29 results found
Kim JA, Wales DJ, Thompson AJ, et al., 2019, Towards development of fibre-optic surface enhanced Raman spectroscopy probes using 2-photon polymerisation for rapid detection of bacteria, Plasmonics in Biology and Medicine XVI, Publisher: SPIE, ISSN: 0277-786X
In this study, a variety of direct laser written surface-enhanced Raman spectroscopy (SERS) micro-structures, designed for bacteria detection, are presented. Various SERS micro-structures were designed to achieve both a high density of plasmonic hot spots and a strong probability of interaction between the hot spots and the target bacterial cells. Twophoton polymerization was used for initial fabrication of the polymeric skeletons of the SERS micro-structures, which were then coated with a 50 nm-thick gold layer via e-beam evaporation. The micro-structures were fabricated on glass coverslips and were assessed using a confocal Raman microscope. To this end, Rhodamine 6G was used as an analyte under 785 nm laser illumination. The optimal SERS micro-structures showed approximately 7×103 enhancement in Raman signal (analytical enhancement factor, AEF) at a wavenumber of 600 cm-1. Real-time detection of E. coli in solution was demonstrated using the fabricated SERS platform with low laser powers and a short acquisition time (785 nm, 5 mW, 50 ms).
Consortium H, Drake L, Frost G, et al., 2019, Health outcomes in Undernutrition: the role of Nutrients, Gut dysfunction and the gut microbiome (HUNGer), Health outcomes in Undernutrition: the role of Nutrients, Gut dysfunction and the gut microbiome (HUNGer), Publisher: Imperial College London
The HUNGer consortium is comprised of a multi-disciplinary, multi-national consortium of world leading researchers, with expertise in physiology and nutrition, through to clinical research, public health and agriculture in LMIC settings. The HUNGer consortium was awarded the MRC Confidence in Global Nutrition and Health award in 2018.The HUNGer consortium is developing a programme of work that will directly address United Nations Sustainable Development Goal 2 (SDG-2): End hunger, achieve food security and improve nutrition, and promote sustainable agriculture. We believe there are a number of critical unanswered questions regarding the role of the gut in undernutrition, which if answered could significantly improve the effective management and prevention of undernutrition.The following document represents the consensus opinion of the HUNGer consortium concerning the key challenges that currently limit the effective management and prevention of undernutrition and the most promising potential solutions.
Tudor A, Delaney C, Zhang H, et al., 2018, Fabrication of soft, stimulus-responsive structures with sub-micron resolution via two-photon polymerization of poly(ionic liquid)s, Materials Today, Vol: 21, Pages: 807-816, ISSN: 1369-7021
Soft, stimulus-responsive 3D structures created from crosslinked poly(ionic liquid)s (PILs) have been fabricated at unprecedented sub-micron resolution by direct laser writing (DLW). These structures absorb considerable quantities of solvent (e.g., water, alcohol, and acetone) to produce PIL hydrogels that exhibit stimulus-responsive behavior. Due to their flexibility and soft, responsive nature, these structures are much more akin to biological systems than the conventional, highly crosslinked, rigid structures typically produced using 2-photon polymerization (2-PP). These PIL gels expand/contract due to solvent uptake/release, and, by exploiting inherited properties of the ionic liquid monomer (ILM), thermo-responsive gels that exhibit reversible area change (30 ± 3%, n = 40) when the temperature is raised from 20 °C to 70 °C can be created. The effect is very rapid, with the response indistinguishable from the microcontroller heating rate of 7.4 °C s−1. The presence of an endoskeleton-like framework within these structures influences movement arising from expansion/contraction and assists the retention of structural integrity during actuation cycling.
Thompson AJ, Power M, Yang G-Z, 2018, A micro-scale fiber-optic force sensor fabricated using direct laser writing and calibrated using machine learning, Optics Express, Vol: 26, Pages: 14186-14200, ISSN: 1094-4087
Fiber-optic sensors have numerous existing and emerging applications spanning areas from industrial process monitoring to medical diagnosis. Two of the most common fiber sensors are based on the fabrication of Bragg gratings or Fabry-Perot etalons. While these techniques offer a large array of sensing targets, their utility can be limited by the difficulties involved in fabricating forward viewing probes (Bragg gratings) and in obtaining sufficient signal-to-noise ratios (Fabry-Perot systems). In this article we present a microscale fiber-optic force sensor produced using direct laser writing (DLW). The fabrication entails a single-step process that can be undertaken in a reliable and repeatable manner using a commercial DLW system. The sensor is made of a series of thin plates (i.e. Fabry-Perot etalons), which are supported by springs that compress under an applied force. At the proximal end of the fiber, the interferometric changes that are induced as the sensor is compressed are read out using reflectance spectroscopy, and the resulting spectral changes are calibrated with respect to applied force. This calibration is performed using either singular value decomposition (SVD) followed by linear regression or artificial neural networks. We describe the design and optimization of this device, with a particular focus on the data analysis required for calibration. Finally, we demonstrate proof-of-concept force sensing over the range 0-50 μN, with a measurement error of approximately 1.5 μN.
Vysniauskas A, Lopez Duarte I, Thompson AJ, et al., 2018, Surface functionalisation with viscosity-sensitive BODIPY molecular rotor, Methods and Applications in Fluorescence, Vol: 6, ISSN: 2050-6120
Surface functionalisation with viscosity sensitive dyes termed ‘molecular rotors’ can potentially open up new opportunities in sensing, for example for non-invasive biological viscosity imaging, in studying the effect of shear stress on lipid membranes and in cells, and in imaging contacts between surfaces upon applied pressure. We have functionalised microscope slides with BODIPY-based molecular rotor capable of viscosity sensing via its fluorescence lifetime. We have optimised functionalisation conditions and prepared the slides with the BODIPY rotor attached directly to the surface of glass slides and through polymer linkers of 5 kDa and 40 kDa in mass. The slides were characterised for their sensitivity to viscosity, and used to measure viscosity of supported lipid bilayers during photooxidation, and of giant unilamellar vesicles lying on the surface of the slide. We conclude that our functionalised slides show promise for a variety of viscosity sensing applications.
Thompson AJ, Yang G-Z, 2018, Tethered and Implantable Optical Sensors, Implantable Sensors and Systems, Editors: Yang, Publisher: Springer, Pages: 439-505, ISBN: 978-3-319-69747-5
Optical imaging and sensing modalities have been used in medical diagnosis for many years. An obvious example is endoscopy, which allows remote wide-field imaging of internal tissues using optical fibers and/or miniature charge-coupled device (CCD) cameras. While techniques such as endoscopy provide useful tools for clinicians, they do not typically allow a complete diagnosis to be made. Instead, physical biopsies may be required to confirm or refute the presence of disease. Furthermore, endoscopic procedures are both invasive and time-consuming. As such, much research is currently directed toward the development of devices that can provide a complete in vivo diagnosis without the requirement for a physical biopsy. Ideally, such devices should also be minimally or non-invasive, and they should provide immediate identification of disease at the point of care. Additionally, there is significant interest in the development of implantable diagnostic devices that can be left within patients’ bodies for extended periods of time (for several days or longer). Such systems could be used for automated disease diagnosis, and example applications include the detection of post-surgical infections as well as monitoring of the health status of patients undergoing chemotherapy. This chapter focuses on the development of optical instruments that can provide in situ diagnosis at the point of care, with an emphasis on progress towards miniature devices that may function as implants in the future.
Power MC, Thompson A, Anastasova-Ivanova S, et al., 2018, A monolithic force-sensitive 3D microgripper fabricated on the tip of an optical fiber using 2-photon polymerization, Small, Vol: 14, Pages: 1703964-1-1703964-10, ISSN: 1613-6810
Microscale robotic devices have myriad potential applications including drug delivery, biosensing, cell manipulation, and microsurgery. In this work, a tethered, 3D, compliant grasper with an integrated force sensor is presented, the entirety of which is fabricated on the tip of an optical fiber in a single-step process using 2-photon polymerization. This gripper can prove useful for the interrogation of biological microstructures such as alveoli, villi, or even individual cells. The position of the passively actuated grasper is controlled via micromanipulation of the optical fiber, and the microrobotic device measures approximately 100 µm in length and breadth. The force estimation is achieved using optical interferometry: high-dimensional spectral readings are used to train artificial neural networks to predict the axial force exerted on/by the gripper. The design, characterization, and testing of the grasper are described and its real-time force-sensing capability with an accuracy below 2.7% of the maximum calibrated force is demonstrated.
