Details of the previous recipients of the RMS Summer Studentship
Three students were successful in applying for an RMS Summer Studentship last year. Many congratulations to the successful applicants, who were as follows:
Ben Watson, University of Strathclyde
Optical microscopy has used the same manufacturing methods for milling and sanding glass elements to produce high-quality optics for over a century. Recent developments in 3D printing have opened the possibility of printing optical components, but the surface quality of these 3D prints remains unknown.
To address this, I designed and printed several planoconvex lenses using a consumer-grade 3D printer, and then experimented with various post-processing methods to improve the quality of the lens surface. I then used a confocal microscope set up in reflection mode to image the topology of the lens surface following different post-processing methods. By the end of my studentship, I had developed a workflow for manufacturing 3D printed lenses and written a custom analysis script that was used to characterise and quantify their surface quality.
Hale-Seda Radoykova, King’s College London
Accurately detecting and measuring structures in fluorescence microscopy images is important yet challenging. One of the interests of the Culley lab is to develop image analysis techniques to help researchers with these tasks.
The aim of this summer project was to acquire images of fluorescently labelled tubulin in Schizosaccharomyces pombe cells and to produce an image processing pipeline adapted to quantifying the microtubules in these images.
Catherine Read, University of York
The focus of this project was to compare behaviour of the core components of the pyrenoid in two related model algal organisms, Chlamydomonas reinhardtii and Chlorella. Both express native forms of the key fixation enzyme Rubisco (large and small chains) and a linker protein (EPYC1) which constitutively phase-separates into a pyrenoid. The non-equilibrium physics of this process inside the cell and the equilibrium physics of phase separation in vitro have not yet been compared quantitatively.
Six Summer Studentships were awarded in 2021, they were to:
Barbara Altenhuber, University of Leeds
The aim of this project was to determine the localisation of the activity-regulated cytoskeleton-associated protein (Arc) and establish a workflow to determine the in situ structure of Arc by cryogenic correlated light and electron microscopy (cryoCLEM). Arc is a key regulator of synaptic plasticity and assembles within postsynaptic receptor supercomplexes. Recent evidence suggests Arc self-assembles into virus-like capsids in neurons, which mediate a novel transport mechanism of shipping mRNA between neurons. However, the subcellular location of Arc in the brain has not been determined because of the poor specificity of Arc antibodies. Moreover, the in situ structure of Arc in the brain is unknown.
Chiara Pillen, University of Sheffield
The proposed project focused on detailing the unique advantages of a brand-new optical super-resolution imaging modality known as self-activated nanodiamond-based stochastic optical reconstruction microscopy (sandSTORM).
Imaging cellular or sub-cellular structures at nanometer-scale of detail is a key aspiration of super-resolution microscopy. The proposed project developed one of the recently invented super-resolution protocols into a versatile and highly efficient imaging tool, capable of adaptation into clinical diagnostics and high-content imaging.
Mollie Brown, University of Strathclyde
This project proposed to develop a simple MATLAB code for the automated adjustment of image intensity throughout the whole depth of the dataset. The Mesolens image datasets are very large (approx. 200GB for one 6mm x 6mm x 3mm volume) so we will begin by extracting a small volume of interest to prove principle. Once demonstrated on a small volume, we will upscale to study the whole data volume.
This image processing let us more accurately segment the islets from the surrounding tissue, and we were, for the first time, be able to perform a precise analysis of islet number, shape, volume and distribution within the whole pancreas.
Elene Lominadze, University of Exeter
This project explored the potential for the new prototype to be used as a serious research tool. The RAP microscope takes brightfield images of standard 96-well microtiter plates in rapid succession. The research aspect looked into the feeding habits of a model organism, playneries dumerulli (sea worm larvae) using a two-step process. First, brightfield images were acquired of the larvae. These images clearly showed the movement of the larvae across the floor of each well. Different food stocks (algae) placed in each well promoted different types of behaviour in the larvae. The assessment of this behaviour is determined by the second step in which a machine learning algorithm was applied to the brightfield images to identify the location, speed and direction of the larvae. From this tracking information it was possible to assign one of three behaviours to each larva (resting, feeding or foraging). The goal was to identify which food stock promote which behaviours in the larvae.
