Technologies and Techniques for Single Cell Proteomics and Lipidomics: Nanodigestion and Analysis of a Single Cell Plasma Membrane
Lead Research Organisation:
Imperial College London
Department Name: Chemistry
Abstract
The human genome project and those aimed as sequencing the genomes of other organisms tell us the codes that are present in an organism for generating proteins. Of course nearly every cell in the body contains a complete copy of those codes yet there are numerous cell types within the body performing a wide range of different functions, even within the same tissue we can clearly identify different cell types that are performing widely different functions. What makes these cell types different is fundamentally the different level of expression of the genes that they contain, in other words the genes that are switched on and therefore the proteins that are manufactured within those cells. However that is not the whole story. Even if we know what genes are switched on in a cell, the down stream activity of those proteins is really what is important in determining cell functionality. Proteins will move within the cell, they will interact and transform depending on those interactions. In addition the cells contain a wide variety of other chemical species, not least of which are lipids. While not directly coded by the genome, the production of lipids within the cell is controlled by the proteins present and interactions involving lipids are equally important in cell function as those involving proteins.One important area where understanding of the mechanisms behind cell function is at the cell membrane, as it is here that the cell interacts with its environment and with other cells. The ability to determine which molecular species are present within the cell membrane, particularly in areas where we can identify some sort of activity will be key to developing this understanding. This proposal is an ambitious project to construct instrumentation that can take individual cells, extract those molecules from identified areas of the plasma membrane, and analyse them using optical techniques to determine the chemical structures that they contain. The proposed instrumentation draws together a number of individual technologies from across Imperial College: The whole process will take place in microfluidic devices where fluids can be handled in nano-litre volumes to digest and separate molecules from cells and from each other: Multi-dimensional fluorescence imaging techniques will be used to highlight the interesting and active areas on the cell membrane and to monitor the digestion process: Optical trapping will be used to hold and manipulate the individual cells within the microfluidic flow to allow targeting of specific areas of the cell membrane: 2d non-linear infra-red spectroscopy techniques will be used to analyse the digested components and determine their structure.
Organisations
- Imperial College London (Lead Research Organisation)
- Biotechnology and Biological Sciences Research Council (Co-funder)
- University of California (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- STFC Laboratories (Collaboration)
- ASTON UNIVERSITY (Collaboration)
- Oxford Gene Technology (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- AstraZeneca (Collaboration)
- University of Tokyo (Collaboration)
- DURHAM UNIVERSITY (Collaboration)
- UNIVERSITY OF GLASGOW (Collaboration)
- BRUNEL UNIVERSITY LONDON (Collaboration)
- Nanoink (Collaboration)
- UNIVERSITY OF LEEDS (Collaboration)
- GlaxoSmithKline (GSK) (Collaboration)
Publications
Benninger RK
(2007)
Fluorescence-lifetime imaging of DNA-dye interactions within continuous-flow microfluidic systems.
in Angewandte Chemie (International ed. in English)
Benninger R
(2007)
Fluorescence-Lifetime Imaging of DNA-Dye Interactions within Continuous-Flow Microfluidic Systems
in Angewandte Chemie International Edition
Lanigan PM
(2008)
Spatially selective sampling of single cells using optically trapped fusogenic emulsion droplets: a new single-cell proteomic tool.
in Journal of the Royal Society, Interface
Fournier F
(2008)
Protein identification and quantification by two-dimensional infrared spectroscopy: implications for an all-optical proteomic platform.
in Proceedings of the National Academy of Sciences of the United States of America
Niu X
(2009)
Droplet-based compartmentalization of chemically separated components in two-dimensional separations
in Chemical Communications
Lanigan PM
(2009)
A microfluidic platform for probing single cell plasma membranes using optically trapped Smart Droplet Microtools (SDMs).
in Lab on a chip
Fournier F
(2009)
Biological and Biomedical Applications of Two-Dimensional Vibrational Spectroscopy: Proteomics, Imaging, and Structural Analysis
in Accounts of Chemical Research
Guo R
(2009)
Detection of complex formation and determination of intermolecular geometry through electrical anharmonic coupling of molecular vibrations using electron-vibration-vibration two-dimensional infrared spectroscopy.
in Physical chemistry chemical physics : PCCP
Donaldson PM
(2010)
Generation of simplified protein Raman spectra using three-color picosecond coherent anti-stokes Raman spectroscopy.
in The journal of physical chemistry. B
Goyder Miriam Sarah
(2011)
Capillary electrophoresis with multiple readout techniques for protein analysis
Guo R
(2011)
Potential for the detection of molecular complexes and determination of interaction geometry by 2DIR: application to protein sciences.
in Faraday discussions
Salehi-Reyhani A
(2011)
A first step towards practical single cell proteomics: a microfluidic antibody capture chip with TIRF detection.
in Lab on a chip
Kaplinsky Joseph John
(2012)
Single cell analysis and cell sorting using microfluidic devices with application to circulating tumour cells
Lanigan PM
(2012)
Dynamical hologram generation for high speed optical trapping of smart droplet microtools.
in Biomedical optics express
Guo R
(2012)
Geometry determination of complexes in a molecular liquid mixture using electron-vibration-vibration two-dimensional infrared spectroscopy with a vibrational transition density cube method.
in Physical chemistry chemical physics : PCCP
Goyder MS
(2012)
Affinity chromatography and capillary electrophoresis for analysis of the yeast ribosomal proteins.
in BMB reports
Salehi-Reyhani Ali
(2012)
Tools for single cell proteomics
Burgin Edward Philip
(2012)
The design of a digital single-molecule detection platform, with direct application to single cell analysis
Salehi-Reyhani A
(2013)
Scaling advantages and constraints in miniaturized capture assays for single cell protein analysis.
in Lab on a chip
Phillips John Robert
(2013)
Optical traps for single cell analysis
Salehi-Reyhani A
(2015)
Chemical-free lysis and fractionation of cells by use of surface acoustic waves for sensitive protein assays.
in Analytical chemistry
Sowley H
(2019)
Detection of Drug Binding to a Target Protein Using EVV 2DIR Spectroscopy.
in The journal of physical chemistry. B
Osman S
(2021)
Evaluation of FOXO1 Target Engagement Using a Single-Cell Microfluidic Platform.