Schmitz A, Thompson AJ, Berthet-Rayne P, et al., 2017, Shape sensing of miniature snake-like robots using optical fibers, IEEE International Conference on Intelligent Robots and Systems (IROS), Publisher: IEEE, Pages: 947-952, ISSN: 2153-0858
Snake like continuum robots are increasingly used for minimally invasive surgery. Most robotic devices of this sort that have been reported to date are controlled in an open loop manner. Using shape sensing to provide closed loop feedback would allow for more accurate control of the robot's position and, hence, more precise surgery. Fiber Bragg Gratings, magnetic sensors and optical reflectance sensors have all been reported for this purpose but are often limited by their cost, size, stiffness or complexity of fabrication. To address this issue, we designed, manufactured and tested a prototype two-link robot with a built-in fiber-optic shape sensor that can deliver and control the position of a CO 2 -laser fiber for soft tissue ablation. The shape sensing is based on optical reflectance, and the device (which has a 4 mm outer diameter) is fabricated using 3D printing. Here we present proof-of-concept results demonstrating successful shape sensing - i.e. measurement of the angular displacement of the upper link of the robot relative to the lower link - in real time with a mean measurement error of only 0.7°.
Thompson AJ, Hughes M, Anastasova S, et al., 2017, The potential role of optical biopsy in the study and diagnosis of environmental enteric dysfunction, Nature Reviews Gastroenterology and Hepatology, Vol: 14, Pages: 727-738, ISSN: 1759-5045
Environmental enteric dysfunction (EED) is a disease of the small intestine affecting children and adults in low and middle income countries. Arising as a consequence of repeated infections, gut inflammation results in impaired intestinal absorptive and barrier function, leading to poor nutrient uptake and ultimately to stunting and other developmental limitations. Progress towards new biomarkers and interventions for EED is hampered by the practical and ethical difficulties of cross-validation with the gold standard of biopsy and histology. Optical biopsy techniques — which can provide minimally invasive or noninvasive alternatives to biopsy — could offer other routes to validation and could potentially be used as point-of-care tests among the general population. This Consensus Statement identifies and reviews the most promising candidate optical biopsy technologies for applications in EED, critically assesses them against criteria identified for successful deployment in developing world settings, and proposes further lines of enquiry. Importantly, many of the techniques discussed could also be adapted to monitor the impaired intestinal barrier in other settings such as IBD, autoimmune enteropathies, coeliac disease, graft-versus-host disease, small intestinal transplantation or critical care.
Power M, Seneci CA, Thompson AJ, et al., 2017, Modelling & characterization of a compliant tethered microgripper for microsurgical applications, International Conference on Manipulation, Automation and Robotics at Small Scales, MARSS 2017, Publisher: IEEE
The development of microscale surgical tools could pave the way for truly minimally invasive microsurgical procedures. This work demonstrates the application of direct laser writing (DLW) using two-photon polymerization (TPP), a rapid prototyping microfabrication technique, to create a tethered, passively actuated three-dimensional gripper with potential applications in microbiopsy. A microgripper design was devised, modelled and optimized. The gripper was then fabricated and characterized for validation of the theoretical model. The results demonstrate that modelling the behavior of compliant microtools provides a useful approximation for the observed trends and, thus, can be utilized in the design of TPP tools. Future work on the incorporation of viscoelastic material into the model will further improve agreement between the predicted and experimental performance.
