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Laser Analytics Group


We have invited the following speakers to the Laser Analytics Group:

15 May 2024

Dr Chris Rowlands started his academic career in 2001 at Imperial College, but on the other side of campus, in the Chemistry department. After discovering that he couldn't sketch a hexagon well enough to be any good at synthetic chemistry, he decided to concentrate on physical chemistry, if only because it required remembering the names of fewer chemists. This proved a good career move, and he went on to study for a PhD in the physics and chemistry of chalcogenide glasses at Cambridge University, in the group of Prof. Stephen Elliott. It was there that he learned about glass synthesis, Raman microscopy, analytical chemistry techniques of all kinds, algorithm design, and several new swearwords for use when attempting to get the laser working again. 

After leaving Cambridge in 2010, he spent a year at the University of Nottingham, studying the use of Raman microscopy in diagnosing cancer in the group of Dr Ioan Notingher, before receiving a three-year Wellcome Trust MIT Postdoctoral Research Fellowship to the Massachusetts Institute of Technology, in the group of Prof Peter So. There he discovered the delights (and curses) of multiphoton microscopy, fluorescence lifetime microscopy, super-resolution imaging, light-sheet microscopy and many more fluorescence microscopy techniques. Five years, several papers, two snowpocalypses and multiple swearwords later, his visa ran out, so he came back to the UK to continue his fellowship back in Cambridge, as a guest in the laboratory of Prof Clemens Kaminski. While nominally developing new super-resolution techniques, a suspiciously high fraction of his time was actually spent drinking tea and trying to sneak naughty acronyms into serious scientific journals.

The tea and naughty acronyms were clearly a good career move, because in 2017 he was invited to join the Bioengineering Faculty at Imperial College as a lecturer. His current research is focussed on the development of optical instrumentation, particularly for use in biological applications. Nevertheless, the main focus of the lab is on interesting research, so if there's a good idea and the resources are available to do it, the group will have a go. Science is supposed to be fun after all.

Seeing Deeper, Faster, Better: Breaking the boundaries of optical microscopy

It has been nearly seven years since Dr Christopher Rowlands left CEB to join the faculty at the Department of Bioengineering at Imperial College, and he returns to show us how “everything he knows, he owes to the traditions and tea-breaks of the department”. He will discuss some of the novel instruments under development in his lab, including instruments for performing Raman spectroscopy at unprecedented speeds (even recording label-free images of a beating zebrafish heart), a 3D Structured Illumination Microscope with one moving part, and a method for creating ultrasound scanners with megapixel resolution using a very scary laser. Attempts will be made to make the talk accessible to all, but there may be some gratuitous raytracing. Viewer discretion is advised.

30 November 2023

Dr Andrea Serio is a Lecturer in Neural Tissue Engineering at King’s College London and a Group Leader within the Francis Crick Institute. He studied biotechnology in Italy before obtaining his PhD at the University of Edinburgh in 2014, where he developed human stem cell-based models of glial neuronal interactions to study neurodegenerative disorders with Prof. Siddharthan Chandran. He then moved to Imperial College London, within Prof. Molly Stevens Lab in the Department of Bioengineering where he focused on developing novel tissue engineering platforms and imaging technologies to better model the nervous system in vitro using stem cells. In 2017 he established his independent group in King’s College London, where he now is Reader in Neural Tissue Engineering, before moving to the Francis Crick Institute in 2019, where he now leads the Neural Tissue Engineering & Disease Modelling group. Since 2023 he is also a principal investigator withing the Dementia Research Institute (UK DRI). His interdisciplinary research focuses on combining engineering, biophysics and neurobiology to develop novel platforms and technologies to allow the modelling of complex neural circuitry in vitro.

Shape Matters: Engineering human stem cells models to understand the relationship between form and function in neural cells

Shape and function are two intimately linked properties in all living cells: the need to perform a certain function has shaped each cell to a specific and optimal shape, which in turns also influences how the cell manages its homeostasis. In cells with very polarised or complex shapes, like neurons and glial cells, this relationship is crucial as

several key functions need to be performed across intricate cellular architectures, with challenges that sometimes cannot be met relying solely on diffusion of metabolites or components.

Stem cell-based models and other in vitro experimental systems can effectively recapitulate key aspects of development and have so far allowed a better understanding of key biological mechanisms underpinning human biology and disease. Access to these models has been particularly invaluable for basic and applied neuroscience.

However, conventional culture conditions often fail to approximate cell shape, and overlook some of the engineering constraints that cells in vivo face. Particularly in the case of specialised neurons covering long range connections such as spinal cord motor neurons (MNs), stem cell models often lack fundamental characteristics of their cytoarchitecture, including axonal length.

MN axons can grow up to 1m in length, and this feature necessitates robust axonal transport, local protein translation and mitochondrial dynamics to maintain cellular homeostasis and functionality, which might not be faithfully captured by shorter cells in standard culture conditions.

To directly address this issue, we have developed a novel bioengineered platform to reproducibly obtain arrays of human motor axons ranging from micrometres to centimetres in length, which we have then used to systematically investigate the effect of cell size on axonal biology for the first time.  We have discovered a link between length and metabolism in human MNs in vitro, where axons above a “threshold” size induce specific adaptations in cytoskeleton composition, functional properties, local translation and mitochondrial homeostasis of the axoplasm.

Our findings indicate the existence of a specific length-dependent mechanism that switches several homeostatic processes within human MNs to cope with extremely long axons. This has critical implications for in vitro modelling of several neurodegenerative disorders and shows the importance of physiologically modelling cell shape and biophysical constraints in vitro.

23 November 2023

Dr Liuba Dvinskikh is a research associate at Imperial College London currently working on the development and application of dual-view oblique plane microscopy (dOPM) [1], a single-objective light-sheet fluorescence microscopy technique, for cleared tissue imaging to study immune cell infiltration in ovarian cancer. Prior to that, Liuba built a dOPM system at the Institute of Cancer Research, London, for imaging heterogenous 3D cancer spheroid models. Liuba's PhD work was focused on remote-refocusing light-sheet fluorescence microscopy, applied to high-speed volumetric imaging of calcium dynamics in cardiomyocytes. Previously, Liuba completed a BSc in Physics, followed by a MSc in Optics and Photonics. Her research interests are focused on the development and application of novel optical instrumentation concepts for fast, high-resolution 3D biomedical imaging.

Fast and high-resolution 3D imaging with light-sheet fluorescence microscopy

The optical sectioning, parallelized acquisition and low phototoxicity of light-sheet fluorescence microscopy (LSFM), or selective plane illumination microscopy (SPIM) [2] has resulted in its increasing use across a wide range of biomedical imaging applications across a variety of spatio-temporal scales: from subcellular organelles to whole organs, and from events spanning milliseconds to week-long timelapses. The development and application of optical instrumentation solutions such as aberration-free remote refocusing [3-4], oblique plane microscopy (OPM) [5], and multi-directional illumination [6] and detection have enabled fast imaging with high and near-isotropic resolution in 3D with improved FOV and imaging depth. In this talk I will review the concepts of single and dual-objective light-sheet fluorescence microscopy in the context of my work on high-speed calcium imaging [7-9] and imaging of 300 µm thick cleared tissue samples with subcellular resolution.  

[1] Sparks et al. (2020a) Biomed. Opt. Express 11 (12)  DOI: 10.1364/BOE.409781
[2] Huisken et al. (2004) Science 305(5686):1007-9 DOI: 10.5281/zenodo.7425649
[3] Botcherby et al. (2007) Opt. Lett 32 (14), DOI: 10.1364/OL.32.002007 
[4] Botcherby et al (2008) Opt. Commun. 281(4) DOI: 10.1016/j.optcom.2007.10.007  
[5] Dunsby C. (2008) Opt. Express 16(25)  DOI 10.1364/OE.16.020306
[6] Huisken and Stainier (2007) Opt.Lett 32(17) DOI: 10.1364/OL.32.002608
[7] Sparks et al. (2020b). J. Biophotonics 13 (6) DOI: 10.1002/jbio.201960239  
[8] Dvinskikh et al. (2023b) Sci. Rep. 13 (3342) DOI: 10.1038/s41598-023-29419-w 
[9] Dvinskikh et al (2023a) Front Physiol 14 DOI: 10.3389/fphys.2023.1079727

12 October 2023

Mateo Sanchez Lopez received his PhD in organic chemistry in 2014 from the University of Santiago de Compostela. The focus of his thesis was on the design and synthesis of fluorescent DNA binders. Mateo developed a new synthetic methodology that enabled a straightforward synthesis of bisbenzamidines and new fluorescent probes. Moreover, he created new chemical approaches to control the interaction of these small molecules with the DNA. Mateo envisioned a pioneering strategy that consists of using an organometallic catalyst in living cells to trigger a biological event, such as DNA binding. For this work, Mateo was awarded with the Eli Lilly Prize for PhD students.