in Analytical chemistry
| Title | Doctoral Training Centre Den 2010 Video |
| Description | Video of finalist group from the SCP group pitching scientific ideas to judges comprising of Heads of Research Councils. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2010 |
| Title | MAC chip animatiosn |
| Description | A series of animations showing the use of the MAC chip platform step by step. These animations follow one single cell taken from the blood of a cancer patient and follow it through optical trapping, optical lysis and finally single molecules detection of the proteins within. Each animation is overlayed with real video footage from a device for comparison. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2013 |
| Impact | These animations have been used by multiple members of the group for presentation purposes and have received a lot of interest. For example the animations were used by a PhD student in his end of PhD postgraduate symposium which lead to him receiving the second place prize for final year PhD talk. |
| Title | Promotional video for the Chemical Biology Centre SCP/RASOR Technology Showcase event, 30 June 2010 |
| Description | Demonstration of track writing |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2010 |
| Title | Recordings of trapping optimisation and blob manipulation |
| Description | Recordings of trapping optimisation and blob manipulation - see supplementary data on Biomedical Optics Express, 2012, 3, 1609-1619 paper for examples. |
| Type Of Art | Image |
| Description | The main aim of the project was to construct instrumentation that can take individual cells, extract those molecules from identified areas of the plasma membrane, and analyse them using optical techniques to determine the chemical structures that they contain. Prototype versions of three unique proteomics platforms (labelled platforms 'Microfludic Antibody Capture (MAC) Chip' and 'Smart Droplet Microtools (SDMs)' and label free platform '2DIR') were established and evaluated. The first is a microfluidic chip-based fluorescently labelled platform with a single molecule read-out. Fluids can be handled in nano-litre volumes to digest and separate molecules from cells and from each other. Fluorescence imaging techniques are used to highlight interesting areas on the cell membrane and to monitor the digestion process. This technology has the ability to reliably use single-molecule read-out in an antibody affinity assay and the ability to reliably use nanodigestion to spatially select parts of the cell membrane for read-out. The second is a labelled platform which was developed for spatially selective chemical digestion of single cells (nanodigestion) using SDMs, oil microdroplets coated with amphiphilic monolayers. SDMs are manipulated using optical traps in microfluidic environments and allow us to perform biopsies on the cellular scale. We have demonstrated that following controlled cell-SDM interactions protein transfer to the SDM from the target cell occurs via specific contact points with SDMs acting as storage vehicles for the uptaken plasma membrane material. Each SDM can then be used downstream for proteomics analysis. The third is a label free platform using 2DIR and spectroscopic methods for a readout of proteins separated by reverse phase chromatography and capillary separation. The strength of this platform lies in the novel approach to protein identification coupled with intrinsic ability to add value over and above protein counting. We have successfully increased the sensitivity of the 2DIR platform by over three orders of magnitude, discovered another potential non-linear spectroscopic route to protein identification using Coherent Anti Stokes Raman CARS spectroscopy and determined the utility of the method for measuring phosphorylation and other potential added value approaches to proteomics analysis. |
| Exploitation Route | The main application of the technology is in healthcare where the technology can be adapted for use as clinical diagnostic tools. We are currently running a clinical evaluation of the technology applied to detection of sexually transmitted diseases. This has the potential to allow earlier and more effective intervention and to improve patient care. We also plan to develop this technology further for the detection of infectious diseases. Another clinical area where the technology is directly applicable is in oncology. We plan to use our single cell proteomic technology to track CTCs in breast cancer patients to follow development of resistance to drug treatment. This will allow clinicians to decide earlier and more accurately what drug regimen to use and when to change from one drug to another. There are two main ways in which this research is being exploited. Firstly there is its application for the study of biology in order to further our understanding of a range of important biological functions. For example heterogeneity and specialisation of cells in bacterial populations where it is believed that not all cells are behaving identically at any one time and that there can be co-operativity between them. Similarly in humans, cells of one type although nominally identical are in fact not, which gives rise to variable function and response to drugs. By studying cell to cell variation it is also possible to understand better the molecular networks that make cells function, and as our measurement methods are both accurate and precise, the data can be used for better modelling of biological processes to allow the development of predictive models which can help to put our understanding of biology onto a much more rigorous footing. In fact we have already been successful in generating funding to apply these methods to some biological networks as described. The second route for exploitation is in healthcare. The very high sensitivity of these methods means that they can be adapted for use as a diagnostic tool. We are currently running a clinical evaluation of the technology applied to detection of sexually transmitted diseases. The benefit is that the miniaturisation allows for a rapid readout as well as a sensitive readout so that there is the potential for clinicians to obtain a test result in a few minutes. This means that positive patients can be treated on the spot without having to be sent home first, and that negative patients can obtain rapid reassurance. There are a number of other infectious diseases which could also benefit from this approach and we plan to develop this technology further for detection of infection. The second clinical area where the technology is directly applicable is in oncology. Patients with solid tumours usually have circulating tumour cells (CTCs) in their bloodstream. It is these CTCs which create secondary tumours (metastases) which are usually the cause of death. CTCs potentially give an insight into the state of health of the patient and how they are responding to treatment. We plan to use our single cell proteomic technology to track CTCs in breast cancer patients to follow development of resistance to drug treatment. This will allow clinicians to decide earlier and more accurately what drug regimen to use and when to change from one drug to another. Equipment prototypes built as part of the research has also been turned into a facility and a consortium of around 50 research collaborators are making use of the facility for subsequent biological projects. The equipment is also available for further technological development. As of 2017 we are now putting the technology to active use in collaborations with clinicians. We have a project with NHLI/Brompton hospital in using the MAC chip to follow the development of senescence in immune cells recovered from sputum from patients with COPD. Another study has been completed in collaboration with ICR and The Marsden hospital to show that we can analyse the heterogeneity in tumour xenograft samples. Finally we are starting a new project in collaboration with Kings College to undertake analysis of the status of immune cells in human tumour xenografts. |
