai H, Jensen K, Freemont PS, Kitney R, Reeve B, Ellis Tet al., 2016, Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 113, Pages: E3431-E3440, ISSN: 0027-8424
de Murieta IS, Bultelle M, Kitney RI, 2016, Toward the First Data Acquisition Standard in Synthetic Biology, ACS SYNTHETIC BIOLOGY, Vol: 5, Pages: 817-826, ISSN: 2161-5063
Bultelle MA, Sainz De Murieta I, Kitney RI, 2015, Introducing synbis - The synthetic biology information system, Pages: 838-842
Kelwick R, Kopniczky M, Bower I, Chi W, Chin MHW, Fan S, Pilcher J, Strutt J, Webb AJ, Jensen K, Stan G-B, Kitney R, Freemont Pet al., 2015, A Forward-Design Approach to Increase the Production of Poly-3-Hydroxybutyrate in Genetically Engineered Escherichia coli, PLOS ONE, Vol: 10, ISSN: 1932-6203
Sainz De Murieta I, Bultelle MA, Kitney RI, 2015, A dicom extension supporting data acquisition in synthetic biology, Pages: 948-951
Tay D, Poh CL, Kitney RI, 2015, A novel neural-inspired learning algorithm with application to clinical risk prediction, JOURNAL OF BIOMEDICAL INFORMATICS, Vol: 54, Pages: 305-314, ISSN: 1532-0464
Tay D, Poh CL, Van Reeth E, Kitney RIet al., 2015, The Effect of Sample Age and Prediction Resolution on Myocardial Infarction Risk Prediction, IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS, Vol: 19, Pages: 1178-1185, ISSN: 2168-2194
Wong A, Wang H, Poh CL, Kitney RIet al., 2015, Layering genetic circuits to build a single cell, bacterial half adder, BMC Biology, Vol: 13, ISSN: 1741-7007
Dickinson RJ, Kitney RI, 2014, Information driven care pathways and procedures, IFMBE Proceedings, Vol: 41, Pages: 1322-1325, ISSN: 1680-0737
Luboz V, Kyaw-Tun J, Sen S, Kneebone R, Dickinson R, Kitney R, Bello Fet al., 2014, Real-time stent and balloon simulation for stenosis treatment, VISUAL COMPUTER, Vol: 30, Pages: 341-349, ISSN: 0178-2789
Tay D, Poh CL, Goh C, Kitney RIet al., 2014, A biological continuum based approach for efficient clinical classification, JOURNAL OF BIOMEDICAL INFORMATICS, Vol: 47, Pages: 28-38, ISSN: 1532-0464
Kelay T, Kesavan S, Collins RE, Kyaw-Tun J, Cox B, Bello F, Kneebone RL, Sevdalis Net al., 2013, Techniques to aid the implementation of novel clinical information systems: A systematic review, INTERNATIONAL JOURNAL OF SURGERY, Vol: 11, Pages: 783-791, ISSN: 1743-9191
Tay D, Poh CL, Kitney RI, 2013, An Evolutionary Data-Conscious Artificial Immune Recognition System, 15th Genetic and Evolutionary Computation Conference (GECCO), Publisher: ASSOC COMPUTING MACHINERY, Pages: 1101-1108
Baldwin G, Bayer T, Dickinson R, Ellis T, Freemont PS, Kitney RI, Polizzi K, Stan GBet al., 2012, Synthetic Biology - A Primer, ISBN: 9781848168640
Kitney R, Freemont P, 2012, Synthetic biology - the state of play, FEBS LETTERS, Vol: 586, Pages: 2029-2036, ISSN: 0014-5793
Yang X, Han R, Guo Y, Bradley J, Cox B, Dickinson R, Kitney Ret al., 2012, Modelling and performance analysis of clinical pathways using the stochastic process algebra PEPA, BMC BIOINFORMATICS, Vol: 13, ISSN: 1471-2105
MacDonald JT, Barnes C, Kitney RI, Freemont PS, Stan G-BVet al., 2011, Computational design approaches and tools for synthetic biology, INTEGRATIVE BIOLOGY, Vol: 3, Pages: 97-108, ISSN: 1757-9694
Wang B, Kitney RI, Joly N, Buck Met al., 2011, Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology, NATURE COMMUNICATIONS, Vol: 2, ISSN: 2041-1723
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