Super-resolution Microscopy: Novel Developments and Optimisations

This thesis describes the design, development and optimisation of a multifunctional localisation based super-resolution microscope at Cambridge Advanced Imaging Centre. The microscope is optimised to perform single and dual-colour imaging with high localisation precision and accuracy. Moreover, three-dimensional imaging capability is included in the microscope using the double-helix point spread function and the light field imaging modality. The thesis also describes the application of the microscope to image challenging biological samples, in collaboration with the research groups at the Department of Physiology, Development and Neuroscience. This includes, studying dynamics of a DNA-binding transcription factor for the Notch signalling pathway, deep within the whole salivary glands of Drosophila. Characterisation and optimisation of the microscope and the subsequent image analysis pipeline, to extract dynamics of single molecules at such depths is also discussed. Another application of the microscope, discussed in the thesis, is the study of chromatin architecture in primary spermatocytes of Drosophila. This includes optimisation of imaging conditions and data analysis software to reconstruct features with different densities of labelling dye in the imaged nuclei. Calibration and application of dual-colour localisation microscopy, to visualise the arrangement of active transcription sites in chromatin fibres is also discussed. Finally, the thesis also presents the application of light field imaging technique to extend the depth of field of localisation microscopy to over 20 μm. Modification of the microscope for light field imaging and a method to localise point emitters with high precision in all three spatial dimensions is discussed. The effectiveness of the technique for single molecule imaging is shown by detecting emissions from single fluorophores in labelled cells

Impact of Terrorism on International tourism demand

Tourists seek safe and secure destinations and avoid that of overwhelmed with terrorism. This study quantifies the relationship between terrorism and international tourism demand in 200 destination countries and regions for the period of 1995 to 2020. To achieve the objective, the study implied two-dimensional analyses by using the gravity model through Pooled ordinary least square estimator to pay special attention towards demand distribution. Our empirical results depict that, terrorism and terrorism in a destination country has a statistically insignificant relationship on international tourism demand, more specifically, here radical decline in GDP was observed in the sub-period 2006 – 2020 due to the global financial crisis and its aftershocks which badly affects tourist’s attraction to destination countries. This study pinpoints new insights for national tourism policymakers and business purposes.          &nbsp

Maximizing the field of view and accuracy in 3D Single Molecule Localization Microscopy.

Super-resolution techniques that localize single molecules in three dimensions through point spread function (PSF) engineering are very sensitive to aberrations and optical alignment. Here we show how double-helix point spread function is affected by such mis-alignment and aberration. Specifically, we demonstrate through simulation and experiment how misplacement of phase masks in infinity corrected systems is a common source of significant loss of accuracy. We also describe an optimal alignment and calibration procedure to correct for these errors. In combination, these optimizations allow for a maximal field of view with high accuracy and precision. Though discussed with reference to double-helix point spread function (DHPSF), the optimization techniques are equally applicable to other engineered PSFs

BRDF of human skin in the visible spectrum

© Emerald Publishing Limited. Purpose - Significant research has been carried out in terms of development of new bidirectional reflectance distribution function (BRDF) instruments; however, there is still little research available regarding spectral BRDF measurements of human skin. This study aims to investigate the variation in human skin reflectance using a new fibre optic-based spectral-BRDF measurement device. Design/methodology/approach - Design of this system mainly involves use of multiple fibre optics to illuminate and detect light reflected from a sample, whereas a hemispherical dome was 3D printed to mount the fibres at various slant/tilt angles. To investigate the spectral differences in BRDF of human skin, 3 narrowband filters in the visible spectrum were used, whereas measurements were taken from the back of the hand for Caucasian and Asian skin types. Findings - The experiments demonstrate that the BRDF of human skin varies with wavelengths in the visible spectrum and it is also different for Caucasian and Asian skin types. Both skin types exhibit off-specular reflection with increase in angle of incidence and show less variation with respect to viewing angles when the angle of incidence is normal to the surface. Research implications - A database of spectral BRDF measurements of human skin will help not only in creating realistic skin renderings but also in development of novel skin reflectance models for biomedical and machine vision applications. The measurements would also provide means to validate the predictions from existing light transport/spectral simulation models for human skin and will ultimately help in the accurate diagnosis and simulation of various skin disorders. Originality/value - The proposed system provides fast scatter measurements by utilising multiple fibres to detect light simultaneously at different angles while also allowing easy switching between incident light directions. Due to its flexible design and contact-based measurements, the device is independent of errors due to sample movements and does not require any image registration. Also, measurements taken from the device show that the BRDF of skin varies significantly in the visible spectrum and it is different for Caucasian and Asian skin types

Activation of the Notch Signaling Pathway In Vivo Elicits Changes in CSL Nuclear Dynamics.