| Sectors | Healthcare Pharmaceuticals and Medical Biotechnology |
| URL | http://www.singlecellanalysis.ac.uk/ |
| Description | Application of Microfluidic Antibody Capture (MAC) chips to Circulating Tumour Cells (CTCs) and the detection of infectious diseases. Opened up a new subject area, Single Cell Analysis. This work is now being used for the non invasive analysis of living cells in sputum from COPD patients. We have shown that we are able to identify senescence in cells from patients with COPD compared with healthy subjects. |
| Sector | Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic |
| Description | Applications of 2DIR/Proteome on a chip to cardiovascular problems |
| Amount | £200,000 (GBP) |
| Funding ID | RE/08/002 |
| Organisation | British Heart Foundation (BHF) |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2008 |
| End | 03/2014 |
| Description | Applications of 2DIR/Proteome on a chip to cardiovascular problems |
| Amount | £200,000 (GBP) |
| Funding ID | RE/08/002 |
| Organisation | British Heart Foundation (BHF) |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2008 |
| End | 03/2014 |
| Description | Cellular Information Processing and Decision Making from Noise to Robust Phenotypes |
| Amount | £260,264 (GBP) |
| Funding ID | RGP0061/2011 |
| Organisation | Human Frontier Science Program (HFSP) |
| Sector | Charity/Non Profit |
| Country | France |
| Start | 12/2011 |
| End | 11/2014 |
| Description | Cellular Information Processing and Decision Making from Noise to Robust Phenotypes |
| Amount | £260,264 (GBP) |
| Funding ID | RGP0061/2011 |
| Organisation | Human Frontier Science Program (HFSP) |
| Sector | Charity/Non Profit |
| Country | France |
| Start | 12/2011 |
| End | 11/2014 |
| Description | Chembecell Ltd |
| Amount | £150,000 (GBP) |
| Organisation | Imperial Innovations |
| Sector | Private |
| Country | United Kingdom |
| Start | 01/2007 |
| End | 02/2010 |
| Description | Chembecell Ltd |
| Amount | £150,000 (GBP) |
| Organisation | Imperial Innovations |
| Sector | Private |
| Country | United Kingdom |
| Start | 01/2007 |
| End | 02/2010 |
| Description | Clinical Demonstration of Point of Care Diagnostics Using Microfluidic Chips with Single Molecule Sensitivity for the Detection of Infectious Diseases |
| Amount | £277,094 (GBP) |
| Funding ID | P31601 |
| Organisation | Agency for Science, Technology and Research (A*STAR) |
| Department | Biomedical Research Council |
| Sector | Academic/University |
| Country | Singapore |
| Start | 07/2010 |
| End | 01/2013 |
| Description | Clinical Demonstration of Point of Care Diagnostics Using Microfluidic Chips with Single Molecule Sensitivity for the Detection of Infectious Diseases |
| Amount | £277,094 (GBP) |
| Funding ID | P31601 |
| Organisation | Agency for Science, Technology and Research (A*STAR) |
| Department | Biomedical Research Council |
| Sector | Academic/University |
| Country | Singapore |
| Start | 07/2010 |
| End | 01/2013 |
| Description | Collaboration with Tsinghua University |
| Amount | £22,500 (GBP) |
| Funding ID | EP/K503381/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2012 |
| End | 03/2013 |
| Description | Collaboration with Tsinghua University |
| Amount | £22,500 (GBP) |
| Funding ID | EP/K503381/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2012 |
| End | 03/2013 |
| Description | Collaboration with Tsinghua University |
| Amount | £22,500 (GBP) |
| Funding ID | EP/K503381/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2012 |
| End | 03/2013 |
| Description | Detection of binding and geometry determination of drug-protein interactions in a kinase binding site from EVV 2DIR Data |
| Amount | £500,000 (GBP) |
| Funding ID | 1373757 |
| Organisation | AstraZeneca |
| Sector | Private |
| Country | United Kingdom |
| Start | 09/2012 |
| End | 09/2016 |
| Description | Detection of binding and geometry determination of drug-protein interactions in a kinase binding site from EVV 2DIR Data |
| Amount | £500,000 (GBP) |
| Funding ID | 1373757 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2012 |
| End | 09/2016 |
| Description | Detection of binding and geometry determination of drug-protein interactions in a kinase binding site from EVV 2DIR Data |
| Amount | £500,000 (GBP) |
| Funding ID | 1373757 |
| Organisation | AstraZeneca |
| Sector | Private |
| Country | United Kingdom |
| Start | 09/2012 |
| End | 09/2016 |
| Description | Diagnosing Cancer one Cell at a Time with Single Molecule Spectroscopy |
| Amount | £132,578 (GBP) |
| Funding ID | EP/F500416/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2012 |
| End | 09/2016 |
| Description | Elements of a Vesicle Machine |
| Amount | £201,409 (GBP) |
| Funding ID | EP/H024425/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2010 |
| End | 03/2011 |
| Description | GATA Protein Complexes in Stem Cell Development |
| Amount | £100,000 (GBP) |
| Funding ID | RE/08/002 |
| Organisation | British Heart Foundation (BHF) |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2010 |
| End | 09/2013 |
| Description | GATA Protein Complexes in Stem Cell Development |
| Amount | £100,000 (GBP) |
| Funding ID | RE/08/002 |
| Organisation | British Heart Foundation (BHF) |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2010 |
| End | 09/2013 |
| Description | Membrane Biophysics Platform |
| Amount | £1,356,571 (GBP) |
| Funding ID | EP/G00465X/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2009 |
| End | 01/2014 |
| Description | Next Generation Analytical Tools: Application to Protein Oxidations that affect Human Health and Wellbeing |
| Amount | £3,885,167 (GBP) |
| Funding ID | EP/I017887/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2011 |
| End | 02/2016 |
| Description | Novel Tools for Single Cell Manipulation |
| Amount | £101,750 (GBP) |
| Funding ID | EP/I031561/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2011 |
| End | 08/2012 |
| Description | Optical Control of Emulsion Drops for Nanofluidics and Microfabrication |
| Amount | £1,624,366 (GBP) |
| Funding ID | EP/I013377/1, EP/I013237/1, EP/I013342/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2011 |
| End | 03/2015 |
| Description | Phosphorylation regulation of protein association using coherent two-dimensional infrared spectroscopy |
| Amount | £100,000 (GBP) |
| Funding ID | EP/F500416/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2009 |
| End | 09/2013 |
| Description | Sculpting Dynamic Amphiphilic Structures |
| Amount | £4,772,920 (GBP) |
| Funding ID | EP/J017566/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2012 |
| End | 05/2017 |
| Description | Single Cell Proteomics for Studying Circulating Tumour Cells and Monitor Disease Progression on Breast Cancer Patients |
| Amount | £157,773 (GBP) |
| Funding ID | PIEF-GA-2011-302649 CTCPROTEOMIC |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 08/2012 |
| End | 09/2014 |
| Description | Single Cell Proteomics for Studying Circulating Tumour Cells and Monitor Disease Progression on Breast Cancer Patients |
| Amount | £157,773 (GBP) |
| Funding ID | PIEF-GA-2011-302649 CTCPROTEOMIC |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 08/2012 |
| End | 09/2014 |
| Description | Single cell analysis |
| Amount | £3,500 (GBP) |
| Funding ID | EP/I037172/1 and EP/I037210/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2012 |
| End | 03/2013 |
| Description | The MAPK interactome and its role in hypertrophic responses studied by single cell proteomics |
| Amount | £100,000 (GBP) |
| Funding ID | RE/08/002 |
| Organisation | British Heart Foundation (BHF) |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2010 |