As Mateo was eager to learn molecular biology and directed evolution, in 2015 he joined the group of Prof Alice Ting at the Massachusetts Institute of Technology (MIT), and later in the Department of Genetics at Stanford University. Mateo was awarded with an EMBO long-term postdoctoral fellowship, and his work was focused on the development of new molecular tools for cell biology and neuroscience. As an example, Mateo developed a new platform for the directed evolution of the TEV protease, which yielded faster mutants. For this work, he was awarded XIII Suschem prize in 2021. In 2020 Mateo joined the Synthetic Biology Centre in the department of Bioengineering at Imperial College London, to work with Prof Tom Ellis to gain further expertise in the development of molecular biology using engineering principles. Mateo was awarded with a Marie-Curie Sklodowska-Action supported by the EU Horizon 2020. The project Evolving together involved the design of genetic circuits to study DNA repair mechanisms.

Mateo has recently been awarded a Wellcome Trust Career Development Award and is starting his independent group in the Department of Chemistry at Cambridge.

Developing new molecular tools for the mapping and manipulation of active neuronal circuits

One of the greatest challenges of this century is to understand how the brain computes, transmits, and stores information at single cell resolution while performing different tasks. Which neurons are active during sleep? Is it possible to manipulate neurons in order to recall a specific memory? A lack of molecular technology currently hampers our understanding of the complex processes and connections by which our brains move from simple signals to complex tasks like dreaming or memory formation. 

Over the past 20 years scientists have developed a large suite of genetically encoded calcium indicators (GECIs) that have revolutionized neuroscience. GECIs allow the real-time imaging of neuronal activity in the brains of living animals by displaying transient increases in fluorescence intensity when calcium levels rise in individual firing neurons. GCaMPs are widely used in neuroscience, but only very small fields of view can be imaged and circuit components may be distributed across large and disparate brain regions, making it difficult to track neuronal activity using real-time calcium imaging. Moreover, they do not enable further manipulation of the target neuron. Manipulation is essential in order to establish a causal relationship of the tagged neuronal network to the behaviour of interest. 

In this seminar, I will talk about state-of-the-art in activity-dependent reporters such as FLARE1 (Fast Light- and-Activity Regulated Expression), FLiCRE2,3 (Fast Light and Calcium-Regulated Expression) and scFLARE4 (single-chain FLARE). All these tools consist of a light- and calcium-gated transcription factor that drives the expression of a reporter gene, which in turn, can be used for the discovery and manipulation of neuronal circuits. 

1.        Wang, W. et al. A light- A nd calcium-gated transcription factor for imaging and manipulating activated neurons. Nat. Biotechnol. 35, 864–871 (2017). 

2.        Sanchez, M. I. & Ting, A. Y. Directed evolution improves the catalytic efficiency of TEV protease. Nat. Methods 17, 167–174 (2020). 

3.        Kim, C. K. et al. A Molecular Calcium Integrator Reveals a Striatal Cell Type Driving Aversion. Cell 183, 2003-2019.e16 (2020). 

4.        Sanchez, M. I., Nguyen, Q. A., Wang, W., Soltesz, I. & Ting, A. Y. Transcriptional readout of neuronal activity via an engineered Ca2+-activated protease. Proc. Natl. Acad. Sci. U. S. A. 117, 33186–33196 (2021). 

2 June 2023

Liu Bin is Deputy President (Research and Technology) and a Tan Chin Tuan Centennial Professor at the National University of Singapore (NUS).  Prior to her current appointment, she served as Senior Vice Provost (Faculty & Institutional Development) from 2022 to 2023, Vice President (Research and Technology) from 2019 to 2021 and Head of the NUS Department of Chemical & Biomolecular Engineering from 2017 to 2021.

Liu Bin is an internationally acclaimed leader in the field of organic functional materials and is highly recognised for her contributions in polymer chemistry and applications of organic nanomaterials for biomedical, environmental and energy research.  Since 2014, she has been named annually among the World's Most Influential Scientific Minds by Thomas Reuters and the Top 1% Highly Cited Researchers by Clarivate.  She is a prolific researcher with over 450 publications and holds 30 patents with 16 of them licenced to different companies in the US, UK, and Asia.  In 2014, she co-founded Luminicell, a NUS spin-off company that produces organic luminescent nanoparticles for use in biomedical applications.

She has an impressively extensive list of accolades, including the National Science and Technology Young Scientist Award (2008), the L'Oréal Women in Science National Fellowship (2011), the President's Technology Award (2016), and the American Chemical Society ACS Nano Lectureship Award (2019).  In 2021, she bagged the Kabiller Young Investigator's Award in Nanoscience and Nanomedicine, and the Royal Society of Chemistry Centenary Prize.  She was one of 12 women in the world who received the 2023 International Union of Pure and Applied Chemistry Distinguished Women in Chemistry or Chemical Engineering award.

At NUS, Liu Bin has been instrumental in the development of vibrant innovation clusters across the University's colleges, faculties, and schools, including the NUS Sustainability Cluster, as well as the strengthening of efforts to build up and develop the University's talent pool.  She is especially passionate about nurturing the next generation of research leaders and encouraging more women to pursue careers in science and engineering.

Aggregation-Induced Emission: Materials and Biomedical Applications

Recent years have witnessed the fast growth of fluorogens with aggregation-induced emission characteristics (AIEgens) in biomedical research. The weak emission of AIEgens as molecular species and their bright luminescence as nanoscopic aggregates distinguish them from conventional organic luminophores and inorganic nanoparticles, making them wonderful candidates for many high-tech applications. In this talk, I summarize our recent AIE work in the development of new fluorescent bioprobes for biosensing and imaging. The AIE dot probes with different formulations and surface functionalities show advanced features over quantum dots and small molecule dyes in noninvasive cancer cell detection, long-term cell tracing, and vascular imaging. In addition, our recent discovery that AIEgens with high brightness and efficient reactive oxygen species generation in the aggregate state further expanded their applications to image-guided cancer surgery and therapy. By combing the accurate prediction of material performance via first-principle calculations and Bayesian optimization-based active learning, a self-improving discovery system was realized for high-performance photosensitizers, which significantly accelerated our materials innovation for biomedical research.

18 April 2023

Somenath Bakshi is an Assistant Professor in the Department of Engineering at the University of Cambridge. He did his PhD in University of Wisconsin Madison under Professor James Weisshaar – developing super-resolution imaging technologies to study central cellular processes in microbes. After finishing his PhD, he moved to Harvard University for his postdoc with Professor Johan Paulsson in the Department of Systems Biology. During his postdoc Somenath developed high-throughput time lapse imaging technologies to study stress-response in bacteria. In 2019, he moved to Cambridge, and established the Laboratory of Systems and Synthetic Microbiology. His work focuses on the analysis of the genetic and metabolic factors underlying the emergence of antibiotic resistance, and engineering diagnostic and therapeutic strategies to combat the spread of antibiotic resistance. He is also the head of the recently established Smart Microscopy Laboratory, which is a cross-school platform for bringing together engineers, computer scientists, and biologists to develop targeted imaging solutions for specific biological problems.

Connecting the dynamics of microbial systems across scales

Biological reactions often involve low-copy molecular reactants, leading to stochastic outcomes. As a result, there is substantial heterogeneity among cells, even when they experience the same external conditions. Recent theoretical and experimental investigations have demonstrated that for microbial systems such heterogeneity is of important consequence to the population fitness and therefore also important for their evolution. We are establishing an experimental framework to connect the single-cell level picture of microbes to the short-term and long-term behaviours of their populations. We are using this approach to analyse the extent and role of cellular heterogeneity in determining the population dynamics of microbial systems in the context of - 1. Emergence of antibiotic persistence 2. Fitness costs of plasmids carrying antibiotic resistance genes and 3. The arms race between bacteria and bacteriophages. In this talk I will describe the background and motivation for this approach, the key challenges, the necessary technical advancements, and illustrate its potential with selected key findings.

14 March 2023

Ritwick studied Microbiology and Biochemistry in Mumbai (India) and obtained his PhD in 2010 from Indian Institute of Science, Bangalore. Ritwick then moved to the Department of Biosystems Science and Engineering of ETH-Zürich in Basel (Switzerland) as a postdoctoral fellow with Renato Paro. In 2014, Ritwick started his own independent group at the Max Planck Institute of Immunobiology and Epigenetics in Freiburg (Germany), before moving to the MRC Toxicology Unit of University of Cambridge in 2019. Ritwick received the ERC Consolidator Grant in 2018 and Alfred Tissières Young Investigator Award in 2019. Ritwick leads a multi-disciplinary group of 16 lab members composed of postdocs, PhD students and research assistants.

Transcriptional lockdown, condensates and neurodegeneration

Human cells exposed to stress downregulate their gene expression in a manner similar to the pandemic-associated lockdowns. We termed this phenomenon as Stress-Induced Transcriptional Attenuation (SITA), and identified regulators of SITA. The talk will discuss our recent work on novel nuclear condensates formed by SITA regulators and their significance in neurodegeneration.

3 March 2023

Sarah has been working in the field of neurodegeneration for 13 years, focussing on two overlapping neurodegenerative disorders - frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS).  She has published 24 papers, including a first-author article in Science in 2014, and in 2015 was awarded the UCL Early Careers Neuroscience Prize.  In 2016 she joined King's College London as a Lecturer and was appointed a Fellow of the UK Dementia Research institute in 2017.  Her research has focussed primarily on the FTD/ALS pathomechanisms emanating from mutation in the gene C9ORF72, leading the first study to dissect the RNA and protein gain-of-function mechanisms from this mutation, generating elegant genetic tools to identify the arginine-rich polypeptides as the most toxic species. Her work since has been trying to pinpoint the precise mechanism responsible for this neurotoxicity, specialising in quantitative microscopy from human pathological analysis to single molecule transport in cell models.

Using single molecule, biophysical and cell approaches to unveil structure-function alterations to the nuclear pore in C9ORF72 TDP-43 proteinopathy

Cytoplasmic mislocalisation and aggregation of the RNA-binding proteins TDP-43 in central nervous system post-mortem tissue is characteristic of the vast majority of amyotrophic lateral sclerosis (ALS) cases, but also other neurodegenerative diseases like the overlapping disorder frontotemporal dementia (FTD) and Alzheimer’s disease and traumatic brain injury. Although predominantly nuclear at steady-state, many RNA-binding proteins, like TDP-43, shuttle between the cytoplasm and nucleus as part of their role in RNA homeostasis. Thus, nucleocytoplasmic transport dysfunction has long been implicated in this proteinopathy. In addition, more recent evidence suggests dysfunction directly at the nuclear pore – the large multiprotein complex through which all nucleocytoplasmic transport occurs. We have been studying the earliest changes induced by the toxic de novo dipeptide repeat proteins (DPRs) produced from the C9ORF72 repeat expansion mutation in ALS/FTD in a reductionist system using super-resolution and single molecule imaging, biophysical properties of the selection barrier of the nuclear pore and translating these in patient iPSC derived neuron and cell models to unveil the true molecular mechanisms at play at the nuclear pore. These findings may represent the earliest cellular changes that initiate TDP-43 mislocalisation and initiate the pathological cascade that leads to neurodegeneration from the C9ORF72 repeat expansion mutation in ALS/FTD.

30 September 2022

Nicole Robb is an Assistant Professor at the University of Warwick Medical School and a visiting lecturer at the University of Oxford.  She completed a BSc in Microbiology at Imperial College London before doing a DPhil at the University of Oxford, where she specialised in the field of influenza virology.  Following a post-doc in Physics at the University of Oxford she was awarded a Royal Society Dorothy Hodgkin Fellowship to set up her group at the University of Warwick.  Her current research interests include super resolution microscopy, rapid pathogen detection and using biophysical and biochemical techniques to study viral replication.  She holds several patents on viral diagnostic technology and is co-founder of a University of Oxford spinout company that is working on rapid viral testing.  She is also PhD Course Director of the University of Warwick's Institute for Global Pandemic Planning (IGPP), a new interdisciplinary initiative formed to research solutions to mitigate the effects of pandemics.

Rapid virus detection using single-particle imaging and machine learning

The increasing frequency and magnitude of viral outbreaks in recent decades, epitomized by the current COVID-19 pandemic, has resulted in an urgent need for rapid and sensitive viral diagnostic methods. We have recently discovered a novel, calcium-mediated interaction of the surface of enveloped viruses with DNA, which we use for the rapid fluorescent labelling and optical detection of viruses. Machine learning algorithms can then be used to distinguish between images of single intact particles of different viruses. Our assay achieves labeling, imaging and virus identification in just a couple of minutes and does not require any lysis, purification or amplification steps. We are able to differentiate SARS-CoV-2 from negative clinical samples, as well as from other common respiratory pathogens such as influenza and seasonal human coronaviruses, with high accuracy. In addition, we can also distinguish between viral strains and variants, making this a useful screening tool. Single-particle imaging combined with deep learning therefore offers a promising alternative to traditional viral diagnostic methods.

23 May 2022

Ommar Omarjee left sunny Mauritius in 2010 to study and train as an immunologist in Lyon,France. During his PhD thesis with Professor Alexandre Belot, he characterised novel single-gene defects implicated in rare familial forms of autoimmunity and inflammation. In order to pursue translational human immunology research, Ommar joined the group of Professor Christoph Hess in 2020 to better understand the immuno-metabolic dysregulation underpinning immune disorders in patients.

ER Contact Sites

Cellular metabolism critically defines immune cell function. How cellular metabolism is orchestrated at the ultrastructural level in immune cells remains largely unknown. Recently, we identified contact sites between the endoplasmic reticulum (ER) and mitochondria as critical subcellular hubs integrating metabolic and signaling requirements in memory CD8+ T cells, specifically underpinning their rapid recall capacity. This finding established the ER as a critical ultrastructural component selectively enabling a pivotal memory CD8+ T cell feature. Building on this observation, the overarching goal of this project is to assess how basic ER biology links with key aspects of CD8+ T cell function in the context of primary immune deficiencies (PIDs).

17 March 2022

Miguel Anaya is a Royal Academy of Engineering Research Fellow at the Department of Chemical Engineering and Biotechnology, and a Research Fellow at Darwin College, University of Cambridge. He graduated from Autonomous University of Madrid in 2012 with a B.S.+M.S. in Physics (one year at the Free University of Berlin), and he obtained a second M.S. in Materials Science in 2013 at the University of Seville (First Class Honours). He completed his PhD at the Spanish National Research Council in 2018 under the supervision of Professor Hernan Miguez, with recognition from the Spanish Royal Society of Physics as the best Thesis in Experimental Physics.

Miguel leads a team focussed on the modelling, fabrication, and characterisation of perovskite-based devices at the Optoelectronic Materials and Device Spectroscopy Group (StranksLab). For his work, he has received the SPIE Scholarship, the E-MRS Student Award and an EPSRC Impact Award, and he has been recently distinguished as Emerging Investigator 2021 by the Royal Society of Chemistry.

Halide Perovskites for Sustainable Optoelectronic Devices: from energy to healthcare

Halide perovskites are generating enormous excitement for their use in high-performance yet inexpensive optoelectronic applications. Nevertheless, in spite of their performance, these thin film materials have a plethora of micro- and nano-scale heterogeneities and their impact on performance and stability need to be understood. 

Here, we will describe a series of multimodal microscopy measurements to determine the relationship between material structure, chemistry and photophysical properties. We will present how we can understand and optimise vacuum deposited perovskite materials and apply them for tandem solar cells of superior performance. From a more fundamental point of view, we will show how synchrotron nanoprobe and optical spectroscopic methods correlated at the nanoscale explain why this emerging family of semiconductors is remarkably tolerant to defects. These observations reflect that the quest of highly pristineness in traditional semiconductors such as c-Si or GaN is not necessarily a condition for low temperature processed halide perovskites to perform well when integrated into devices. We will comment on the implications these findings have for the fabrication of highly efficient solar cells, LEDs and high-energy radiation detectors.

25 October 2021

Alexander Borodavka is an experienced postdoctoral researcher with a demonstrated history of working in the higher education industry. He is skilled in research in virology, biochemistry, and biophysics. Alexander is a strong research professional who graduated from the University of Leeds.

Biomolecular Condensates Go Viral: Putting the Spotlight on the RNA Assembly in Viruses with Segmented RNA Genomes

Accurate RNA folding is essential for virus replication. Rotaviruses are viruses infecting humans and animals. Rotavirus genomes are distributed between 11 distinct RNA molecules, all of which must be selectively copackaged during virus assembly. This likely occurs through sequence-specific RNA-RNA interactions facilitated by the viral RNA chaperone NSP2. The RNA chaperone NSP2 binds viral transcripts, regulating their interactions with each other. NSP2 must release RNAs after they base pair prior to their packaging. Using single-molecule fluorescence tools, we dissected the individual steps of the RNA chaperone activity of NSP2. Structural proteomics and cryo-EM studies of the NSP2–RNA complex revealed that NSP2 regulates RNA unfolding and the release of the RNA using its charged C-terminal region. Some aspects of the viral RNA chaperone regulation resemble the conserved autoregulation mechanisms employed by bacterial RNA chaperones. Moreover, RNA chaperone NSP2 readily undergoes liquid-liquid phase separation together with the viral protein NSP5, forming complex protein/RNA-rich condensates that support rotavirus transcript enrichment and genome replication. During viral replication, these condensates can be reversibly dissolved using small molecule modulators of LLPS, resulting in significantly reduced viral replication. Some aspects of the assembly of rotavirus replication factories mirror the formation of other ribonucleoprotein granules. 

10 May 2021

Eva Sevcsik received her Master’s degree in chemistry from Graz University of Technology in 2003. She performed her doctoral research at the Austrian Academy of Sciences in Graz, followed by postdoctoral studies at Yale University. In 2011, she joined the group of Gerhard Schütz at TU Wien as a postdoctoral associate. Eva Sevcsik is now Assistant Professor at the Institute of Applied Physics at TU Wien. She is part of the “BioInterface” network at TU Wien and her research is devoted to the development and application of micro- and nanostructured biointerfaces to manipulate the spatial organization of membrane proteins in living cells. Using these surfaces in combination with single molecule microscopy techniques, she studies the fundamental elements of plasma membrane organization and function, with a specific interest in the molecular mechanisms governing early T cell signaling. 

Spatial requirements for T-cell receptor triggering probed via a DNA origami-based biointerface

The nanoscale spatial organization of ligands and receptors is emerging as an important theme in regulating cell behavior yet inherently challenging to investigate. Antigen recognition by T-cells illustrates this conundrum: while central to adaptive immunity and with most molecular players already identified, knowledge on its operational principles is still limited. We have devised a DNA origami-based biointerface which allows the experimenter to adjust protein distances with nanometer precision as a means to enhance or disturb signaling while being responsive to large scale reorganization processes during cell activation. Applying this biointerface to study the spatial requirements of T-cell activation we find that the smallest signaling-competent receptor unit consists of two stably ligated T-cell receptors (TCRs) within a distance of 20 nanometers. Spatial organization of the physiological ligand pMHC, however, is not a relevant parameter of antigen-mediated T-cell activation as single, well-isolated pMHC molecules efficiently stimulate T-cells.

24 March 2021

Professor Melody Clark is an Individual Merit Promotion Scientist (IMP) and Project Leader at BAS.  She has a genetics degree and PhD from London University.  After a string of short-term postdoctoral contracts working on areas ranging from plant chromosomes to the high-profile Japanese pufferfish genome project, she finally landed a job as a Project Leader at the British Antartic Survey (BAS) in August 2003.  She currently leads the Adaptations group, which studies two main areas: how animals adapt to the extreme cold and how they may react in the fact of predicted climate change, also how molluscs produce their shells (essential protection if there's a large iceberg in the area for the Antarctic species, not really a problem for the temperate species we study).  Grant income is currently running at over £7M in the past 10 years, with the most recent signficant grant being PI and Coordinator of the EU Marie Curie Initial Training Network FP7-PEOPLE-2013-ITN Project no: 605051: CACHE; CAlcium in a CHanging Environment, from November 2013 with a budget of circa €3.7M.  In 2007 she was awarded the Senior Prize for Outstanding Women in Marine Biological Sciences Prize, awarded by the EU-FP6 Network of Excellence, Marine Genomics Europe.

Why do we need high-resolution microscopy to study cold adaptation in Antarctic marine species?

Antarctic marine species live almost permanently below 0°C. At one level, these animals appear to be very successful: there is incredibly biodiversity in the Southern Ocean (estimated at, in excess of, 20,000 species). However, at the cellular level, they appear to have real problems at such cold temperatures, which we think is due to compromised proteostasis. This talk will outline the evidence for cellular problems experienced by multicellular life at 0°C. Some of the issues include reduced efficiency of protein folding and viscosity of the intracellular milieu, which is why we need to design high-resolution microscopy systems to study the folding of individual proteins at 0°C. 

23 February 2021

Professor Roy Quinlan joined the University of Durham in 2001 and was one of those responsible for founding the Biophysical Sciences Institute, which was then established in 2007.  He is a Biochemistry graduate and PhD from the University of Kent where he worked on microtubules with Professor Keith Gull FRS, before taking up an Alexander von Humboldt Fellowship at the German Cancer Research Centre to work on Intermediate Filaments with Professor Werner Franke in 1981.  He joined Dr Murray Stewart at the LMB Cambridge determining the coiled coil pitch of myosin LS2, but continued to investigate structural aspects of GFAP and lamins.  In 1988, he was appointed as a lecturer to the Department of Biochemistry in Dundee.  Here his interest in the cytoskeleton and particularly intermediate filaments in astrocytes, cardiomyocytes and the lens led to the discovery of the functionally important interaction of the small heat shock protein chaperones with intermediate filaments and its role in mediating the biomechanical properties of cells.  In the lens, these proteins are key to its function as an optical element of the eye.  The strong correlation between structure and function in this tissue provides the platform for current research interests to model lens cell organisation in 3 and 4 dimensions and integrating the cytoskeletal and chaperone functions into a scaled model of this tissue.

Aging through the lens of the eye

Twins studies evidence that genetics contributes approx. one quarter to longevity – the rest is environment and circumstance. If you were planning to live your three score and ten years, what would you consider to be essential, desirable and optional features? Biological systems are incredible when it comes to adaption and survival. It is the exceptions that can give us the most insight into how the essential, desirable and optional features can be to preserve function and life for centuries, not just decades. This seminar will take the eye lens as an example of just such an “exception” and how it delivers and preserves transparency and refraction over a lifetime whilst sacrificing what some might consider as essential features to the living cell – namely nuclei, mitochondria, ER and Golgi. In return I hope you can answer this question “Is there a role for RNA after the nucleus is gone?”

21 January 2021

Dr Lakdawala trained as a molecular virologist at the Salk Institute in San Diego, CA on viral ubiquitin ligases. In 2009, she began a post-doctoral fellowship with Dr. Subbarao at the NIH to study influenza airborne transmission and virus assembly dynamics in live cells using light sheet microscopy with Dr Hari Shroff. Seema started an independent laboratory at the University of Pittsburgh School of Medicine in 2015 studying influenza virus assembly and pathogenesis. The Lakdawala Lab has published multiple papers on influenza assembly and recently described a new architecture of the viral genome. Their research has been featured in the popular press (WESA, Gizmodo, and This Week in Virology) and is funded by the NIH, American Lung Association, and Charles E Kaufman Foundation. 

Visualizing Influenza Virus Assembly Using Light Sheet Microscopy

16 December 2020

Raffaele Mezzenga completed his master degree in Materials Science (Summa Cum Laude) from Perugia University, while actively working for the European Center for Nuclear Research (CERN) and NASA on elementary particle-polymer interactions (NASA Space Shuttle Discovery mission STS91). In 2001 he obtained a PhD in the field of Polymer Physics from EPFL Lausanne, focusing on the thermodynamics of reactive polymer blends. He then spent 2001-2002 as a postdoctoral scientist at University of California, Santa Barbara, working on the self-assembly of polymer colloids. In 2003 he moved to the Nestlé Research Center in Lausanne as research scientist, working on the self-assembly of surfactants, natural amphiphiles and lyotropic liquid crystals. In 2005 he was hired as Associate Professor in the Physics Department of the University of Fribourg, and he then joined ETH Zurich on 2009 as Full Professor. His research focuses on the fundamental understanding of self-assembly processes in polymers, proteins, lyotropic liquid crystals, food and biological colloidal systems. Prof. Mezzenga has held several visiting professor positions across the globe, such as in Finland, Australia, Singapore and Italy. He is recipient of several international distinctions among which the AOCS Young Scientist Research Award, both the Dillon Medal and Fellowship of the American Physical Society, the Biomacromolecules/Macromolecules Young Investigator Award of the American Chemical Society, and the Swiss Science National Foundation Professorship Award. 

Amyloid liquid crystals

Chirality is ubiquitous in nature and plays crucial roles in biology, medicine, physics and materials science. Understanding and controlling chirality is therefore an important research challenge with broad implications. Unlike other chiral colloids, such as nanocellulose, collagen or filamentous viruses, amyloid fibrils have been shown to form nematic phases but appeared to miss, until very recently, their twisted form, the cholesteric or chiral nematic phases, despite a well-defined chirality at the single fibril level. In this talk I will discuss our recent discovery of cholesteric phases in amyloids fibrils and the new implications that this discovery brings to the fields of liquid crystals and liquid-liquid phase separation. By selecting amyloid fibrils as model filamentous chiral colloids, an unprecedented breadth of liquid crystalline morphologies is observed, where up to six distinct configurations of the nematic field are observed under identical conditions. Amyloid-rich droplets -also known as tactoids- nucleating from an isotropic phase via liquid-liquid phase separation show homogeneous, bipolar, radial, uniaxial chiral and radial chiral nematic fields, with additional parabolic focal conics in bulk. Furthermore, tactoids of different symmetry undergo order–order transitions by flow-induced deformations of their shape. Tactoids align under extensional flow, undergoing extreme deformation into highly elongated prolate shapes, with the cholesteric pitch decreasing as an inverse power-law of the tactoids aspect ratio. Variational and scaling theories allow rationalizing the experimental evidence as a subtle interplay between surface and bulk energies and to debate on the thermodynamic nature of theses transitions. Along with the role model in neurodegenerative diseases and vital cellular functions, played by pathological and functional amyloids, respectively, these unique filamentous protein aggregates are also emerging as un unparallel model system to deepen our understanding of liquid-liquid phase separation and chiral liquid crystals under confinement, opening to a more comprehensive exploitation in advanced technologies and related functional materials.

24 November 2020

Erwin Peterman is a professor in Physics of Living Systems at the Vrije Universiteit Amsterdam. Currently he is also Head of the Physics and Astronomy Department. He studied Molecular Sciences at Wageningen University and did his PhD in the biophysics of photosynthesis at Vrije Universiteit Amsterdam. After a postdoc in the lab of W.E. Moerner (UC San Diego, Stanford University) he returned to the Vrije Universiteit and has become professor there. He is a single-molecule biophysicists who combines the development of advanced, often laser-based, techniques and their application to important biological problems. His instrument development focusses on single-molecule fluorescence microscopy, optical tweezers and acoustic force spectroscopy. He is cofounder of LUMICKS b.v. a company that develops single-molecule instrumentation and has sold them to labs all over the world. In his biological applications, Peterman focusses on understanding intracellular transport and the role of motor proteins therein and DNA and DNA-binding proteins.

Single-molecule tracking of transmembrane proteins in the chemosensory cilia of C. elegans

Being able to adequately react to one’s environment is essential for survival and procreation. Cilia are vital for the cell’s ability to sense its environment and rely on a process called intra flagellar transport (IFT) for their development, maintenance and function in signal-transduction. As a model, we study C. elegans chemosensory cilia. Motor proteins transport ciliary components along the polarized microtubule axoneme of the cilium. Among the cargoes of IFT are transmembrane proteins involved in signal transduction. We demonstrate the robust, extensive and reversible ciliary retraction upon external chemical stimulation. To elucidate the dynamics underlying this dramatic shift in protein distribution, we performed single-molecule imaging of the transmembrane protein OCR-2 in live C. elegans. Analysis of the single-molecule trajectories shows that, in dendrite and transition zone, active transport is the prevailing motility mode of OCR-2. In the proximal and distal segments, however, motility is a much more complex, location-specific interplay between active transport, normal diffusion and sub diffusion. At the tip, confinement of the membrane proteins plays an important role. Together, our data demonstrates an intricate interplay between modes of transportation that ensure the proper ciliary distribution of OCR-2. These insights in the dynamics of cellular signal-transduction contributes to a wider understanding of IFT dynamics and to cilia as chemosensory organelles.

19 November 2020

Ariel J Ben-Sasson is a research fellow and an acting instructor at the Baker Lab, at the Institute for Protein Design, at the University of Washington. Ariel has joined the Baker Lab in late 2013 as an HFSP Cross Disciplinary Fellow. His research interests are in the areas of protein engineering, self-assembling systems, and functional/conductive bio-materials. Prior to joining the Baker Lab Ariel received his PhD and MSc at the Organic Materials and Devices lab at the Nano-Science program at the Technion – Israel Institute of Technology, and BSc (cum laude) in the Biomedical Engineering Department (2005). Ariel developed methods to design and implement self-assembling systems of synthetic polymers to logic devices and developed the first block-copolymers based Vertical Organic Field Effect Transistor (VOFET). This research garnered awards from the SPIE, EMRS, MRS, TSMC and the Azrieli Fellowship, and several refereed publications and patents.

Designed 2D Binary Protein Materials Geared to Modulate Cells Behaviour

Co-assembling genetically encoded protein materials represent a paradigm shift in engineering of complex biomaterials [1].  Compared to their single-component counterparts such as S-layers and designed analogues, binary systems afford facile components production and functionalization, as well as control over the onset, location, and composition aspects of the formation process that is only initiated by mixing two different building blocks. We leverage these novel binary system properties to go beyond homogeneous protein materials formation, whether in a tube or inside a living cell, and demonstrate formation of biologicallyactive hybrid arrays on mammalian cell membranes and their synthetic counterparts.  In this talk I will describe our methodology to protein material design, the in-silico design machinery (Rosetta) we use to modify or generate molecular shapes and functions, and the set of geometrical constraints that together enable the design of infinitely propagating ordered structures to a predefined shape. I will next describe the experimental set-up for array formation on cell membranes. I introduce the concept of pseudo-symmetrical objects (namely objects which partly possess more than one symmetry) to diversify building blocks functionality: cyclic symmetry to properly anchor to cell receptors, and dihedral symmetry
to robustly propagate in 2D. This work culminates in demonstrating array assembly on cells to tunable dimensions, receptors clustering, biological pathway activation, and endocytosis blocking, which paves the way for novel approaches to interact with and reshape synthetic and living systems.

[1] Ben-Sasson, A. J. et al. Design of Biologically Active Binary Protein 2D Materials.  bioRxiv 2020.09.19.304253 (2020) doi:10.1101/2020.09.19.304253.

12 November 2020

Sebastian Ahnert is a physicist by background, and has just joined CEB as a University Lecturer. His research interests lie on the interface of theoretical physics, biology, mathematics and computer science. He is particularly interested in using algorithmic descriptions of structures and functional systems in order to quantify and classify their complexity. Currently he is also a Senior Research Fellow at The Alan Turing Institute in London, where he leads an effort to develop applications of machine learning to molecular biology. Before coming to CEB he held a joint position between the Cavendish Laboratory and the Sainsbury Laboratory at Cambridge.

The topology and evolution of protein complexes

Proteins play many different roles in every biological cell, and as part of their function many proteins assemble into complexes, which are also referred to as protein quaternary structure. We explore the space of the possible topologies of protein complexes by considering three fundamental ways in which their interfaces can evolve. We show that different combinations of these three steps can give rise to a large variety of possible topologies, and that almost all complexes observed in nature exhibit one of these topologies. This approach also results in a comprehensive classification system of protein complexes. We can also make predictions about topologies that are likely to exist in nature, but have not yet been observed. This predictive power can also be used in tandem with other evidence, such as the stoichiometry and symmetry of a complex of which the topology is not yet known. An example of this is the cellulose synthase complex. Its symmetry and modular organisation can be determined from microscope images, but its exact topology is still a matter of debate. Our approach offers specific predictions of its topology. Lastly we also present a new approach to infer likely evolutionary pathways of complexes by combining topological information with protein domain assignments and sequence alignments. 

3 December 2019

Christophe Leterrier has been working on the organization of the axon since his PhD, where he studied the axonal targeting of the CB1 cannabinoid receptor. For his postdoc, he worked on revealing new cytoskeletal components of the axon initial segment, as well as their nanoscale organization (1). He started the NeuroCyto lab in 2017, with the aim of deciphering the axonal cytoskeleton architecture using advanced microscopy techniques (2,3). The team currently focuses the organization of axonal actin and its partners (4) in order to understand the function of newly discovered axonal actin structures: rings, hotspots and trails (5).

1. Leterrier et al., Cell Rep 13, 2781–2793 (2015)
2. Leterrier et al., Nat. Rev. Neurosci 18, 713–726 (2017)
3. Culley et al., Nat. Methods 15, 263–266 (2018)
4. Ganguly et al., J. Cell Biol. 104, 20576–417 (2015)
5. Papandréou & Leterrier, Mol. Cell. Neurosci 91, 151–159 (2018).

Actin-based structures in the axon: a nanoscale view

The intricate morphology and molecular identity of axons is maintained for decades, but also continuously adapts to changes in the environment and activity of neurons. Axons fulfill these paradoxical demands thanks to a unique cytoskeletal organization that ensures the coordinated transport, anchoring and mobility of axonal components. While axonal microtubules are readily seen by electron microscopy, a number of axonal actin structures have been recently discovered, thanks to the development of optical super-resolution microscopy techniques. We use Single Molecule Localization Microscopy (SMLM) to map the nanoscale architecture of actin-based structures within the axon. In the axon initial segment, a key compartment for the maintenance of neuronal polarity, we resolved a highly organized assembly encompassing the periodic actin/spectrin scaffold and its partners: ankyrin, myosin. We have also visualized new actin structures along the axon shaft: rings, hotspots and trails, and are now resolving their molecular organization and functions. For this, we develop a combination of versatile labeling, correlative acquisition and quantitative analysis strategies that allow for high-content, nanoscale interrogation of the axonal architecture.

