Hardware, software, and applications of super-resolution microscopy

Modern microscopy techniques can image beyond the diffraction limit, in three spatial dimensions, and capture sub-cellular resolution videos, providing new biological insight and assisting in drug development. However, such advanced instruments typically require expert engineers and physicists to operate them, limiting their throughput and practicality for answering biological questions. Moreover, analysis of the raw data is complicated and there are significant barriers to publishing and sharing the data with others. This thesis addresses these problems, presenting two tools designed to reduce the level of expertise required to acquire and publish modern microscopy data. The development of a structured illumination microscope (SIM) is described, with a particular emphasis on control and reconstruction software designed to make SIM accessible to biologists who are new to super-resolution microscopy. The microscope's ease-of-use has led to a wide variety of biological investigations, which are presented as case studies to assist readers of this thesis in designing their own SIM experiments. The current practice for publishing 3D data is to show 2D intensity projections or fly-through videos, which present the data only from the author's perspective and do not give readers the opportunity to explore the results themselves. To solve this problem, Chapter 3 introduces my new volumetric rendering program, FPBioimage, which runs in a web browser. By creating a tool that is intuitive and easy to use, FPBioimage enables researchers around the world to immediately view their colleagues' experimental results, even when separated by thousands of miles. Two biological studies are discussed in detail to highlight the ability of these tools to answer the latest questions in cell biology. SIM's combination of high speed and high resolution video capture reveals a pinching phenomenon in the endoplasmic reticulum which was previously unknown, responsible for active flow of luminal proteins. FPBioimage is used to show metal organic frameworks successfully delivering sensitive drugs to cells, establishing a new method of cancer treatment. All software presented in this thesis is freely available, and has been carefully written to be reusable by other researchers. This is evidenced by OMERO, an online microscopy data repository, adopting FPBioimage as their default volumetric renderer. The open-source license under which the software is distributed means that developers can continue to build on the programs, extending the capabilities as new technology becomes available.Integrated Photonic and Electronic Systems Centre for Doctoral Training (IPES CDT

A new online tool for visualization of volumetric data

This work was sponsored by the Engineering and Physical Sciences Research Council (EPSRC) UK, the Medical Research Council (MRC) UK and the Wellcome Trust

Computer-aided discovery of a metal-organic framework with superior oxygen uptake.

Current advances in materials science have resulted in the rapid emergence of thousands of functional adsorbent materials in recent years. This clearly creates multiple opportunities for their potential application, but it also creates the following challenge: how does one identify the most promising structures, among the thousands of possibilities, for a particular application? Here, we present a case of computer-aided material discovery, in which we complete the full cycle from computational screening of metal-organic framework materials for oxygen storage, to identification, synthesis and measurement of oxygen adsorption in the top-ranked structure. We introduce an interactive visualization concept to analyze over 1000 unique structure-property plots in five dimensions and delimit the relationships between structural properties and oxygen adsorption performance at different pressures for 2932 already-synthesized structures. We also report a world-record holding material for oxygen storage, UMCM-152, which delivers 22.5% more oxygen than the best known material to date, to the best of our knowledge

Design of a Functionalized Metal-Organic Framework System for Enhanced Targeted Delivery to Mitochondria.

Mitochondria play a key role in oncogenesis and constitute one of the most important targets for cancer treatments. Although the most effective way to deliver drugs to mitochondria is by covalently linking them to a lipophilic cation, the in vivo delivery of free drugs still constitutes a critical bottleneck. Herein, we report the design of a mitochondria-targeted metal-organic framework (MOF) that greatly increases the efficacy of a model cancer drug, reducing the required dose to less than 1% compared to the free drug and ca. 10% compared to the nontargeted MOF. The performance of the system is evaluated using a holistic approach ranging from microscopy to transcriptomics. Super-resolution microscopy of MCF-7 cells treated with the targeted MOF system reveals important mitochondrial morphology changes that are clearly associated with cell death as soon as 30 min after incubation. Whole transcriptome analysis of cells indicates widespread changes in gene expression when treated with the MOF system, specifically in biological processes that have a profound effect on cell physiology and that are related to cell death. We show how targeting MOFs toward mitochondria represents a valuable strategy for the development of new drug delivery systems

The structure and global distribution of the endoplasmic reticulum network is actively regulated by lysosomes