Kuimova MK, Mika JT, Thompson AJ, et al., 2016, Measuring the viscosity of the Escherichia coli plasma membrane using molecular rotors, Biophysical Journal, Vol: 111, Pages: 1528-1540, ISSN: 1542-0086
The viscosity is a highly important parameter within the cell membrane, affecting the diffusion ofsmall molecules and, hence, controlling the rates of intra-cellular reactions. There is significantinterest in the direct, quantitative assessment of membrane viscosity. Here we report the use offluorescence lifetime imaging microscopy (FLIM) of the molecular rotor BODIPY C10 in themembranes of live Escherichia coli (E. coli) bacteria to permit direct quantification of the viscosity.Using this approach we investigated the viscosity in live E. coli cells, spheroplasts and liposomesmade from E. coli membrane extracts. For live cells and spheroplasts the viscosity was measured atboth room temperature (23o C) and the E. coli growth temperature (37o C), while the membraneextract liposomes were studied over a range of measurement temperatures (5-40o C). At 37o C werecorded a membrane viscosity in live E. coli cells of 950 cP, which is considerably higher than thatpreviously observed in other live cell membranes (e.g., eukaryotic cells, membranes of Bacillusvegetative cells). Interestingly, this indicates that E. coli cells exhibit a high degree of lipid orderingwithin their liquid-phase plasma membranes.
Thompson AJ, Koziej L, Williams H, et al., 2016, Towards optical fibre based Raman spectroscopy for the detection of surgical site infection, BiOS, SPIE Photonics West, Publisher: SPIE
Surgical site infections (SSIs) are common post-surgical complications that remain significant clinical problems, as they are associated with substantial mortality and morbidity. As such, there is significant interest in the development of minimally invasive techniques that permit early detection of SSIs. To this end, we are applying a compact, clinically deployable Raman spectrometer coupled to an optical fibre probe to the study of bacteria, with the long term goal of using Raman spectroscopy to detect infection in vivo. Our system comprises a 785 nm laser diode for excitation and a commercial (Ocean Optics, Inc.) Raman spectrometer for detection. Here we discuss the design, optimisation and validation of this system, and describe our first experiences interrogating bacterial cells (Escherichia coli) in vitro. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
Thompson AJ, Herling TW, Kubankova M, et al., 2015, Molecular Rotors Provide Insights into Microscopic Structural Changes During Protein Aggregation., Journal of Physical Chemistry B, Vol: 119, Pages: 10170-10179, ISSN: 1520-6106
Changes in microscopic viscosity represent an important characteristic of structural transitions in soft matter systems. Here we demonstrate the use of molecular rotors to explore the changes in microrheology accompanying the transition of proteins from their soluble states into a gel phase composed of amyloid fibrils. The formation of beta-sheet rich protein aggregates, including amyloid fibrils, is a hallmark of a number of neurodegenerative disorders, and as such, the mechanistic details of this process are actively sought after. In our experiments, molecular rotors report an increase in rigidity of approximately three orders of magnitude during the aggregation reaction. Moreover, phasor analysis of the fluorescence decay signal from the molecular rotors suggests the presence of multiple distinct mechanistic stages during the aggregation process. Our results show that molecular rotors can reveal key microrheological features of protein systems not observable through classical fluorescent probes operating in light switch mode.
Brydegaard M, Thompson AJ, Andersson-Engels S, et al., 2015, Complete parameterization of temporally and spectrally resolved laser induced fluorescence data with applications in bio-photonics, CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, Vol: 142, Pages: 95-106, ISSN: 0169-7439
Mika JT, Thompson AJ, Hofkens J, et al., 2015, Measurement of the Viscosity of E. coli Membranes using Molecular Rotors and Flim, 59th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 542A-542A, ISSN: 0006-3495
Tang T-YD, Hak CRC, Thompson AJ, et al., 2014, Fatty acid membrane assembly on coacervate microdroplets as a step towards a hybrid protocell model, NATURE CHEMISTRY, Vol: 6, Pages: 527-533, ISSN: 1755-4330