2 December 2019

Sid is a German Research Foundation/DFG Fellow at the Centre for Misfolding Diseases and Maxwell Centre. He is developing a research programme on ultrafast non-dissipative nanofluidic detection of protein-misfolding. He is also a Visiting Researcher at the Single-Molecule Optics group, Leiden Institute of Physics and High Magnetic Field Laboratory, Radboud University. During his postdoctoral research at the Leiden Institute of Physics, he developed a new research line to study persistent current in resistive nanomaterials. The visiting position at Leiden enables him to continue this research. Before moving to Leiden, he was in the Debye Institute of Nanomaterials Science, Utrecht as a Postdoctoral Researcher working on non-dissipative single-molecule detection techniques. He received a PhD in Physics on 'Nanoscale Photonics' from the International Max Planck Research School for Physics of Biological and Complex Systems, Göttingen, Germany. During his PhD, he has developed methods on single-molecule nanofluidics and light-matter interaction in nanostructures. He has an MPhil in Mechanical Engineering from the University of Birmingham, UK where he worked on AFM correlated electron microscopy technique for contact-free nanotribological characterisation of complex collagen networks of articular cartilage. Before that, he was a Junior Research Fellow in the Indian Institute of Science, Bangalore where he developed a single-photon lithography technique to fabricate high-aspect-ratio nanostructures for nanomechanical sensing. His research interests are experimental and theoretical nanophotonics, nanofluidics, nanomechanics, nanofabrications and didactic teaching. He is keen on developing an open platform of liberal arts for curiosity-driven research and studying a student dependent customised supervision methods, which turned into as Open Academic Research. Overleaf has awarded him an Overleaf Advisor position for his contribution to collaborative research communication.

Decomposing complex-systems using continuum and quantum mechanics

Complex-systems require a broad range of computational and experimental tools. At continuum domain, multi-variable decomposition often NP hard and at nanoscale domain, uncertainty principle acts as the biggest barrier. His research interest is to develop quantum coherent (in other words non-dissipative) methods to detect single molecules for
ultra-fast dynamics. Some of the key interdisciplinary topics of his research are confined light-matter interaction, single-molecule nanofluidics, noninvasive functional dynamic mapping of cells, mesoscopic persistent current in macromolecules, and a living-lab of research-education.

Siddharth will give two examples of continuum mechanics - nanotribology of soft-matter (like PDMS and articular cartilage) and nanomechanics of atomic defects in inorganic solid-state-matter. The nanoscale continuum is fragile in fluid when single-molecules flow at the border of continuum and quantum world, it is intriguing to play at this interface to see who wins. In quantum mechanics, phonons represent vibrational relaxation of a quantum systems. Can we see an interface where phonons and electrons couple to each other? To answer this, Siddharth will also touch upon experimental and theoretical insight of light-matter interaction in nanomaterials, like carbon nanodots, graphene quantum dots, and ZnO nanorods. In order to play in these fields, manipulation of optics and electron-optics is important. Siddharth will also show how to use single-photon optics to beat the resolution of conventional optical lithography by demonstrating a method for ultra-high aspect nanostructures and electron-beam to enclose nanotrenches to create nanofluidic channels. If time permits, Siddharth will talk about single nanoparticle electrostatic traps, mesoscopic persistent current, and a living-lab situation to understand the evolution of research-based education from the perspective of quantum coherence.

22 July 2019

Professor Jianbin Tang is from the Department of Chemical & Biological Engineering, Zhejiang University. He obtained his PhD from Zhejiang University in 2006 and did his postdoctoral research in the University of Wyoming from 2006 to 2008. Currently, his research focuses on synthesis of nanomaterials for cancer drug delivery and molecular imaging. He has published over 100 scientific papers in Nature Biomedical Engineering, Advanced Materials, JACS, ACS Nano, etc, with a total citations of over 5600.

Anticancer Prodrugs: Targeted Delivery and Selective Release

The talk is about the design and delivery of tumor-specific anticancer prodrugs. The therapeutic effect of chemotherapy drugs with severely hindered by their side effects resulting from poor selectivity. A tumor-specific anticancer prodrug in combination with a drug delivery system can greatly decrease the side effect of chemotherapy drugs and enhance their therapeutic effect. A series of tumor-specific anticancer prodrugs were designed and synthesized and the drug activation in vivo was investigated by fluorescent imaging. Additionally, several tumor signal amplification strategies were developed to further increase the selectivity of anticancer prodrugs. With these tumor signal amplification drug delivery systems, an excellent anticancer efficacy was achieved against multidrug resistant cancer models.

14 June 2019

Vidya Ganapati is an Assistant Professor of Engineering at Swarthmore College. She was previously a Postdoctoral Associate at Verily Life Sciences. She received her Ph.D. and M.S. in Electrical Engineering & Computer Science at the University of California, Berkeley, and her B.S. at the Massachusetts Institute of Technology. She has been a recipient of the CITRIS Athena Early Career Award, the Department of Energy Office of Science Graduate Fellowship, and the UC Berkeley Chancellor's Fellowship. Her current research interests include using optimization, machine learning, and simulation for optical system design, with applications in bioimaging and photovoltaics.

Deep Learned Optical Multiplexing for Microscopy 

Fourier ptychographic microscopy is a technique that achieves a high space-bandwidth product, i.e. high resolution and high field-of-view. In Fourier ptychographic microscopy, variable illumination patterns are used to collect multiple low-resolution images. These low-resolution images are then computationally combined to create an image with resolution exceeding that of any single image from the microscope. Due to the necessity of acquiring multiple low-resolution images, Fourier ptychographic microscopy has poor temporal resolution. Our aim is to improve temporal resolution in Fourier ptychographic microscopy, achieving single-shot imaging without sacrificing space-bandwidth product. We use example-based super-resolution to achieve this goal by trading off generality of the imaging approach.

In example-based super-resolution, the function relating low-resolution images to their high-resolution counterparts is learned from a given dataset. We take the additional step of modifying the imaging hardware in order to collect more informative low-resolution images to enable better high-resolution image reconstruction. We show that this "physical preprocessing" allows for improved image reconstruction with deep learning in Fourier ptychographic microscopy.

In this work, we use deep learning to jointly optimize a single illumination pattern and the parameters of a post-processing reconstruction algorithm for a given sample type. We show that our joint optimization yields improved image reconstruction as compared with sole optimization of the post-processing reconstruction algorithm, establishing the importance of physical preprocessing in example-based super-resolution.

26 February 2019

Dr Ricardo Henriques is a group leader since 2013 at both University College London and the Francis Crick Institute in the UK. His group undergoes research in optical and computational biophysics, with a special interest in super-resolution microscopy and host-pathogen interactions. He graduated in Physics, specialising in biophotonics and robotics. He finished his PhD in 2011 on the topic of advancing super-resolution microscopy technologies (Musa Mhlanga lab). He then pursued postdoc research at Institut Pasteur Paris, studying HIV-1 T-cell infection through nanoscale imaging (Christophe Zimmer lab). 

'Democratising high-quality live-cell super-resolution microscopy enabled by open-source analytics in ImageJ'

In this talk I will present high-performance open-source approaches we have recently developed to enable and enhance optical super-resolution microscopy in most modern microscopes, these are NanoJ-SRRF, NanoJ-SQUIRREL and NanoJ-Fluidics. SRRF (reads as surf) is a new super-resolution method capable of enabling live-cell nanoscopy with illumination intensities orders of magnitude lower than methods such as SMLM or STED. The capacity of SRRF for low-photoxicity, allows unprecedented imaging for long acquisition times at resolution equivalent or better than SIM.  For the second part of the talk, I will introduce SQUIRREL, an analytical approach that provides quantitative assessment of super-resolution image quality, capable of guiding researchers in optimising imaging parameters. By comparing diffraction-limited images and super-resolution equivalents of the same acquisition volume, this approach generates a quality score and quantitative map of super-resolution defects. To illustrate its broad applicability to super-resolution approaches, we demonstrate how we have used SQUIRREL to optimise several image acquisition and analysis pipelines. Finally, I will showcase a novel fluidics approach to automate complex sequences of treatment, labelling and imaging of live and fixed cells at the microscope. The NanoJ-Fluidics system is based on low-cost LEGO hardware controlled by ImageJ-based software and can be directly adapted to any microscope, providing easy-to-implement high-content, multimodal imaging with high reproducibility. We demonstrate its capacity to carry out complex sequences of experiments such as super-resolved live-to-fixed imaging to study actin dynamics; highly-multiplexed STORM and DNA-PAINT acquisitions of multiple targets; and event-driven fixation microscopy to study the role of adhesion contacts in mitosis.

11 February 2019

Silvia Vignolini is a Reader in Chemistry and Bio-inspired materials at the Department of Chemistry at the University of Cambridge. 

'Colour engineering: from nature to applications'

The most brilliant colours in nature are obtained by structuring transparent materials on the scale of the wavelength of visible light. By controlling/designing the dimensions of such nanostructures, it is possible to achieve extremely intense colourations over the entire visible spectrum without using pigments or colorants. Colour obtained through structure,
namely structural colour, is widespread in the animal and plant kingdom. Such natural photonic nanostructures are generally synthesised in ambient conditions using a limited range of biopolymers. Given these limitations, an amazing range of optical structures exists: from very ordered photonic structures, to partially disordered, to completely
random ones.  In this seminar, Silvia will introduce some striking example of natural photonic structures and review our recent advances to fabricate bio-mimetic photonic structures using the same material as nature. Biomimetic with cellulose-based architectures enables us to fabricate novel photonic structures using low cost materials in ambient conditions.  Importantly, it also allows us to understand the biological processes at work during the growth of these structures in plants.

28 January 2019

Claire Durrant is a Research Associate at the John van Geest Centre for Brain Repair at the University of Cambridge.

'Organotypic hippocampal slice cultures as tools to investigate mechanisms of presynaptic disruption in sporadic and familial Alzheimer's disease models'

Loss of presynaptic proteins in the hippocampus is an early and clinically-relevant alteration in the brains of patients with Alzheimer’s disease (AD). Long term organotypic hippocampal slice cultures (OHSCs) from neonatal amyloid mice provide an excellent platform to examine mechanisms of synaptic disruption, largely retaining the cellular composition and neuronal architecture of the in vivo hippocampus, but with in vitro advantages of accessibility to live imaging, sampling and intervention.

OHSCs were made from P6-P9 wild-type, TgCRND8 or APP NL-G-F knockin mice and maintained in culture for up to 2 months. Transgenic cultures were monitored for spontaneous pathology development and the mechanisms behind presynaptic disruption were probed via pharmacological manipulation of Aβ production and genetic knockdown of tau. Wild-type cultures were treated with a battery of environmental factors associated with risk of sporadic AD, such as pro-inflammatory compounds, and assessed for AD-related pathological changes.

In both TgCRND8 and APP-knockin OHSCs there is a progressive accumulation of intra-axonal Aβ. In TgCRND8 cultures, this correlates with a decline in presynaptic proteins and alterations in mRNA levels for synaptic proteins. Beta-secretase inhibitor abolished accumulation of Aβ1-42 but surprisingly did not rescue synaptophysin levels. This raises the question of whether BACE1-independent APP products, or APP overexpression as in Down syndrome and APP duplication patients, underlie some synaptic defects. Elucidation of any synaptic changes in the APP-knockin model is ongoing, providing an effective experimental system to test this hypothesis. LPS or IL1β treatment of wild-type slices resulted in a significant loss of synaptophysin protein, similar to that seen in the TgCRND8 model.

OHSCs represent an important new system for understanding mechanisms of presynaptic disruption in AD. Comparison between genetic and sporadic models of AD may help identify common pathways to target for therapeutic intervention. Future work will examine mechanisms resulting in synaptophysin depletion, particularly in relation to the involvement of tau, relative contribution of APP overexpression and mutations, as well as alternative APP processing products.

13 August 2018

Andrew Barentine is a PhD student of Biomedical Engineering in the Bewersdorf lab at Yale University School of Medicine. 

'3D Nanoscopy at 10000 Cell a Day'

Single-Molecule-Switching (SMS) nanoscopy methods retrieve spatial information from within a cell at 20-80 nm resolution, about 10-fold better than conventional microscopy. However, the slow recording speed typical of SMSN imaging (tens of minutes) limits the number of cells which can be imaged, dramatically weakening the statistical power of quantitative SMS-based investigation. sCMOS cameras and high laser powers have recently enabled acquisition at speeds an order of magnitude faster than with EMCCD cameras. However, the large data volume produced by sCMOS cameras, ~70 TB/day, has prevented extended high-speed SMS. In addition to the difficulty of data storage, the localization analysis bottleneck is compounded for high-quality fits, as the non-negligible sCMOS read-noise requires a more complicated noise model. We developed a platform for high-speed and high-throughput SMSN, included in the Python Microscopy Environment (PYME), which enables automated super-resolution imaging of ~10000 3D fields of view a day. We leverage distributed storage and a fully GPU-accelerated sCMOS-specific routine to localize 49500 loc./s, which is real-time at 800 Hz for up to 62 emitters/frame. We demonstrated our advances using an automated biplanar-astigmatism microscope designed to produce high-volumes of 3D and two-color SMS data, allowing us to image entire nuclei in less than 10 seconds. In addition to real-time localization of full-bandwidth sCMOS data, we developed a distributed post-localization analysis architecture integrated in PYME. With our other advances, we can now quantify unprecedented numbers of SMS images, which we are using to investigate the organization of the interphase nucleus. 

 26 April 2018

Jonathan Powell is the Head of Biomineral Research and Fellow of Hughes Hughes.  John Wills is a Herchel Smith Fellow and Fellow of Girton College.

 'In Situ Cytometry Studies of the Endogenous Nano-chaperone Pathway for Gut Immune Cell Surveillance'

In 2015 we reported on our discovery of an endogenous nanomineral that chaperones luminal antigen and bacterial MAMPs to intestinal immune cells, as a part of normal immunosurveillance (Nature Nanotechnology. 2015 Apr;10(4):361-9). We have since shown that this pathway is promiscuous, across species and operates far beyond the ileal lymphoid patches as we originally described it. We have also shown that in humans there is hijack of the pathway by engineered food additive and xcipient nanoparticles, to which humans are so commonly orally exposed. The recipient immune cells for both the endogenous and exogenous nanoparticles normally express the immuno-modulatory receptor PD-L1, but we showed that this fails in Crohn’s disease (Sci Rep. 2016 May 26;6:26747). These and ensuing studies face marked technical challenges: the endogenous chaperone is friable and labile and destroyed by processing so in situ analyses of frozen or anhydrous tissues is required. Signals- such as cytokines and chemokines that diffuse from cells- provide strong clues as to whether recipient cells of particles are initiating cell-cell signalling so gradients must be established, again in situ and quantitatively. Quantitative cell content with precise locational data and nearest neighbour phenotypes are also required. All of these- and more- are addressed by our development of in situ cytometry (ISC). Like similar quantitative histology and histochemistry techniques, ISC utilises open source software to segment cells and analyse their content and location simultaneously. Through integration of carefully controlled sample preparation, imaging, image analysis and machine learning, we are able to provide fully quantitative cell-by-cell outputs for the complex tissue types and variable tissue regions that make up the gastrointestinal tract, and demonstrate detailed nanoparticle interactions in situ.  

26 April 2018

Dr Madeline Lancaster is a Group Leader in the Cell Biology Division of the Medical Research Council (MRC) Laboratory of Molecular Biology, part of the Cambridge Biomedical Campus in Cambridge, UK. Madeline studied biochemistry at Occidental College, Los Angeles, USA, before completing a PhD in 2010 in biomedical sciences at the University of California, San Diego, USA. She then joined the Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) in Vienna, Austria as a postdoctoral researcher, before joining the LMB in 2015.

Human brain development exhibits a number of unique characteristics, such as dramatic size expansion and variation in relative abundance of specific neuron populations. In an effort to better understand human brain development, we developed a human model system, called cerebral organoids. Cerebral organoids, or “mini-brains”, are 3D tissues generated from human pluripotent stem cells that allow modelling of brain development in vitro. We have been able to demonstrate that brain organoids are particularly powerful not only for examining human specific mechanisms, but also pathogenesis of neurological disease. More recently, we have developed improvements to better control their differentiation using micropatterning to guide their development while maintaining self-organization. Current findings reveal the timed generation of excitatory neurons and inhibitory interneurons as well as their proper migration and positioning. We are now using this system to perform the first functional tests of putative brain evolution genes in this human model system. These studies are revealing some interesting roles for these factors in regulation of human neurogenesis.

Research in the Lancaster lab focuses on human brain development using a new model system, called cerebral organoids. These ‘mini-brains’ are 3D tissues generated from stem cells that allow modelling of human brain development in vitro. The laboratory uses mini-brains to study the most fundamental differences between human brain development and that of other mammalian species – what makes us human. We are also studying neurodevelopmental disorders such as autism and intellectual disability, and the cellular mechanisms underlying neurodevelopmental disease progression and potential therapeutic avenues.

Lab webpage: 

20 March 2018

Sam Stranks is a Royal Society URF in the Cavendish. He completed his PhD (DPhil) in Physics at Oxford University, followed by a JRF at Worcester College Oxford and a Marie Curie Fellowship at MIT. He received the 2017 European Physical Society Early Career award for his contributions to the perovskite field. 

Halide perovskites are generating enormous attention for their potential use in inexpensive yet high-performance photovoltaics and light-emitting diodes. However, device performance is still limited by non-radiative losses. In this work, I'll discuss our recent work revealing the origin of non-radiative decay in the bulk and at interfaces through imaging. I'll describe how we can tactically remove the losses through passivation approaches, which could push devices towards their limits. 