The endoplasmic reticulum (ER) comprises morphologically and functionally distinct domains, sheets and interconnected tubules. These domains undergo dynamic reshaping, in response to changes in the cellular environment. However, the mechanisms behind this rapid remodeling are largely unknown. Here, we report that ER remodeling is actively driven by lysosomes, following lysosome repositioning in response to changes in nutritional status: the anchorage of lysosomes to ER growth tips is critical for ER tubule elongation and connection. We validate this causal link via the chemo- and optogenetically driven re-positioning of lysosomes, which leads to both a redistribution of the ER tubules and its global morphology. Therefore, lysosomes sense metabolic change in the cell and regulate ER tubule distribution accordingly. Dysfunction in this mechanism during axonal extension may lead to axonal growth defects. Our results demonstrate a critical role of lysosome-regulated ER dynamics and reshaping in nutrient responses and neuronal development.This research was funded by Infinitus (China) Company Ltd. (supporting M.L. and C.F.K.); a UKRI Engineering and Physical Sciences Research Council (EPSRC) grant (EP/L015889/1) awarded to the Centre for Doctoral Training in Sensor Technologies and Applications (supporting F.W.v.T.); a Sir Henry Wellcome Postdoctoral Fellowship from the Wellcome Trust (215943/Z/19/Z, to J.Q.L.); the Netherlands Organization for Scientific Research (NWO) (supporting W.N.); the European Research Council (ERC) (supporting L.K.); Wellcome Trust Collaborative Grant (203249/Z/16/Z to C.E.H. and C.F.K.); and the UK Dementia Research Institute, which receives its funding from UK DRI Ltd., funded by the UK Medical Research Council, Alzheimer’s Society, and Alzheimer’s Research UK (supporting E.A. and C.F.K.). D.H.’s research is supported by a PSL-Cambridge grant and an ERC grant, agreement no. 88267

Intramitochondrial proteostasis is directly coupled to α-synuclein and amyloid β1-42 pathologies.

Mitochondrial dysfunction has long been implicated in the neurodegenerative disorder Parkinson's disease (PD); however, it is unclear how mitochondrial impairment and α-synuclein pathology are coupled. Using specific mitochondrial inhibitors, EM analysis, and biochemical assays, we report here that intramitochondrial protein homeostasis plays a major role in α-synuclein aggregation. We found that interference with intramitochondrial proteases, such as HtrA2 and Lon protease, and mitochondrial protein import significantly aggravates α-synuclein seeding. In contrast, direct inhibition of mitochondrial complex I, an increase in intracellular calcium concentration, or formation of reactive oxygen species, all of which have been associated with mitochondrial stress, did not affect α-synuclein pathology. We further demonstrate that similar mechanisms are involved in amyloid-β 1-42 (Aβ42) aggregation. Our results suggest that, in addition to other protein quality control pathways, such as the ubiquitin-proteasome system, mitochondria per se can influence protein homeostasis of cytosolic aggregation-prone proteins. We propose that approaches that seek to maintain mitochondrial fitness, rather than target downstream mitochondrial dysfunction, may aid in the search for therapeutic strategies to manage PD and related neuropathologies.Infinitus China Ltd

C-terminal calcium binding of α-synuclein modulates synaptic vesicle interaction.

Alpha-synuclein is known to bind to small unilamellar vesicles (SUVs) via its N terminus, which forms an amphipathic alpha-helix upon membrane interaction. Here we show that calcium binds to the C terminus of alpha-synuclein, therewith increasing its lipid-binding capacity. Using CEST-NMR, we reveal that alpha-synuclein interacts with isolated synaptic vesicles with two regions, the N terminus, already known from studies on SUVs, and additionally via its C terminus, which is regulated by the binding of calcium. Indeed, dSTORM on synaptosomes shows that calcium mediates the localization of alpha-synuclein at the pre-synaptic terminal, and an imbalance in calcium or alpha-synuclein can cause synaptic vesicle clustering, as seen ex vivo and in vitro. This study provides a new view on the binding of alpha-synuclein to synaptic vesicles, which might also affect our understanding of synucleinopathies

Design of a functionalized metal-organic framework system for enhanced targeted delivery to mitochondria

Mitochondria play a key role in oncogenesis and constitute one of the most important targets for cancer treatments. Although the most effective way to deliver drugs to mitochondria is by covalently linking them to a lipophilic cation, the in vivo delivery of free drugs still constitutes a critical bottleneck. Herein, we report the design of a mitochondria-targeted metal-organic framework (MOF) that greatly increases the efficacy of a model cancer drug, reducing the required dose to less than 1% compared to the free drug and ca. 10% compared to the non-targeted MOF. The performance of the system is evaluated using a holistic approach ranging from microscopy to transcriptomics. Super-resolution microscopy of MCF-7 cells treated with the targeted MOF system reveals important mitochondrial morphology changes that are clearly associated with cell death as soon as 30 minutes after incubation. Whole transcriptome analysis of cells indicated widespread changes in gene expression when treated with the MOF system, specifically in biological processes that have a profound effect on cell physiology and that are related to cell death. We show how targeting MOFs towards mitochondria represents a valuable strategy for the development of new drug delivery systems

OptiJ: Open-source optical projection tomography of large organ samples

Abstract: The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples

OptiJ: Open-source optical projection tomography of large organ samples

The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples