Building a collaborative research culture at Kavli INsD: We've started small but with impact.
Dr Corinne Lutomski
Dissecting neuropsychiatric disorders in a mass spectrometer
I aim to understand the central mechanisms of neuropsychiatric disorders, and how key receptors in the brain accept and interpret extracellular signals to guide mood and behavior. My research uses mass spectrometry to decipher how the collection of interactions in cells, between proteins, lipids and metabolites, drive such processes. A critical challenge of this work is to sequence large proteins and identify small molecule interactors within intact assemblies in the same experiment. My research requires me to (i) develop new methods for investigating protein-effector networks within the context of their native cellular environments (i.e. the brain), and (ii) build new technology in mass spectrometry to be able to controllably dissect these assemblies inside the mass spectrometer. I envision that new workflows in native mass spectrometry will transform the way we use molecular composition; we can harness this technology to reveal new diagnostics for neuropsychiatric disorders, leading to targeted interventions based on an individual’s biology.
#massspectrometry #topdownMS #neuroscience
Dr Tarick El-baba
Charting molecular interactions underlying higher brain function using native mass spectrometry
My research aims to develop native mass spectrometry techniques to decipher the collection of interactions - between proteins, lipids, and metabolites - that drives cellular processes of the mind. By capturing and dissecting molecular interactions directly from neuronal membranes, I am to delineate changes to molecular interactions associated with learning, perception, and memory. In the long term, I am keen to leverage these discoveries to devise novel treatment strategies for debilitating psychiatric conditions such as depression, addiction, and anxiety.
#nativemassspectrometry #topdownproteomics #neurochemistry #neuroscience
Dr Sean Burnap
Exploring host-pathogen interactions using mass photometry and crosslinking mass spectrometry
Viruses are decorated with spike proteins that enable their interaction with receptors on host cells and subsequent infection. Viral spike proteins are often highly modified with sugar molecules, termed glycans, yet the exact role that these sugars play in facilitating interactions remains largely unexplored. Using glyco-engineering approaches coupled with crosslinking mass spectrometry and mass photometry, my research aims to dissect, with molecular detail, the role glycans play in mediating host-pathogen interactions.
#glycotime #XLMS #glycans #viruses
Dr Bethan Cole
Preclinical development of TRPC3 inhibitors to treat spinocerebellar ataxia
Spinocerebellar ataxias (SCAs) are a group of autosomal dominant neurodegenerative disorders affecting the cerebellum, the region of the brain responsible for fine motor control and coordination. The progressive dysfunction of the cerebellum associated with SCAs leads to severely impaired quality of life and for many patients is fatal. There is a large unmet clinical need for therapeutics to treat or slow the progression of SCAs, and there are currently no preventative treatments available. The Becker lab has identified the non-selective cation channel TRPC3 as being a promising therapeutic target to treat a range of genetically distinct SCA subtypes. We are generating and optimising drug leads to target TRPC3 using a combination of medicinal chemistry, in vitro electrophysiological assays and in vivo preclinical testing methods. Ultimately, the aim is to translate these drugs into clinical testing in SCA patients.
#ionchannels #TRPC3 #ataxia #electrophysiology #drugscreening
Dr Oliver Pambos
Super-resolution fluorescence microscopy to understand transcription in living cells
My research combines super-resolution microscopy with sophisticated data analytics to study the behaviour of single molecules in live cells beyond the diffraction limit of light - the fundamental limit beyond which light cannot be focused. By controlling the temporal pattern of laser light illuminating the cell, the observation time of individual molecules is extended from a few seconds to several minutes. At these timescales we are capturing for the first time the entire process individual RNA polymerase proteins transcribing entire genes, one molecule at a time. This is enabling us to answer fundamental biological questions about how this protein machinery works by directly observing it at work in living cells.
#nanometers
250 nanometers: the diffraction limit of visible light
25 nanometers: the spatial resolution when tracking individual molecules
15 minutes: the maximum duration over which we can follow a single molecule
10 milliseconds: duration of the pulse of laser light used to locate single molecules
1 minute: the time to transcribe an individual gene in E.coli
Dr Manish Kushwah
Mechanism and dynamics of polymerisation for membrane binding proteins using label-free single molecule imaging.
Membrane binding proteins (MBPs) are a large sub-section of proteins that reversible bind cell membranes and undergo large scale self-association leading to polymerization which is inextricably linked to their function in various cellular processes. Due to the inherent heterogeneity of the intermediates, cryo-EM reconstruction of pre-assembled polymers has been the desired method to study protein polymerisation. I am interested in developing method that allow quantitative understanding the dynamics of protein polymerization and for this, I am using mass photometry, a label-free, single molecule counting method that provides quantitative estimate the abundance of all species of our model protein system, dynamin, under non-polymerizing and polymerizing conditions to derive the mechanism of polymerisation. We have also developed label-free single particle tracking using mass photometry, which allows us to validate our mechanism on membranes. Taken together, we are able to develop a framework that can provides dynamics of polymerisation method for various membrane binding proteins.
#Protein-polymerisation #membrane biophysics #dynamin #single-particle-tracking #label-free imaging
Dr Jussi-Pekka Tolonen
Cerebellar organoids: The next generation of disease models in childhood-onset ataxias
Ataxia and other cerebellar movement disorders are often severely debilitating diseases.
To combat a pressing lack of treatment options in ataxia, our goal is to identify novel targets for drug development.
As the first step, we are using exciting stem cell-based models of the developing cerebellum, cerebellar organoids, to study signalling pathways that play a key role in ataxia.