| End | 09/2014 |
| Description | The MAPK interactome and its role in hypertrophic responses studied by single cell proteomics |
| Amount | £100,000 (GBP) |
| Funding ID | RE/08/002 |
| Organisation | British Heart Foundation (BHF) |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2010 |
| End | 09/2014 |
| Title | Chip surface passivation protocols |
| Description | To limit the amount of non-specific binding to surface to maintain sensitivity silane, PEG and 3D polymer based surface chemistry was investigated. It was determined that silane based chemistry is appropriate for DNA assays whereas PEG based chemistries are better suited for protein assays. |
| Type Of Material | Improvements to research infrastructure |
| Provided To Others? | No |
| Impact | These passivated slides are required for use with the MAC chip platform a vital part of the Proxomics project. |
| Title | DNA capture probes |
| Description | DNA capture probes for unamplified single cell mRNA detection of GFP and p53 |
| Type Of Material | Cell line |
| Provided To Others? | No |
| Title | Microfluidic Antibody Capture Chips |
| Description | Designed and built microfluidic antibody capture chips, an all optical platform for the quantification of protein in single cells. Cells are loaded into these devices, transported to analysis chambers using an optical trap and then ruptured with the use of a high powered optical lysis laser. The intracellular contents are then quantified by the use of a miniaturized ELISA format. Proteins bind to antibodies on the surface of the device and a secondary fluorescent antibody, present in solution completes the sandwich system. Total Internal Reflection Fluorescence (TIRF) microscopy is then used to detect and count the amount of protein that has bound to the antibody spot. |
| Type Of Material | Technology assay or reagent |
| Provided To Others? | No |
| Impact | The use of MAC chips dominates an entire work stream in the Proxomics project and has resulted in a number of publications. |
| Title | Microfluidic antibody capture (MAC) chip design |
| Description | A microfluidic antibody capture chip was designed to allow to isolation of single cells from a population, their subsequent lysis and binding of a protein or proteins of interest to an antibody patch. Separate designs for the isolation of single, few (1-5) and many (10-100) cells from flow were also made. |
| Type Of Material | Technology assay or reagent |
| Provided To Others? | No |
| Impact | MAC chips dominate an entire workstream of the proxomics project and have resulted in a number of publications. |
| Title | Microfluidic chips design for handling Smart Droplet Microtools and cells |
| Description | Microfluidic chips design for handling Smart Droplet Microtools and cells |
| Type Of Material | Technology assay or reagent |
| Provided To Others? | No |
| Impact | Smart Droplet microtools and the associated platform have led to the publication of several papers. |
| Title | PTEN antibody Cell lines |
| Description | Production of hybridoma cell lines with EMBL antibody facility, Monoterotondo, Italy (GST-PTEN Hybridoma 10D9/C8, GST-PTEN Hybridoma 4F7/B3 and GST-PTEN Hybridoma 10D9/G4). |
| Type Of Material | Cell line |
| Provided To Others? | No |
| Title | Protocols for cell handling onto chips |
| Description | Cells were detached from flasks using gentle tryptic agents and filtered using a nylon mesh. Cells are suspended in media using a CO2 independent buffer. Cells are delivered via capillary tubing. |
| Type Of Material | Improvements to research infrastructure |
| Provided To Others? | No |
| Impact | Cells are used in microfluidic devices for both the MAC chip and SDM platforms both of which have resulted in publications |
| Title | SAWN LC/MS |
| Description | Combination of the SAW nebulsation with mass spectroscopy for a more gentle sample prep |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2012 |
| Provided To Others? | Yes |
| Impact | The technique may potential be used in standard proteomic mass spectroscopy work flows where electrospray is deemed unsuitable |
| Title | Screening and development of microfluidic-chip compatible antibody reagents |
| Description | Screening and development of microfluidic-chip compatible antibody reagents for detection and quantification of proteins on the ATK network axis for single cell studies. [AKT, PTEN, p53, MDM2, MAP4K4, GATA, ER]. |
| Type Of Material | Antibody |
| Provided To Others? | No |
| Title | Single Cell Antibody printing |
| Description | All antibodies were printed by an OmniGrid Micro microarrayer (Digilab, UK) using 946MP2 pins (ArrayIt, USA). Spotting solution was optimised for DNA, antibody, protein or cell-lysate printing. |
| Type Of Material | Improvements to research infrastructure |
| Provided To Others? | No |
| Impact | Antibody printing is a vital step in the MAC chip platform. This platform is a vital part of the proxomics project and has resulted in a number of publications. |
| Title | Single Cell Trapping array |
| Description | A microfluidic device optimised for capturing cells in an array for subsequent single cell analysis |
| Type Of Material | Technology assay or reagent |
| Provided To Others? | No |
| Impact | Will be of interest in the field of microfluidics and single cell analysis. Poster describing the method was shortlisted for poster prize at Microfluidics 2014 conference |
| Title | Sorting of Low Abundance Cells from Small Clinical Samples for downstream single cell analysis |
| Description | We have shown that it is possible to use the laser trap in combination with surface markers to select cells of interest from a heterogeneous mix. The cells are selected by type and then moved into the analysis section of the MAC chip for assessment of their signalling status as read out by protein copy number and PTM condition. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | We are now in a position to demonstrate the utility of this approach in clinical contexts. A pilot project with ICR has been completed and a paper submitted and is under review. Two other projects are underway, one with NHLI/Brompton Hospital on COPD and another with Kings College on the activation status of immune cells in human tumours. |
| Title | Surface Acoustic Wave Nebulisation |
| Description | A novel form of biological molecule ionisation for mass spectrometric analyses. Has the potential to supplement existing methods in specialised applications |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2012 |
| Provided To Others? | Yes |
| Impact | Enabled the investigation of fragile molecules and hopefully allow larger fragments to be analysed via Mass Spec |
| Title | TIRF-FLIM system |
| Description | Combined total internal reflection fluorescence lifetime imaging system for improved resolution to conventional fluorescence lifetime imaging techniques |
| Type Of Material | Improvements to research infrastructure |
| Provided To Others? | No |
| Impact | Enhanced the capabilities of standard fluorescence lifetime imaging through improved axial resolution. Technology is of particular use for investigations of dynamics in biological membranes. |
| Title | Validated existing antibodies |
| Description | Validated existing antibodies for protein targets including AKT, GSK-3beta, 14-3-3 beta/alpha, Bad, Chk1, IKK-a, p27 (Kipl), Raf, S6 Ribosomal Protein, L26 Ribosomal Protein, S3 Ribosomal Protein, PTEN, p53, MDM2, Cytokeratins (8,18, 19), GFP, EPCAM, SOX17, Brachyury, Estrogen Receptor alpha, MAP4K4, GATA, ER. |
| Type Of Material | Cell line |
| Provided To Others? | No |
| Title | 2DIR spectra analysis for proteins/peptides comparison and quantification |
| Description | 2DIR spectra analysis for proteins/peptides comparison and quantification |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2008 |
| Provided To Others? | No |