Jade Manning, University of Nottingham
The overall project was based on the hypothesis that the oxygen gradient present within tumours alters the structure and function of the tumour cells in a concentration-dependent manner. The project studied ultrastructural changes in subcellular organelles, particularly the endoplasmic reticulum (ER) and mitochondria, and correlated changes with biochemical markers using spatial mass spectrometry (3D-OrbiSIMS) in cryogenic conditions.
Jade’s summer project was to embed 3D spheroid cultures for resin section transmission electron microscopy, imaging the centre sections of the spheroid in order to visualise changes in the hypoxic core. She analysed the mitochondria and ER in 2-D, focusing particularly on the shape and spacing within the mitochondrial cristae and ER sheets respectively. The 3D cell models were both established lines or patient lines including the use of CRISPR-Cas9 engineered knockout lines of known hypoxia modulating proteins such as hypoxia inducible factor 1/2ɑ and FOSL2.
Jack Pearce, Diamond Light Source
For this summer project, Jack used a combination of advanced X-ray and electron microscopy techniques to characterise the structure of dental tartar at the nanoscale. Experiments were carried out using the FIB-SEM at ePSIC, Diamond Light Source to collect 3D volume imaging data on different dental tartar samples with a range of different porosities, from a dense packed matrix to a more open structure. The structural density was assessed using image segmentation and analysis techniques. The results were then correlated to results of nano X-ray microscopy experiments at Beamline I14, Diamond Light Source, using a combination of ptychographic and phase contrast imaging and X-ray fluorescence to analyse the tartar nanostructure and assess quantitative differences in the calcium compositions of the different sample matrices.
Rana Salem is a student at Glasgow Caledonian University. Her project was a collaboration between the university’s Department of Applied Science and the Centre for Textile Conservation at the University of Glasgow.The aim was to assess the impact of oxidative and reductive cleaning methods on the cotton cellulose fibres taken from historic textile garments using a series of microscopic and metric measurements. The eight-week project designed for Rana concerned the examination of a cotton shirt (circa. 1900) and new scoured cotton pre-and post-cleaning with sodium borohydride (reductive) and hydrogen peroxide (oxidative).
Watch Rana's project webinar on the University of Glasgow's Zoom platform (access code: ?x822xE$)
The application of machine learning (ML) algorithms to imaging data and specifically microscopy data is an exciting and rapidly evolving area. One application of ML in microscopy is the improvement of contrast in images by the reduction of noise. Two key challenges in ML are producing suitable training data and evaluating output from the ML algorithms. In this project a novel camera architecture based on non-destructive readout (NDR) was used to produce both ground truth and noisy data simultaneously. These two data sets were then used to train and evaluate various ML algorithms. The NDR produces sets of rapidly acquired images where each frame is the previous frame plus any newly captured photons. This means that in a typical NDR sequence each frame acts an improved version of the previous frame. We can then train a ML algorithm on the same real data but with varying degrees of noise and signal, giving us the ideal test best for ML in microscopy. This work will aid the understanding of noise sources within the camera, quantifying them and finding ways to increase the signal-to-noise ratio in post processing to improve image quality and resolution in the future.
Watch George's project presentation RMS_Pres_Final.mp4
Poppy Cairney is a student at the University of Southampton. Experimentally, her project was going to be capturing TIRF movies of spreading platelets and using tracking software to analyse the dynamics of actin structures ± PAK inhibitors. Unfortunately, due to the constraints of Covid-19, Poppy was provided with some training videos and resources on TIRF microscopy (e.g. iBiology material) and then had several Zoom calls to discuss the technique and why it would be applied to this question. To replicate the image analysis steps, Poppy was provided with some previously captured movies which she processed and analysed using the same techniques she would have in the ‘wet’ project. These were from samples ± GTPase inhibitors, which are in the same pathway as the PAK inhibitors.
Jenny is a student at the University of Strathclyde. Her project involved testing out one of Nvidia’s new “Jetson” computers with a 3D printed microscope. The Jetson unit is expressly designed for low-cost/high computational power applications. The unit is like a super-powered Raspberry Pi, and the project initially involved testing it as a direct replacement for the Raspberry Pi used in various 3D printed, low cost, microscopes. Once this was done, Jenny used the additional onboard processing power to enable it to run some of the machine-learning based algorithms that are provided with the system. The project gave Jenny a chance to do some core research that will feed into future research and project work, and, most importantly, allowed Jenny to develop some skills that will be useful for her in both her studies and career.