#Ataxia #PurkinjeCells #Organoids #CalciumSignalling
Dr Elise Padbury
Exosome biogenesis in Spinocerebellar ataxia
My work is focused on the generation and release of exosomes from clinically relevant human stem cell models of spinocerebellar ataxia. By employing TIRF microscopy and proteomics, we are analysing how disease-causing mutations in the mGluR1-TRPC3 signalling pathway influence the quantity, characteristics and contents of exosomes, with the ultimate aim of identifying disease-specific markers for the early detection and monitoring of ataxic patients.
#Extracellularvesicles #Exosomes #TRPC3 #Cerebellarataxia #TIRF
Dr Roi Asar
Understanding the fundamental physical principles that govern biomolecular interactions and function.
Currently, our work focuses on a mechanistic understanding of the interaction between Spike glycoprotein of SARS-Cov-2 and its cell receptor ACE2. Quantification of such interaction (in the range of nanomolar) as well as resolving binding stoichiometries and avidity is still experimentally challenging. We are using mass photometry (MP), a method for label-free mass measurement of single biomolecules in solution by light scattering. MP enables us to detect, track and measure the mass of individual proteins and their complexes in solution and on membranes, which provides new information on the interaction structure and dynamics.
#Mass photometry #Single molecule Label-free detection #Biomolecular interactions
Dr Carolyn Nielsen
The main exploratory immunology projects with samples from a blood-stage malaria RH5 protein/adjuvant vaccine clinical trial.
My exploratory immunology research focuses on human T and B cell responses to malaria vaccines. I am particularly interested in heterogeneity in vaccine immunogenicity and efficacy as mediated by vaccine platform and regimen. My current work focuses on integrating flow cytometry, systems serology, and single cell RNA sequencing approaches to understand how delayed booster dosing regimens can improve humoral immunogenicity.
#immunogenicity #vaccine #immunology
Dr Hafez El Sayyed
Single Particle Tracking to understand genetic reception
I use single particle tracking to understand how genetic information from conception to expression is maintained and safeguarded. Tracking one transcription molecule at a time allows us to understand various protein kinetics in its natural host providing more life-cell insight and how bacterial proteins diffuse and interact with their partners by measuring their individual molecule movement in real time.
#tracking #PALM #Microbiology #nucleic acid #transaction
hafez.elsayyed@physics.ox.ac.uk
Dr Benedict Tanudjojo
Phenotypic manifestation of ⍺-synuclein strains derived from PD and MSA in iPSC-derived DA neurons
The progressive accumulation and subsequent aggregation of a small neuronal protein, alpha-synuclein, contributes majorly to the symptoms that characterise Parkinson’s disease (PD) and related neurodegenerative disorders. To date, only partially effective symptomatic therapies exist. Therefore, there is an urgent unmet need to inform curative strategies by attempting to answer the question of how does aggregated alpha-synuclein kill neurons? To investigate the mechanisms underlying neuronal death, we generated a model using human neurons derived from patient stem cells, which recapitulated key disease features. Our study demonstrated that the extent of aggregation was dependent on the abundance of alpha-synuclein within neurons—and importantly, that the toxicity of alpha-synuclein was determined by subtle differences in the three-dimensional structure of aggregates. We screened for proteins that interacted with structurally different alpha-synuclein aggregates and discovered 56 candidates, one of which we further explored. In summary, our findings provide an insight into the complex nature of aggregation and how it ultimately leads to the demise of neurons. We define (i) alpha-synuclein levels, (ii) aggregate morphology and (iii) divergent interacting partners as the most important players in our model.
#Seeded aggregation #iPSC #Synuclein strain
Benedict completed his DPhil in July 2022 entitled: Molecular mechanisms of alpha-synuclein aggregation in Parkinson’s disease with Professor Georg Tofaris and is now an alumnus of the Kavli INsD
Dr Rana Abdul Razzak
Synthesis of Artificial Ribosome using DNA
My project aims at building DNA architectures that can synthesize functional molecules, such as peptides. Compared to the natural ribosome, our artificial ribosomes can use both naturally occurring and synthetic building blocks for the synthesis of engineered peptides. Engineered peptides can be used to modulate the activity of enzymes implicated in the pathology of diseases (Science, 2004, Vol.304 (5669), p.448-452) or they can be used as precursors in the synthesis of proteins via ligation chemistries ((a)Biopolymers, 2001, Vol.60 (3), p.194-205; (b)Chemical Society reviews, 2012, Vol.41 (21), p.7001-7015). The programable assembly of DNA allows the synthesis of the peptides in a sequence-controlled manner.
#DNA #Protein synthesis #Programable assembly
Dr Jade Marsh
Investigating disease modifying strategies for Parkinson’s disease
My research is dedicated to investigating two key pathological processes implicated in Parkinson's disease: alpha-synuclein aggregation and the accumulation of dysfunctional mitochondria. One of my objectives is to develop disease-relevant cellular based assays and leverage them to (i) discover the molecular effectors that govern alpha-synuclein proteostasis and (ii) identify therapeutic compounds that can restore alpha-synuclein proteostasis. The other objective of my research is to (i) characterise novel compounds that target a known regulator of mitochondrial clearance using cellular models and (ii) identify and validate an EV-based biomarker that can indicate successful engagement of the target. Through this research, we aim to develop effective strategies to intervene in the disease progression.
#cellular-based disease models (e.g. iPSC-derived dopaminergic neurons) #extracellular vesicles #target-engagement biomarkers #phenotypic-based compound screening #Parkinson’s disease