| Title | Cube-integral method for structural determination with EVV 2DIR spectroscopy |
| Description | A new computational approach based on full electrostatic interactions between first-principle transition density cubes. It has been applied to accurate geometry determination from experimental EVV 2DIR spectra. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2012 |
| Provided To Others? | No |
| Title | Hologram generation in GLSL (on the GPU) |
| Description | Hologram generation in GLSL (on the GPU) |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2012 |
| Provided To Others? | No |
| Title | MD trajectory of wide-type Trp-cage, and liquid molecular complexes |
| Description | MD trajectory of wide-type Trp-cage, and liquid molecular complexes to understand the aromatic-aromatic interaction. H2 bonding calculations on tyrosine, tryptophan. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2012 |
| Provided To Others? | No |
| Description | Dr Alex Breeze |
| Organisation | AstraZeneca |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Dr Alex Breeze is a supervisor of a joint student funded by AstraZeneca and Centre for Doctoral Training in Chemical Biology. Project is 'Detection of binding and geometry determination of drug-protein interactions in a kinase binding site from EVV 2DIR Data'. |
| Start Year | 2012 |
| Description | Dr Alex Lubansky |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Alex Lubansky is a collaborator and a co-I on the grant 'Optical Control of Emulsion Drops for Nanofluidics and Microfabrication'. |
| Start Year | 2011 |
| Description | Dr Andy Thomas |
| Organisation | AstraZeneca |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Dr Andy Thomas is a supervisor of a joint student funded by AstraZeneca and Centre for Doctoral Training in Chemical Biology. Project is 'Protein-protein interactions in cancer studied by femtosecond laser analogues of 2D NMR'. |
| Start Year | 2011 |
| Description | Dr Andy Ward |
| Organisation | STFC Laboratories |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Dr Andy Ward, STFC Laboratories, is a collaborator and a co-I on the grant 'Optical Control of Emulsion Drops for Nanofluidics and Microfabrication'. |
| Start Year | 2011 |
| Description | Dr Annette Jepson |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Annette Jepson is a co-I on the Biomedical Research Council (BRC) grant: 'Clinical Demonstration of Point of Care Diagnostics Using Microfluidic Chips with Single Molecule Sensitivity for the Detection of Infectious Diseases'. |
| Start Year | 2010 |
| Description | Dr Buddhapriya Chakrabarti |
| Organisation | Durham University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Buddhapriya Chakrabarti is a collaborator and a co-I on the grant 'Optical Control of Emulsion Drops for Nanofluidics and Microfabrication'. |
| Start Year | 2011 |
| Description | Dr Corinne Spickett |
| Organisation | Aston University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Corinne Spickett is a collaborator and co-I on the grant 'Next Generation Analytical Tools: Application to Protein Oxidations that affect Human Health and Wellbeing'. |
| Start Year | 2011 |
| Description | Dr David Tew |
| Organisation | GlaxoSmithKline (GSK) |
| Department | Research and Development GSK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Dr David Tew is a collaborator at GSK. The collaboration uses the Microfluidic Antibody Capture (MAC) chip technology for miniaturised drug screens using human primary cells/tissue. |
| Start Year | 2013 |
| Description | Dr Gordon Love |
| Organisation | Durham University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Gordon Love is a collaborator and a co-I on the grant 'Optical Control of Emulsion Drops for Nanofluidics and Microfabrication'. |
| Start Year | 2011 |
| Description | Dr Graham Taylor |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Graham Taylor is a co-I on the Biomedical Research Council (BRC) grant: 'Clinical Demonstration of Point of Care Diagnostics Using Microfluidic Chips with Single Molecule Sensitivity for the Detection of Infectious Diseases' |
| Start Year | 2010 |
| Description | Dr John Sanderson |
| Organisation | Durham University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr John Sanderson is a collaborator and co-I on grant 'Sculpting Dynamic Amphiphilic Structures'. |
| Start Year | 2012 |
| Description | Dr Lian Hutchings |
| Organisation | Durham University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Lian Hutchings is a collaborator and a co-I on the grant 'Optical Control of Emulsion Drops for Nanofluidics and Microfabrication'. |
| Start Year | 2011 |
| Description | Dr Panagiotis Pantelidis |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Panagiotis Pantelidis is a co-I on the Biomedical Research Council (BRC) grant: 'Clinical Demonstration of Point of Care Diagnostics Using Microfluidic Chips with Single Molecule Sensitivity for the Detection of Infectious Diseases'. |
| Start Year | 2010 |
| Description | Dr Peter Kelleher |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Peter Kelleher is a co-I on the Biomedical Research Council (BRC) grant: 'Clinical Demonstration of Point of Care Diagnostics Using Microfluidic Chips with Single Molecule Sensitivity for the Detection of Infectious Diseases'. |
| Start Year | 2010 |
| Description | Dr Pietro Cicuta |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Pietro Cicuta is a collaborator and co-I on grant 'Sculpting Dynamic Amphiphilic Structures'. |
| Start Year | 2012 |
| Description | Dr Simon Connell |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr Simon Connell is a collaborator and co-I on grant 'Sculpting Dynamic Amphiphilic Structures'. |
| Start Year | 2012 |
| Description | NanoInk |
| Organisation | Nanoink |
| Country | United States |
| Sector | Private |
| PI Contribution | The collaboration was a short project to determine whether their dip-pen nanolithography platform would be useful in our single cell research. The instrument we tested over the course of 6 weeks was capable of printing <15micron diameter antibody spots compared to our 100micron diameter 'conventional' spots. It was concluded that the spots would enable a significant reduction in assay volume which could significantly benefit the project going forward. |
| Start Year | 2012 |
| Description | Oxford Gene Technology |
| Organisation | Oxford Gene Technology |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Knowledge exchange on single cell proteomics technology with Oxford Gene Technology. |
| Start Year | 2012 |
| Description | Professor Andy Pitt |
| Organisation | Aston University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Professor Andy Pitt is a collaborator and co-I on the grant 'Next Generation Analytical Tools: Application to Protein Oxidations that affect Human Health and Wellbeing'. |
| Start Year | 2011 |
| Description | Professor Colin Bain |
| Organisation | Durham University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Professor Colin Bain is a collaborator and a co-I on the grant 'Optical Control of Emulsion Drops for Nanofluidics and Microfabrication'. |
| Start Year | 2011 |
| Description | Professor Jon Cooper |
| Organisation | University of Glasgow |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Professor Jon Cooper is a collaborator and co-I on the grant 'Next Generation Analytical Tools: Application to Protein Oxidations that affect Human Health and Wellbeing'. |
| Start Year | 2011 |
| Description | Professor Michael Stumpf |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Professor Michael Stumpf is a collaborator on the grant 'Cellular Information Processing and Decision Making from Noise to Robust Phenotypes'. |
| Start Year | 2011 |
| Description | Professor Mustafa Khammash |