Thompson AJ, Tang T-YD, Herling TW, et al., 2014, Quantitative sensing of microviscosity in protocells and amyloid materials using fluorescence lifetime imaging of molecular rotors, Conference on Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XII, Publisher: SPIE- Society of Photo-optical Instrumentation Engineers, ISSN: 0277-786X
Molecular rotors are fluorophores that have a fluorescence quantum yield that depends upon intermolecular rotation. The fluorescence quantum yield, intensity and lifetime of molecular rotors all vary as functions of viscosity, as high viscosities inhibit intermolecular rotation and cause an increase in the non-radiative decay rate. As such, molecular rotors can be used to probe viscosity on microscopic scales. Here, we apply fluorescence lifetime imaging microscopy (FLIM) to measure the fluorescence lifetimes of three different molecular rotors, in order to determine the microscopic viscosity in two model systems with significant biological interest. First, the constituents of a novel protocell – a model of a prebiotic cell – were studied using the molecular rotors BODIPY C10 and kiton red. Second, amyloid formation was investigated using the molecular rotor Cy3. © (2014) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
Coda S, Thompson AJ, Kennedy GT, et al., 2014, Fluorescence lifetime spectroscopy of tissue autofluorescence in normal and diseased colon measured ex vivo using a fiber-optic probe, Biomedical Optics Express, Vol: 5, Pages: 515-538
We present an ex vivo study of temporally and spectrally resolved autofluorescence in a total of 47 endoscopic excision biopsy/resection specimens from colon, using pulsed excitation laser sources operating at wavelengths of 375 nm and 435 nm. A paired analysis of normal and neoplastic (adenomatous polyp) tissue specimens obtained from the same patient yielded a significant difference in the mean spectrally averaged autofluorescence lifetime −570 ± 740 ps (p = 0.021, n = 12). We also investigated the fluorescence signature of non-neoplastic polyps (n = 6) and inflammatory bowel disease (n = 4) compared to normal tissue in a small number of specimens.
Karim NHA, Mendoza O, Shivalingam A, et al., 2014, Salphen metal complexes as tunable G-quadruplex binders and optical probes, RSC ADVANCES, Vol: 4, Pages: 3355-3363, ISSN: 2046-2069
Coda S, Kelly DJ, Lagarto JL, et al., 2013, Autofluorescence lifetime imaging and metrology for medical research and clinical diagnosis
We report the development of instrumentation to utilise autofluorescence lifetime for the study and diagnosis of disease including cancer and osteoarthritis. ©2013 The Optical Society (OSA).
Thompson AJ, 2013, Developing endoscopic instrumentation and techniques for in vivo fluorescence lifetime imaging and spectroscopy
Coda S, Thompson AJ, Lenz MO, et al., 2012, Sa1609 Fluorescence Lifetime Imaging and Spectroscopy for Label-Free Contrast of Gastrointestinal Diseases, Gastrointestinal Endoscopy, Vol: 75, Pages: AB219-AB220, ISSN: 0016-5107
Thompson AJ, Coda S, Sorensen MB, et al., 2012, In vivo measurements of diffuse reflectance and time-resolved autofluorescence emission spectra of basal cell carcinomas, JOURNAL OF BIOPHOTONICS, Vol: 5, Pages: 240-254, ISSN: 1864-063X
Coda S, Kennedy GT, Thompson A, et al., 2011, FLUORESCENCE LIFETIME IMAGING FOR LABEL-FREE CONTRAST OF GASTROINTESTINAL DISEASES, International School of Physics "Enrico Fermi", Course CLXXXI "Microscopy Applied to Biophotonics"
INTRODUCTION: Autofluorescence (AF) has been used to distinguish between normal and diseased tissue, but its molecular basis is still unclear and making quantitative intensity measurements is challenging. Fluorescence lifetime imaging (FLIM) measures the decay rate of the autofluorescent signal from tissue, providing quantitative AF contrast. FLIM has been recently implemented by our group in three endoscopic instruments consisting of a confocal laser endomicroscope, a wide-field fibre-optic endoscope and a single point fibre-optic probe. FLIM has the potential to report on tissue structure and function in real-time during endoscopy, providing a label-free means to detect the early onset of diseases that cause changes in tissue AF. We are developing these 3 modalities for in vivo clinical application, supported by ex vivo studies on freshly-biopsied/resected GI tissues.AIMS & METHODS: The aim of this work is to translate our FLIM instrumentation from the optical bench to in vivo clinical application. AF from 43 endoscopic samples from different GI sites was excited using a conventional