Pedro Matos Pereira

Pedro Matos Pereira
University College London | UCL · MRC Laboratory for Molecular Cell Biology

Degree in Applied Chemistry; Master in Biotechnology, PhD in Cell Biology

About

83
Publications
17,220
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Introduction
I take advantage of my background in microbiology, chemistry, biochemistry and cell and molecular biology to explore how pathogens interact and overcome their host. I complement these classical approaches with technology developments through the development of new solutions for Super-Resolution microscopy. Bridging these approaches I aim to bring new insights into the key molecular pathways involved in host-pathogen interactions.
Additional affiliations
January 2014 - present
University College London
Position
  • Research Associate
Description
  • Our research is focused on the development of experimental technology to study biological processes that fall outside of the resolving power of conventional cell biology studies. We specially focus on applications to super-resolution (SR) microscopy.
January 2010 - December 2013
Universidade NOVA de Lisboa
Position
  • PhD Student
January 2008 - present
Universidade NOVA de Lisboa
Position
  • Response of Staphylococcus aureus to cell wall synthesis inhibitors
Description
  • S. aureus PBPs Cell Wall Peptidoglycan HPLC CW purification molecular biology Fluorescence microscopy Atomic Force Microscopy

Publications

Publications (83)
Article
Full-text available
This work demonstrates and guides how to use a range of state-of-the-art artificial neural-networks to analyse bacterial microscopy images using the recently developed ZeroCostDL4Mic platform. We generated a database of image datasets used to train networks for various image analysis tasks and present strategies for data acquisition and curation, a...
Preprint
Deep Learning (DL) is rapidly changing the field of microscopy, allowing for efficient analysis of complex data while often outperforming classical algorithms. This revolution has led to a significant effort to create user-friendly tools allowing biomedical researchers with little background in computer sciences to use this technology effectively....
Article
Full-text available
The first step of cellular entry for the human immunodeficiency virus type-1 (HIV-1) occurs through the binding of its envelope protein (Env) with the plasma membrane receptor CD4 and co-receptor CCR5 or CXCR4 on susceptible cells, primarily CD4+ T cells and macrophages. Although there is considerable knowledge of the molecular interactions between...
Preprint
Full-text available
The first step of cellular entry for the human immunodeficiency virus type-1 (HIV-1) occurs through the binding of its envelope protein (Env) with the plasma membrane receptor CD4 and co-receptor CCR5 or CXCR4 on susceptible cells, primarily CD4+ T cells and macrophages. Although there is considerable knowledge of the molecular interactions between...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
A new fluorescent chemosensor for copper (II) and subsequent anion sensing was designed and fully characterized. The sensor consisted of a 1,8-naphthalimide core, bearing two terminal dipicolylamine (DPA) receptor units for binding metal cations, and an ethoxyethanol moiety for enhanced water solubility. The DPA units are connected to position 4 of...
Article
Full-text available
Localization based super‐resolution microscopy relies on the detection of individual molecules cycling between fluorescent and non‐fluorescent states. These transitions are commonly regulated by high‐intensity illumination, imposing constrains to imaging hardware and producing sample photodamage. Here, we propose single‐molecule self‐quenching as a...
Preprint
Full-text available
Localization based super-resolution microscopy relies on the detection of individual molecules cycling between fluorescent and non-fluorescent states. These transitions are commonly regulated by high-intensity illumination, imposing constrains to imaging hardware and producing sample photodamage. Here, we propose single-molecule self-quenching as a...
Article
Full-text available
Super-Resolution Microscopy enables non-invasive, molecule-specific imaging of the internal structure and dynamics of cells with sub-diffraction limit spatial resolution. One of its major limitations is the requirement for high-intensity illumination, generating considerable cellular phototoxicity. This factor considerably limits the capacity for l...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
Quantitative fluorescence and superresolution microscopy are often limited by insufficient data quality or artifacts. In this context, it is essential to have biologically relevant control samples to benchmark and optimize the quality of microscopes, labels and imaging conditions. Here, we exploit the stereotypic arrangement of proteins in the nucl...
Preprint
Super-Resolution Microscopy enables non-invasive, molecule-specific imaging of the internal structure and dynamics of cells with sub-diffraction limit spatial resolution. One of its major limitations is the requirement for high-intensity illumination, generating considerable cellular phototoxicity. This factor considerably limits the capacity for l...
Article
Full-text available
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Article
Full-text available
Single-molecule localization microscopy (SMLM) techniques allow near molecular scale resolution (~ 20 nm) as well as precise and robust analysis of protein organization at different scales. SMLM hardware, analytics and probes have been the focus of a variety of studies and are now commonly used in laboratories across the world. Protocol reliability...
Article
Single-molecule localization microscopy (SMLM) techniques allow near molecular scale resolution (~ 20 nm) as well as precise and robust analysis of protein organization at different scales. SMLM hardware, analytics and probes have been the focus of a variety of studies and are now commonly used in laboratories across the world. Protocol reliability...
Preprint
Full-text available
Quantitative fluorescence and superresolution microscopy are often limited by insufficient data quality or artifacts. In this context, it is essential to have biologically relevant control samples to benchmark and optimize the quality of microscopes, labels and imaging conditions. Here we exploit the stereotypic arrangement of proteins in the nucle...