| Organisation | University of California |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Professor Mustafa Khammash is a collaborator and a co-I on grant 'Cellular Information Processing and Decision Making from Noise to Robust Phenotypes'. |
| Start Year | 2011 |
| Description | Professor Nigel Saunders |
| Organisation | Brunel University London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Professor Nigel Saunders is a collaborator on the Biomedical Research Council (BRC) grant: 'Clinical Demonstration of Point of Care Diagnostics Using Microfluidic Chips with Single Molecule Sensitivity for the Detection of Infectious Diseases'. |
| Start Year | 2010 |
| Description | Professor Paul O?Shea |
| Organisation | University of Nottingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Professor Paul O?Shea is a collaborator and co-I on grant 'Sculpting Dynamic Amphiphilic Structures'. |
| Start Year | 2012 |
| Description | Professor Peter Olmsted |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Professor Peter Olmsted is a collaborator and co-I on grant 'Sculpting Dynamic Amphiphilic Structures'. |
| Start Year | 2012 |
| Description | Professor Shinya Kuroda |
| Organisation | University of Tokyo |
| Country | Japan |
| Sector | Academic/University |
| PI Contribution | Professor Shinya Kuroda is a collaborator and a co-I on grant 'Cellular Information Processing and Decision Making from Noise to Robust Phenotypes'. |
| Start Year | 2011 |
| Title | 2DIR spectrometer |
| Description | Construction of 2DIR Spectrometer and applying it to the detection of oxidized protein side chains. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2011 |
| Impact | 2DIR has been able to successfully detect oxidised forms of proteins and this has lead to publication. |
| Title | A novel application of a FRET probe available from Invitrogen |
| Description | A novel application of a FRET probe available from Invitrogen (Red/Green Bodipy phosphatidylcholine) has been tested. The probe was designed by the manufacturer to measure phospholipase activity. We incorporated this probe in live cell and model membranes and we demonstrated it can be applied to measure the lateral pressure in lipid bilayers. |
| Type Of Technology | Systems, Materials & Instrumental Engineering |
| Title | Approximate Bayesian Computation (ABC) |
| Description | Parameter inference algorithm for stochastic simulations |
| Type Of Technology | Software |
| Year Produced | 2013 |
| Impact | Use of this algorithm has lead to a collaboration with other academics within Imperial college with the work hopefully leading to a joint paper. |
| Title | Automatic handling system for 2DIR samples |
| Description | Automatic handling system for 2DIR samples |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Automation of chip reader |
| Description | Automation of chip reader |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | Capture Assay Model |
| Description | A software that models the scaling advantages and constraints in miniaturized capture assays for single cell proteomics |
| Type Of Technology | Software |
| Year Produced | 2013 |
| Impact | Used in group to predict assay behaviour and inform assay validation |
| Title | Chip surface passivation protocols |
| Description | To limit the amount of non-specific binding to surface to maintain sensitivity silane, PEG and 3D polymer based surface chemistry was investigated. It was determined that silane based chemistry is appropriate for DNA assays whereas PEG based chemistries are better suited for protein assays. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2011 |
| Impact | These passivated slides are required for use with the MAC chip platform a vital part of the Proxomics project. |
| Title | Cicculating Tumour Cells (CTCs) protocols |
| Description | Protocols were determined to isolate CTCs from whole-blood patient samples and introduce the isolated cells into a microfluidic device for subsequent analysis. |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Computational Fluid Dynamics Model of Diffusing Protein |
| Description | Computational Fluid Dynamics model of protein diffusing from a lysed single cell in a microfluidic chamber and subsequent binding to an antibody patch (using SimuLink/Comsol). |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | DNA printing |
| Description | DNA printing - Array of RNA capture DNA oligoneucleotides |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Design of disposable cell sorter chips |
| Description | A microfluidic cytometer was designed to sort hydro-dynamically focussed single cells. The stream of cells would pass through an optical detection stage. Cells which are fluorescently labelled trigger a downstream switch which diverts the flow of the cells into an isolated storage chamber. The sorted cells may then be measured using the single cell proteomics platform described elsewhere. |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Dualbeam trapping system using steering mirrors and polarisation multiplexing |
| Description | Dualbeam trapping system using steering mirrors and polarisation multiplexing |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Establishment of confocal microscope and wide-field microscope |
| Description | Establishment of confocal microscope and wide-field microscope |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Fabrication of microfluidic processes/ microarray fabrication DNA and protein/ surface chemistry/ blocking optimisation of microarray devices |
| Description | Fabrication of microfluidic processes/ microarray fabrication DNA and protein/ surface chemistry/ blocking optimisation of microarray devices |
| Type Of Technology | Systems, Materials & Instrumental Engineering |
| Title | GLSL codes for dynamic hologram generation |
| Description | GLSL codes for dynamic hologram generation |
| Type Of Technology | Software |
| Year Produced | 2012 |
| Title | Image processing scripts for automation of routine calculations |
| Description | Diffusion script which calculates the time for binding to a spot in a cylindrical chamber by calculating the eigenvalues and eigenfunctions of the diffusion operator using appropriate boundary conditions. |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | ImageJ codes for high dynamic range single molecule counting |
| Description | ImageJ codes for high dynamic range single molecule counting |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | ImageJ codes to identify and count single molecules |
| Description | ImageJ code to identify and count single molecules in acquired TIRF images. Code is able to count in two different regimes ? low binding density where single molecules are punctate and high binding density where bound molecule number is high and single molecules overlap one another. Code is able to output binding curves. |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | LabView controls for the track reader |
| Description | LabView controls for the track reader |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | LabView interface for the automated Capillary Electrophoresis |
| Description | LabView interface for the automated Capillary Electrophoresis |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | LabView trapping system interface |
| Description | Labview Track Writing Stage Control Interface |
| Type Of Technology | Software |
| Year Produced | 2012 |
| Title | Labview Track Writing Stage Control Interface |
| Description | Labview Track Writing Stage Control Interface |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | Labview suite for 2DIR spectrometer full control |
| Description | Labview suite for 2DIR spectrometer full control |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | Laser Systems |