Charlie Sweeting (SPM)
Charlie is currently studying physics and chemistry at Durham University. He proposes to analyse using machine learning a large library of existing high-resolution AFM images of calcite in solution acquired in different conditions and exhibiting a variety of contrasts. The goal is to evaluate how feature extraction and K-Clustering algorithms can disentangle imaging artefacts from genuine, environment-dependent information. The results will be analysed against the metadata information of each image to evaluate its level of success. Further analysis may use multivariate regression (by a random forests approach) to identify the main physical causes of changing topographical images.
Benjamin Hicks (Life Sciences)
Benjamin is a biochemistry student from the University of Bristol. His project will focus on imaging the early steps of the endocytosis of EGF and Transferrin (Tf) via their specific receptors in order to understand whether they are co-internalised in the same vesicles. In order to achieve this, he proposes to combine TIRF-M imaging with CLEM (TIRF-CLEM) to obtain a visualisation of both the composition and structure of budding endocytic vesicles. This project will demonstrate the need for microscopy technology development to answer an outstanding biological question.
Ella Cornish (Physical Sciences)
Ella is studying a Natural Sciences Tripos at the University of Cambridge. Her project proposes to explore the nanoscale properties of a range of wide bandgap semiconductors (AlGaN, Ga2O3, SiC). The morphological properties of the materials will be studied by atomic force microscopy (AFM), while the electrical properties will be investigated by (photo-induced where applicable) tunnelling AFM (TUNA), kelvin probe force microscopy (KFPM) and scanning capacitance microscopy (SCM). This will be complemented by electron beam induced current (EBIC) measurements in the scanning electron microscope. Finally, the optical properties of the features will be assessed using TR-CL. If time allows, selected features will be prepared for investigation by transmission electron microscopy (TEM).
Renat Karimov (Life Sciences)
Renat is reading MPhys Physics at the University of Oxford. His project will obtain new quantitative mechanical maps of the ECM (excessive/abnormal extracellular matrix), and crucially to link these experiments to soft matter physics theory that will allow us to identify the key characteristics of PDAC (pancreatic ductal adenocarcinoma) ECM polymer network ECM (e.g. crosslinking) that play a more crucial role in controlling the fluid of liquid through the ECM structure. Renat will join an existing activity and will be trained in AFM and supervised in the development of the code to analyse the data so that the models incorporate the right physics. At the end of the project we expect to compare the mechanical properties of non-cancer ECM with the properties of ECM that is grown from cancer cells.
Joshua Downe (Life Sciences)
Joshua is a biochemistry undergraduate at the University of Oxford. His project will study marine phytoplankton. Marine phytoplankton contribute significantly to the total carbon fixation on the planet, and are also major players in the occurrence of algal blooms. Studying these organisms, in particular the control of their metabolism in response to exogenous and endogenous agents, and the mechanisms by which they may sense extracellular signals in their environment, is therefore vital to understanding factors controlling algal bloom formation. Calcium (Ca2+) is a universal second messenger in eukaryotes, which plays important roles in signal transduction and environmental sensing. However, whilst considerable work has focussed on the role of Ca2+ signalling in animal and plant biology, relatively little is known of the role of this important signalling process in eukaryotic phytoplankton.
We have recently developed state-of the-art genetically encoded fluorescent Ca2+ biosensors to study the role of Ca2+ signalling in a particularly important group of phytoplankton, the diatoms (Helliwell et al., Current Biology, in press). Using this system we have discovered that diatoms possess a novel nutrient sensing pathway to detect the important macronutrient, phosphate. This process has not previously been described before in eukaryotes. This project will use combine microscopy and cell biology approaches to characterise this pathway further.
Megan Hammett (Physical Sciences)
Megan is a Geology undergraduate from the University of Plymouth. Her project will investigate some of these newly recovered meteorites, collected during fieldwork in the Nullarbor, South Australia in collaboration with the team at Monash University, Melbourne.
The 2018 expedition recovered 32 new finds, including ordinary chondrites, carbonaceous chondrites and achondrites alike, representing 4.7 billion years of Solar System history. Each one is unique; found on aboriginal lands within the Nullarbor plains, these meteorites have never been studied scientifically, and therefore require thorough investigation to officially classify - and name – them.