confocal FLIM microscope in the range 405-420nm, which is compatible with our FLIM endoscopes, and which is the range needed to excite a number of important endogenous GI tissue fluorophores such as porphyrins, flavins, collagen and elastin. The samples were collected from patients undergoing endoscopy, transported to the FLIM laboratory to be imaged and then submitted for histopathology. The following disorders were investigated: Barrett’s oesophagus, gastric cancer, ulcerative colitis, Crohn’s disease, adenomatous polyps and colon cancer. The accuracy of FLIM in discriminating dysplastic/cancerous samples from normal tissue has been tested by measuring the Area Under the Curve (AUC).RESULTS: Our preliminary data show that premalignant or neoplastic samples display either shorter or longer fluorescence lifetime than that of normal tissue. Increased lifetime val
Coda S, Kennedy G, Thompson A, et al., 2011, FLUORESCENCE LIFETIME IMAGING OF GASTROINTESTINAL CANCERS, European-Society-for-Medical-Oncology (ESMO) 13th World Congress on Gastrointestinal Cancer, Publisher: OXFORD UNIV PRESS, Pages: v65-v66, ISSN: 0923-7534
Thompson AJ, Paterson C, Neil MAA, et al., 2011, Adaptive phase compensation for ultracompact laser scanning endomicroscopy, OPTICS LETTERS, Vol: 36, Pages: 1707-1709, ISSN: 0146-9592
Coda S, Kennedy GT, Thompson A, et al., 2011, FLUORESCENCE LIFETIME IMAGING FOR LABEL-FREE CONTRAST OF GASTROINTESTINAL DISEASES, Digestive Disease Week, Publisher: Elsevier, ISSN: 0016-5107
INTRODUCTION: Autofluorescence (AF) is a means to distinguish between normal and diseased tissue, but its molecular basis is unclear and intensity-based contrast is often not sufficiently specific. Fluorescence lifetime imaging (FLIM) maps the decay rate of fluorescence emitted from tissue samples, providing quantitative AF contrast. FLIM has been recently implemented by our group in three endoscopic instruments consisting of a confocal laser endomicroscope, a wide-field fibre-optic endoscope and a single point fibre-optic probe. FLIM has the potential to report on tissue structure and function in real-time during endoscopy, providing a label-free means to detect the early onset of diseases that cause changes in tissue AF. We are developing these 3 modalities for in vivo clinical application, supported by ex vivo studies on freshly-biopsied/resected GI tissues.AIMS & METHODS: In this study, autofluorescence from 25 endoscopic samples from different GI sites was excited using a conventional confocal FLIM microscope in the range 405-420nm, which is compatible with our FLIM endoscopes, and which is the range needed to excite a number of important endogenous GI tissue fluorophores such as porphyrins, flavins, collagen and elastin. The samples were collected from patients undergoing endoscopy, transported to the FLIM laboratory to be imaged and then submitted for histopathology. The following diseases were investigated: Barrett’s oesophagus, gastric cancer, ulcerative colitis, adenomatous polyps and colon cancer. ROC curve analysis was used to statistically test the significance of the differences described.RESULTS: Our preliminary data reveals that lifetime of dysplastic or neoplastic samples may be either shorter or longer than that of normal tissue. Increased lifetime values have been observed in Barrett’s oesophagus, colon cancer and polyps. Gastric cancer and ulcerative colitis have shown a decrease in lifetime. In addition, a broadening of
Thompson A, Manning H, Brydegaard M, et al., 2011, Hyperspectral fluorescence lifetime fibre probe spectroscopy for use in the study and diagnosis of osteoarthritis and skin cancer, SPIE Photonics West 2011, Publisher: Society of Photo-optical Instrumentation Engineers (SPIE), ISSN: 1996-756X
We present the application of two fibre-optic-coupled time-resolved spectrofluorometers and a compact steady-state diffuse reflected light/fluorescence spectrometer to in vivo and ex vivo studies of skin cancer and osteoarthritis. In a clinical study of skin cancer, 27 lesions on 25 patients were investigated in vivo before surgical excision of the region measured. Preliminary analysis reveals a statistically significant decrease in the autofluorescence lifetime of basal cell carcinomas compared to neighbouring healthy tissue. A study of autofluorescence signals associated with the onset of osteoarthritis indicates autofluorescence lifetime changes associated with collagen degradation.
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