A key feature of Notch signaling is that it directs immediate changes in transcription via the DNA-binding factor CSL, switching it from repression to activation. How Notch generates both a sensitive and accurate response-in the absence of any amplification step-remains to be elucidated. To address this question, we developed real-time analysis of CSL dynamics including single-molecule tracking in vivo. In Notch-OFF nuclei, a small proportion of CSL molecules transiently binds DNA, while in Notch-ON conditions CSL recruitment increases dramatically at target loci, where complexes have longer dwell times conferred by the Notch co-activator Mastermind. Surprisingly, recruitment of CSL-related corepressors also increases in Notch-ON conditions, revealing that Notch induces cooperative or "assisted" loading by promoting local increase in chromatin accessibility. Thus, in vivo Notch activity triggers changes in CSL dwell times and chromatin accessibility, which we propose confer sensitivity to small input changes and facilitate timely shut-down

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P < 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy.

Funder: Higher Education Commision, PakistanFunder: Cambridge TrustFunder: Isaac Newton TrustWhile the biochemistry of gene transcription has been well studied, our understanding of how this process is organised in 3D within the intact nucleus is less well understood. Here we investigate the structure of actively transcribed chromatin and the architecture of its interaction with active RNA polymerase. For this analysis, we have used super-resolution microscopy to image the Drosophila melanogaster Y loops which represent huge, several megabases long, single transcription units. The Y loops provide a particularly amenable model system for transcriptionally active chromatin. We find that, although these transcribed loops are decondensed they are not organised as extended 10nm fibres, but rather they largely consist of chains of nucleosome clusters. The average width of each cluster is around 50nm. We find that foci of active RNA polymerase are generally located off the main fibre axis on the periphery of the nucleosome clusters. Foci of RNA polymerase and nascent transcripts are distributed around the Y loops rather than being clustered in individual transcription factories. However, as the RNA polymerase foci are considerably less prevalent than the nucleosome clusters, the organisation of this active chromatin into chains of nucleosome clusters is unlikely to be determined by the activity of the polymerases transcribing the Y loops. These results provide a foundation for understanding the topological relationship between chromatin and the process of gene transcription

Risk of appendicitis in patients with incidentally discovered appendicoliths

Background: An appendicolith-related appendiceal obstruction leading to appendicitis is a commonly encountered surgical emergency that has clear evidence-based management plans. However, there is no consensus on management of asymptomatic patients when appendicoliths are found incidentally. The objective of this study was to determine the risk of appendicitis in patients with an incidental finding of the appendicolith.Methods: A retrospective matched cohort study of patients with appendicolith discovered incidentally on computed tomographic scan from January 2008 to December 2014 at our institution was completed. The size and position of the appendicolith were ascertained. The study group was matched by age and gender to a control group. Both groups were contacted and interviewed regarding development of appendicitis.Results: In total, 111 patients with appendicolith were successfully contacted and included in the study. Mean age was found to be 38±15y with 36 (32%) of the study population being females. Mean length of appendix was 66±16mm, and mean width was 5.8±0.9mm. Mean size of the appendicolith was 3.6±1.1mm (1.4-7.8mm). Fifty-eight percent of appendicoliths was located at the proximal end or whole of appendix, 31% at mid area, and 11% at the distal end of appendix. All patients of the study and control groups were contacted, and at a mean follow-up of 4.0±1.7y, there was no occurrence of acute appendicitis in either group.CONCLUSIONS: Patients with incidentally discovered appendicolith on radiological imaging did not develop appendicitis. Hence, the risk of developing acute appendicitis for these patients does not seem higher than the general population