This mineralogical investigation will require the use of multiple non-destructive techniques (in order to preserve these incredibly rare, extra-terrestrial materials), including optical microscopy and analytical electron microscopy (SEM-EDS; EPMA; FIB-SEM), as well as spectroscopic methods common within planetary sciences (e.g. micro-FT-IR & Raman spectroscopy). The project will generate a detailed compositional and textural analysis of each meteorite. These descriptions will form the main bulk of the official classification documentation submitted to the Meteoritical Society’s Bulletin in order to register the samples as approved, newly discovered meteorites, and will bear the names of all those involved in the investigations.
Stephen Watson (Physical Sciences)
Stephen Watson is working towards his Master’s degree at the University of Glasgow. He proposes to study 3 dimensional magnetic structures using transmission electron microscopy (TEM). Currently magnetic data storage is mostly confined to 2D planar structures, utilising the 3rd dimension offers great prospects for future applications.
Rashid Khashiev (Physical Sciences)
Rashid is a second year student in Natural Sciences (NST) at the University of Cambridge. Rashid’s experience in fluorescence microscopy and computational image analysis will help to carry out the proposed microscopical analysis of embryonic development in the green micro-algae Volvox and other members of the family Volvocaceae.
Tilly Hancock (Physics applied to life)
Tilly is in her second year of a Master’s degree in physics at the University of Bristol. Her interest in the processes of photosynthesis and plants’ self-regulation is the ultimate focus of the proposed project. After first hearing about methods of imaging biological matter, such as laser confocal microscopy, on a STEM summer school, she has become enthused about using microscopy, imaging and spectroscopy for a biological or medical purpose. This project will combine these two interests, using structured light scanning in microscopy to enable to study stomata in plant leaves.
Owen Underwood, (Life Sciences)
Owen is a second year undergraduate in Biochemistry and Molecular Medicine at the University of Nottingham, and the project aims to validate the Teluc BRET imaging technique and investigate receptor pharmacology at the endogenous single cell level. The programme of work will involve investigation of single cell ligand binding using bioluminescence microscopy in previously established live cells engineered with CRISPR/Cas9 to express Teluc/ β2AR or Nluc/ β2AR under endogenous promotion as well as over-expressed receptors. It will provide for high quality training in cutting edge microscopy and CRISPR/Cas9 genome engineering techniques.
Emma McCormick (Physical and Life Sciences)
Emma McCormick is currently in her third year of an MPhys Physics degree at the Department of Physics, University of Strathclyde. Using microscopy to understand the cell biology of Streptomycetes is vital to understand their life cycles, morphological changes caused by secondary metabolite production and quantifying production of extracellular components. The primary aim of this project is to use standing wave microscopy (SWM) to study the morphology of various Streptomycete strains of interest which have various mutations causing changes in their metabolite production.
William Cartwright is a 3rd year Masters student in Physics at the University of Durham. William will be using a novel atomic force microscopy measurement tool to investigate the effect of curvature on the mechanical properties of synthetic extracellular vesicles, a promising tool for nanomedicine.
Rhiannon Heard is in her 3rd year of a Masters in Engineering at the University of Oxford and will use this studentship to conduct a project combining academia and industry. She will spend time in Oxford and at Deben UK using advanced in situ microscopy techniques to characterise the high rate behaviour of polymers under quasistatic conditions.
Nikita Patel is in the 3rd year of her Masters in Pharmacology at University College London. In a project conceived by Nikita, she will further investigate the potential use of mesenchymal stem cells and will use multicolour 3D confocal microscopy to image the lung and spleen in and ex vivo and intravital microscopy to gather completely novel data.
Vinayak Ramdhun is a 2nd year undergraduate at the University of Leicester studying Medical Biochemistry. Sparked by his interest in the central principle of molecular biology, Vinayak will use single-molecule microscopy to dissect the mechanism of promote melting by human GTfs and Pol II in mRNA transcription.
Last year’s RMS studentship recipient has since been offered and accepted a PhD position in Cambridge, partly thanks to the highly successful project that they were able complete with the studentship and that played a big role in them being offered the position. This clearly demonstrates to me how much the studentship makes a difference to the career of students.