14 February 2018

Dr Eggeling holds a PhD in Physics from the University of Göttingen. He worked as a research scientist at the biotech company Evotec and was as a senior scientist at the Max-Planck-Institute for Biophysical Chemistry in the department of Professor Stefan Hell. Since 2012, Christian Eggeling has been a principal investigator in the Human Immunology Unit and the scientific director of the newly established Wolfson Imaging Centre Oxford at the Weatherall Institute of Molecular Medicine. He has been appointed Professor of Molecular Immunology in 2014 and started as a Professor of Super-Resolution Microscopy in the Institute of Applied Optics of the Friedrich Schiller-University and the Leibniz Institute of Photonic Technologies in Jena in 2017. Christian Eggeling’s research is focused on the development of advanced microscopy for the investigation of molecular organization and dynamics in cells, especially on the cellular plasma membranes. He will be talking about tackling challenges and potentials in biomedical research with Super-resolution microscopy:

Understanding the complex interactions of molecular processes underlying the efficient functioning of the human body is one of the main objectives of biomedical research. Scientifically, it is important that the applied observation methods do not influence the biological system during observation. A suitable tool that can cover all of this is optical far-field fluorescence microscopy. Yet, biomedical applications often demand coverage of a large range of spatial and temporal scales, and/or long acquisition times, which can so far not all be covered by a single microscope and puts some challenges on microscope infrastructure. Taking immune cell responses and plasma membrane organization as examples, we outline these challenges but also give new insights into possible solutions and the potentials of these advanced microscopy techniques, e.g. for solving long-standing questions such as of lipid membrane rafts.

7 February 2018

Marcel Bruchez is Professor for Biological Sciences and Chemistry at Carnegie Mellon University and Director of the Molecular Biosensors and Imaging Center.

He will be talking about the "Fluorogen Switch":

Fluorogen activating proteins that activate the fluorescence of triarylmethane dyes have been demonstrated as practical tags for both cell surface and intracellular labelling, with applications ranging from single-molecule imaging to whole-animal optogenetics. The binding of a fluorogenic dye can result in thousands-fold activation, serving as a binding mediated optical switch, which activates fluorescence from otherwise dark molecules. Synthesis of various fluorescent donors linked to a far-red excitable fluorogen at distances far shorter than the Forster radius of the dyes has established a new family of FRET-based multi excitation fluorogenic dyes, with tunable excitation and emission properties suitable for use with a wide variety of conventional and superresolution microscopy methods. Use of environmentally sensitive donor dyes produces targeted and activated ratiometric fluorescent indicators, enabling optical physiology at and beyond the diffraction limit. I will discuss applications of pH sensors in living cells for measurement of endolysosomal trafficking and development and validation ROS generating and sensor dyes for use in live cells and model organisms.

 30 January 2018

George Malliaras from the Department of Engineering will present his work on interfacing with the brain using organic electronics.

One of the most important scientific and technological frontiers of our time is the interfacing of electronics with the human brain. This endeavour promises to help understand how the brain works and deliver new tools for diagnosis and treatment of pathologies including epilepsy and Parkinson's disease. Current solutions, however, are limited by the materials that are brought in contact with the tissue and transduce signals across the biotic/abiotic interface. Recent advances in organic electronics have made available materials with a unique combination of attractive properties, including mechanical flexibility, mixed ionic/electronic conduction, enhanced biocompatibility, and capability for drug delivery. I will present examples of novel devices for recording and stimulation of neurons and show that organic electronic materials offer tremendous opportunities to study the brain and treat its pathologies.

22 January 2018

Professor Thomas Huser from the Biomolecular Photonics Group at the University of Bielefeld will present his latest efforts in unveiling and following structural changes of cellular nanopores in living cells by GPU-enhanced super-resolution structured illumination microscopy.

During the last decade a number of optical imaging techniques have been developed that utilize different physical or photochemical means to overcome the optical diffraction limit. Any single technique is, however, often not well suited to address all needs of a specific biomedical research problem. Single molecule localization microscopy, for instance, provides very high spatial resolution and quantification, but requires a considerable amount of time to conduct which is often not ideal for addressing imaging needs in live cell studies. Super-resolved structured illumination microscopy, on the other hand, is well suited for live cell imaging, but its spatial resolution improvement is, in most cases, limited to a factor of two. In my research group, much of the research interests are driven by specific biomedical needs, e.g. resolving the structure and dynamics of nanopores in the cellular plasma membrane, or investigating the mechanisms and specific sequence in the transmission of virus from infected cells to uninfected cells. To best address these issues from all perspectives, we typically utilize a suite of multimodal methods, e.g. the combination of optical tweezers with optical nanoscopy, or the combination of temporal and spatial methods of improving the spatial resolution and select the best possible method for each research question. 

16 January 2018

Professor Melody Clark has a genetics degree and PhD from London University. After a string of short-term post doc contracts working on areas ranging from plant chromosomes to the high-profile Japanese pufferfish genome project, she finally landed a job as Project Leader at the British Antarctic Survey (BAS) in August 2003.

She currently leads the Adaptations group and will talk about how animals have adapted to life in freezing oceans and how they respond to climate change. In particular, the paradox of the incredible biodiversity in the Southern Ocean and the cellular level problems of protein folding at such low temperatures.

30 August 2017

Dr Ahluwalia is working on optimizing and fabricating high-refractive index contrast waveguides for lab-on-a-chip applications including optical trapping, propulsion, sensing, and superresolution microscopy.

He talked about Nanoscopy over millimeter scale using photonic chip” and provided us with an overview of photonics chip-based dSTORM, chip-based light fluctuating optical nanoscopy, and chip-based SIM (structured illumination microscopy). By retrofitting photonic chips to any standard optical microscope it is possible to convert it into an optical nanoscope (dSTORM, SIM, etc). Chip-based optical nanoscopy enables sub-100 nm optical resolution over extra-ordinary large field-of-view (millimetre scale). This will enable application of high-throughput chip-based optical nanoscopy in diagnostics and pathology.

  •  Dr Marcel Mueller

12 July 2017

Marcel Müller studied physics and worked a post doc at Bielefeld University where he developed the widely known fairSIM plug-in for ImageJ. He then continued his work in Oxford to include 3D-SIM capabilities in software package and started a new post doc in the Dedecker lab in Leuven to work on Multifocus 3D-SIM.

  •  Professor Anatoly Grudinin

7 July 2017

Anatoly Grudinin started his work in the area of fiber optics in 1980 as one of the first researchers who studied nonlinear properties of silica fibers and nonlinear dynamics of picosecond and femtosecond pulse evolution in single-mode optical fibers. In 2003 Anatoly left his professor's chair at the Optoelectronics Research Centre at University of Southampton and founded Fianium, a fiber laser company focused on development and volume manufacturing of ultrafast fiber lasers for bio-medical and industrial applications. 

In this talk “Ultrafast fiber lasers: the hunt for a killer application” he reviewed latest developments and applications of picosecond and femtosecond fiber lasers. Motivated by rapid improvement of performance and attractive features such as compactness and low ownership cost, ultrafast fiber lasers now challenge conventional DPSS ultrafast sources across numerous industrial sectors. They enable development of unique sources such as supercontinuum lasers capable of enabling scientific discovery and replace incumbent illumination technologies within industrial instruments and systems.

16 June 2017

Morten Bache is associate professor in the Nonlinear Optics and Biophotonics Section at DTU Fotonik and Ultrafast Nonlinear Optics team leader. He is an expert in theoretical and numerical modeling of nonlinear optical phenomena with a vast experience in realistic numerical modeling of experiments. During his Ph.D. and a 3 year postdoc in Italy he worked on nonlinear and quantum optics and on ultra-fast spatial and temporal phenomena in quadratic nonlinear materials. His current research concerns ultra-fast femtosecond nonlinear optics in fibers and nonlinear crystals.

12 June 2017

Dr Salter is a W.W. Spooner Research Fellow at New College in Oxford and conducts research into photonic engineering,    particularly adaptive optics systems, laser microfabrication and diamond technology. 

​He gave a talk entitled "​Adaptive optics for femtosecond laser writing inside transparent materials" in which he described methods of writing waveguides into CVD diamond materials and applications. 

22 May 2017

Dr Derivery is a group leader at the Laboratory of Molecular Biology in Cambridge. He pioneers ground breaking new imaging and biophysical tools to study symmetry breaking during development.

Dr Derivery talked about polarized endosome dynamics by spindle asymmetry during asymmetric cell division. During asymmetric division, fate determinants at the cell cortex segregate unequally into the two daughter cells. It has recently been shown that Sara signalling endosomes in the cytoplasm also segregate asymmetrically during asymmetric division. Dr. Derivery and his group unravelled the molecular mechanism of this asymmetric dispatch of signalling endosomes.

11 May 2017

Dr Hassanali is a senior investigator in the Condensed Matter and Statistical Physics section (CMSP) at the International Center for Theoretical Physics (ICTP) in Trieste, Italy.

Dr Hassanali talked about theoretical and computational investigations of quantum and microscopic interactions in molecular systems using ab initio molecular dynamics simulations. Dr Hasanali's team performed ground breaking molecular dynamics and DFT simulations to explain our intriguing discovery that the amyloid systems develop an intrinsic fluorescence in the UV-Vis range that is independent of aromatic residues.  His simulation demonstrated that frequent proton charge exchanges can take place between adjacent C- and N- Termini in amyloids.