| Description | Ytterbium fibre laser at 1070nm was used for optical trapping of single cells. Nd:YAG short pulsed laser was used to set up a cavitation bubble within a microfluidic chamber to lyse a single cell. |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Microfluidic Antibody Capture Chips |
| Description | Designed and built microfluidic antibody capture chips, an all optical platform for the quantification of protein in single cells. Cells are loaded into these devices, transported to analysis chambers using an optical trap and then ruptured with the use of a high powered optical lysis laser. The intracellular contents are then quantified by the use of a miniaturized ELISA format. Proteins bind to antibodies on the surface of the device and a secondary fluorescent antibody, present in solution completes the sandwich system. Total Internal Reflection Fluorescence (TIRF) microscopy is then used to detect and count the amount of protein that has bound to the antibody spot. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2011 |
| Impact | The use of MAC chips dominates an entire work stream in the Proxomics project and has resulted in a number of publications. |
| Title | Microfluidic antibody capture (MAC) chip design |
| Description | A microfluidic antibody capture chip was designed to allow to isolation of single cells from a population, their subsequent lysis and binding of a protein or proteins of interest to an antibody patch. Separate designs for the isolation of single, few (1-5) and many (10-100) cells from flow were also made. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2011 |
| Impact | MAC chips dominate an entire workstream of the proxomics project and have resulted in a number of publications. |
| Title | Microfluidic chips design for handling Smart Droplet Microtools and cells |
| Description | Microfluidic chips design for handling Smart Droplet Microtools and cells |
| Type Of Technology | Systems, Materials & Instrumental Engineering |
| Year Produced | 2011 |
| Impact | Smart Droplet microtools and the associated platform have led to the publication of several papers. |
| Title | Microfluidic structures for handling SDMs and Single cells with traps |
| Description | Microfluidic structures for handling SDMs and Single cells with traps. |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Microfluidics Platform |
| Description | Designed and built microfluidics platform |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Multibeam time multiplex holographic trapping system |
| Description | Multibeam time multiplex holographic trapping system (using spatial light modulator). |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Nanodigestion |
| Description | Fabrication of SDMs and technologies for single cell biopsies (nanodigestion). |
| Type Of Technology | Systems, Materials & Instrumental Engineering |
| Title | Plasmids tagging VHR with HA and Flag |
| Description | Plasmids pcDNA-3.1-Flag-VHR and pcDNA-3.1-HA-VHR, to express N-terminal tagged VHR. |
| Type Of Technology | New Material/Compound |
| Year Produced | 2014 |
| Impact | Enabled tagged VHR to be expressed in cell lines and detected using different antibodies |
| Title | Protocols for CE and sample deposition |
| Description | Protocols for CE and sample deposition with non-tapered ultrathin capillaries |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Protocols for cell handling onto chips |
| Description | Cells were detached from flasks using gentle tryptic agents and filtered using a nylon mesh. Cells are suspended in media using a CO2 independent buffer. Cells are delivered via capillary tubing. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2011 |
| Impact | Cells are used in microfluidic devices for both the MAC chip and SDM platforms both of which have resulted in publications |
| Title | Protocols for protein deposition |
| Description | Protocols for protein deposition with tapered capillary and low voltages/low pressure (improved technique). |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Recasting of existing database for 2DIR |
| Description | Algorithm for protein identification based upon amino acid composition. |
| Type Of Technology | Software |
| Year Produced | 2008 |
| Title | Reflection/transmission optical setup for 2DIR spectrometer |
| Description | Reflection/transmission optical setup for 2DIR spectrometer |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Single Cell Analysis MATLAB code to calculate binding times |
| Description | The single molecule scripts were used to count molecules in sequences of antibody spot images under bleaching conditions. This is done with simple thresholding of connected components using built-in MATLAB image processing routines. Also included are the functions for fitting single molecules to gaussians which gave comparable results but for much more computation. |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | Single Cell Analysis MATLAB code to identify and count single molecules |
| Description | Matlab code to identify and count single molecules in acquired TIRF images. Code is able to count in two different regimes ? low binding density where single molecules are punctate and high binding density where bound molecule number is high and single molecules overlap one another. Code is able to output binding curves. |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | Single Cell Analysis software |
| Description | Algorithm for Single cell trapping and laser lysis |
| Type Of Technology | Software |
| Year Produced | 2011 |
| Title | Single Cell Antibody printing |
| Description | All antibodies were printed by an OmniGrid Micro microarrayer (Digilab, UK) using 946MP2 pins (ArrayIt, USA). Spotting solution was optimised for DNA, antibody, protein or cell-lysate printing. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2011 |
| Impact | Antibody printing is a vital step in the MAC chip platform. This platform is a vital part of the proxomics project and has resulted in a number of publications. |
| Title | Single Cell lysis protocols |
| Description | A technique using a short pulsed laser is employed to lyse single cells. Through a series of physical processes a cavitation bubble expands from the focal point of the laser. The shearing forces experienced by the cell placed approximately 10_m away disrupts the cell and liberates intracellular constituents for analysis. It has been demonstrated that the cell may be fully (all membranes ruptured including nuclear membrane) or partially (only plasma membrane ruptured preserving the nucleus intact) lysed. The optical lysis process is extremely fast whereby the cell is disrupted within a few microseconds. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2011 |
| Impact | Optical lysis is a vital part of the Microfluidic antibody capture platform which has resulted in a number of publications. |
| Title | TIRF-FLIM system |
| Description | Combined total internal reflection fluorescence lifetime imaging system for improved resolution to conventional fluorescence lifetime imaging techniques |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2014 |
| Impact | Enhanced the capabilities of standard fluorescence lifetime imaging through improved axial resolution. Technology is of particular use for investigations of dynamics in biological membranes. |
| Title | Time multiplex multibeam holographic trapping system |
| Description | Time multiplex multibeam holographic trapping system with better holograms and algorithms. |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Track Reader |
| Description | A custom-built UV-based detection platform was constructed to image CE-separated proteins which were depositied into tracks on a metal substrate. |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Track writing |
| Description | Merger of track writing and antibody detection technology. |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Two Single molecule microscope systems |
| Description | Developed a generic platform to undertake the analysis of protein copy number from single cells with single molecule resolution. The system is based upon a widefield total internal fluorescence microscope and sensitive EMCCD camera . |
| Type Of Technology | New/Improved Technique/Technology |
| Title | Two versions of Proteome-on-a chip system |
| Description | One version was fully automated, which is not common with prototypes of separation equipment. |
| Type Of Technology | New/Improved Technique/Technology |
| Description | A Career in Chemistry: 'Star Trek Tractor Beams: no longer science friction'. Chemistry Student Interest and Revision Day, Imperial College London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Primary Audience | |
| Results and Impact | A Career in Chemistry: 'Star Trek Tractor Beams: no longer science friction'. Chemistry Student Interest and Revision Day, Imperial College London, 25 November 2010. |
| Year(s) Of Engagement Activity | 2010 |
| Description | Doctoral Training Centre Den Style Competition |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Primary Audience | |
| Results and Impact | Two SCP students, Joe Kaplinsky and Ali Salehi-Reyhani, along with another Institute of Chemical Biology student, Duncan Casey, won the first prize in a Dragons' Den style competition showcasing student entrepreneurship. Four teams of PhD students competed for £20,000 business development money in a Dragons' Den style competition this week, digitally compered by Evan Davis, host of the BBC programme Dragons' Den. http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_2-7-2010-13-25-51 Podcast with Evan Davis, Dragons' Den -http://www3.imperial.ac.uk/media/podcasts/magazinepodcasts2010. |
| Year(s) Of Engagement Activity | 2010 |
| URL | http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_2-7-2010-13-25-51 |
| Description | Front cover image of Biomedical optics Express |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | |
| Results and Impact | Front cover image of Biomedical optics Express (July 2012, Vol. 3, Issue 7) http://www.opticsinfobase.org/boe/issue.cfm . |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://www.opticsinfobase.org/boe/issue.cfm |
| Description | Front cover image of Journal of The Royal Society Interface Focus |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | |
| Results and Impact | Front cover image of Journal of The Royal Society Interface Focus (6 October 2008, 5, Suppl 2) Smart droplet microtools: a new toolkit for single-cell analysis. http://rsif.royalsocietypublishing.org/content/5/Suppl_2.cover-expansion . |
| Year(s) Of Engagement Activity | 2008 |
| URL | http://rsif.royalsocietypublishing.org/content/5/Suppl_2.cover-expansion |
| Description | Front cover of July 1 Biomedical Optics Express |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | |
| Results and Impact | Front cover of July 1 Biomedical Optics Express. Also, on spotlights page: http://www.opticsinfobase.org/spotlight/. |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://www.opticsinfobase.org/spotlight/ |
| Description | Imperial College Twitter Initiative |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | |
| Results and Impact | Imperial College Twitter Initiative - 17 June 2011, - Aidan Brown - Describing single Molecule Experiment http://www3.imperial.ac.uk/interact/dayinthelife. |
| Year(s) Of Engagement Activity | 2011 |
| URL | http://www3.imperial.ac.uk/interact/dayinthelife |
| Description | Inaugural Lecture |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Primary Audience | Participants in your research or patient groups |
| Results and Impact | Programmable Light, Inaugural Lecture, Imperial College London, 23 May 2012 http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/eventssummary/event_19-4-2012-13-43-23. |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/eventssummary/event_19-4-2012-13-43-23 |
| Description | Institute of Cancer Research News, start of SCP project, 2007 |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | |
| Results and Impact | Institute of Cancer Research News, start of SCP project, 2007 News article. |
| Year(s) Of Engagement Activity | 2007 |
| URL | http://www.ieu.icr.ac.uk/about_us/history/history6.htm |
| Description | Interviews on research paper: Protein Identification and Quantification by Two-Dimensional Infrared Spectroscopy: Implications for An All-Optical Proteomic Platform |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | |
| Results and Impact | Interviewed by ACS Analytical Chemistry, Bio Optics World, Genome Technology, Journal of Proteome Research, Laser Focus World, Nature Methods, ProteoMonitor for feature article on research paper: Protein Identification and Quantification by Two-Dimensional Infrared Spectroscopy: Implications for An All-Optical Proteomic Platform. PNAS 2008, 105(40),15352-15357. ACS Analytical Chemistry, 20 November 2008 (DK) An optical view of proteomics http://pubs.acs.org/action/showStoryContent?doi=10.1021/on.2008.11.18.171784& BioOptics World, 6 October 2008 (DK, KW) 2DIR imaging technique basis for future single-cell protein analysis tool http://www.bioopticsworld.com/articles/2008/10/2dir-imaging-technique-basis-for-future-single-cell-protein-analysis-tool.html Genome Technology, November 2008 (DK) Seeing Proteins with Optical Spectroscopy http://cdnwww.genomeweb.com/seeing-proteins-optical-spectroscopy Imperial College London, 22 September 2008 (DK) New technology paves the way for the future of identifying proteins inside cells (DK) http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_23-9-2008-15-56-2?newsid=44554. http://www.genomeweb.com/proteomics/no-optical-illusion-uk-researchers-developing-new-proteomics-platform http://www.icr.ac.uk/press/press_archive/press_releases_2008/10090.shtml http://www.scientistsolutions.com/t6940-new+technology+paves+way+for+identifying+proteins+within+single+cells.html |
| Year(s) Of Engagement Activity | 2008 |
| URL | http://www.laserfocusworld.com/articles/print/volume-44/issue-11/world-news/spectroscopy-two-dimensi... |
| Description | RSC Highlights in Chemical Biology |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | |
| Results and Impact | RSC Highlights in Chemical Biology, Plucking proteins from single cells, 28 January 2009. http://www.rsc.org/Publishing/Journals/cb/Volume/2009/3/plucking_proteins_from_single_cells.asp Highlighting Lab on a Chip paper: Lanigan P.M.P., Ninkovic T., Chan K., French P.M.W., de Mello A.J., Willison K.R., Parker P.J., Klug D.R., Templer R.H., Neil M.A.A., Ces O. A Microfluidic Platform for Probing Single Cell Plasma Membranes Using Optically Trapped Smart Droplet Microtools (SDMs). Lab on a Chip (Lab Chip, 2009, 9, 1096-1101) . |
| Year(s) Of Engagement Activity | 2009 |
| URL | http://www.rsc.org/Publishing/Journals/cb/Volume/2009/3/plucking_proteins_from_single_cells.asp |
| Description | Single Cell Analysis. Chemistry Open Day for GCSE and A-Level students |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Primary Audience | |
| Results and Impact | Single Cell Analysis. Chemistry Open Day for GCSE and A-Level students, 24 June 2010. |
| Year(s) Of Engagement Activity | 2010 |
| Description | Single Cell Analysis. London Oratory School |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Primary Audience | |
| Results and Impact | Single Cell Analysis. London Oratory School, London, November 2009. |
| Year(s) Of Engagement Activity | 2009 |
| Description | Star Trek Tractor Beams no longer science friction. Chemistry Taster Day |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Primary Audience | |
| Results and Impact | Star Trek Tractor Beams no longer science friction. Chemistry Taster Day. |
| Year(s) Of Engagement Activity | 2012 |