Article
Full-text available
Combining and multiplexing microscopy approaches is crucial to understand cellular events, but requires elaborate workflows. Here, we present a robust, open-source approach for treating, labelling and imaging live or fixed cells in automated sequences. NanoJ-Fluidics is based on low-cost Lego hardware controlled by ImageJ-based software, making hig...
Article
Full-text available
Super-resolution microscopy (SRM) has become essential for the study of nanoscale biological processes. This type of imaging often requires the use of specialised image analysis tools to process a large volume of recorded data and extract quantitative information. In recent years, our team has built an open-source image analysis framework for SRM d...
Article
Full-text available
TMEM16F is a Ca2+ -gated ion channel that is required for Ca2+ -activated phosphatidylserine exposure on the surface of many eukaryotic cells. TMEM16F is widely expressed and has roles in platelet activation during blood clotting, bone formation and T cell activation. By combining microscopy and patch clamp recording we demonstrate that activation...
Chapter
Full-text available
Super-resolution microscopy (SRM) can provide a window on the nanoscale events of virus replication. Here we describe a protocol for imaging hepatitis C virus-infected cells using localization SRM. We provide details on sample preparation, immunostaining, data collection, and super-resolution image reconstruction. We have made all efforts to genera...
Article
Full-text available
The cytoskeleton occupies a central role in cellular immunity by promoting bacterial sensing and antibacterial functions. Septins are cytoskeletal proteins implicated in various cellular processes, including cell division. Septins also assemble into cage-like structures that entrap cytosolic Shigella, yet how septins recognise bacteria is poorly un...
Data
SEPT6-GFP HeLa cells were infected with S. flexneri mCherry for time-lapse microscopy. Each frame was acquired every 2 min. Scale bar, 1 μm.
Data
SEPT6-RFP HeLa cells were infected with P. aeruginosa GFP for time-lapse microscopy, and imaged every 2 min. Scale bar, 1 μm.
Data
SEPT6-RFP HeLa cells were infected with S. aureus GFP for time-lapse microscopy, and imaged every 2 min. Scale bar, 1 μm.
Preprint
Full-text available
Single-molecule localization microscopy (SMLM) techniques allow near molecular scale resolution (~ 20nm) as well as precise and robust analysis of protein organization at different scales. SMLM hardware, analytics and probes have been the focus of a variety of studies and are now commonly used in laboratories across the world. Protocol reliability...
Preprint
Full-text available
Super-resolution microscopy has become essential for the study of nanoscale biological processes. This type of imaging often requires the use of specialised image analysis tools to process a large volume of recorded data and extract quantitative information. In recent years, our team has built an open-source image analysis framework for super-resol...
Preprint
NK cell responses depend on the balance of signals from inhibitory and activating receptors. However, how the integration of antagonistic signals occurs upon NK cell-target cell interaction is not fully understood. Here, we provide evidence that NK cell inhibition via the inhibitory receptor Ly49A is dependent on its relative colocalization at nano...
Preprint
Full-text available
Fluorescence microscopy can reveal all aspects of cellular mechanisms, from molecular details to dynamics, thanks to approaches such as super-resolution and live-cell imaging. Each of its modalities requires specific sample preparation and imaging conditions to obtain high-quality, artefact-free images, ultimately providing complementary informatio...
Article
Full-text available
Super-resolution microscopy techniques break the diffraction limit of conventional optical microscopy to achieve resolutions approaching tens of nanometres. The major advantage of such techniques is that they provide resolutions close to those obtainable with electron microscopy while maintaining the benefits of light microscopy such as a wide pale...
Article
Full-text available
Super-resolution microscopy depends on steps that can contribute to the formation of image artifacts, leading to misinterpretation of biological information. We present NanoJ-SQUIRREL, an ImageJ-based analytical approach that provides quantitative assessment of super-resolution image quality. By comparing diffraction-limited images and super-resolu...
Preprint
TMEM16F, an ion channel gated by high cytoplasmic Ca ²⁺ , is required for cell surface phosphatidylserine exposure during platelet aggregation and T cell activation. Here we demonstrate in Jurkat T cells and HEK293 cells that TMEM16F activation triggers large-scale surface membrane expansion in parallel with lipid scrambling. Following TMEM16F medi...
Preprint
Most super-resolution microscopy methods depend on steps that contribute to the formation of image artefacts. Here we present NanoJ-SQUIRREL, an ImageJ-based analytical approach providing a quantitative assessment of super-resolution image quality. By comparing diffraction-limited images and super-resolution equivalents of the same focal volume, th...
Article
Full-text available
Toxoplasma gondii is the most common protozoan parasitic infection in man. Gamma interferon (IFNγ) activates haematopoietic and non-haematopoietic cells to kill the parasite and mediate host resistance. IFNγ-driven host resistance pathways and parasitic virulence factors are well described in mice, but a detailed understanding of pathways that kill...
Article
Full-text available
Despite significant progress, high-speed live-cell super-resolution studies remain limited to specialized optical setups, generally requiring intense phototoxic illumination. Here, we describe a new analytical approach, super-resolution radial fluctuations (SRRF), provided as a fast graphics processing unit-enabled ImageJ plugin. In the most challe...
Data
Live-cell microtubule dynamics imaged with SRRF. EGFP-labeled microtubules in live HeLa cells imaged at 100 frames per second, yielding 1 super resolution frame per second. First half: top panel TIRF imaging, bottom panel SRRF rendering, inset corresponds to zoom for second half of the movie. Second half: expansions of inset, plot shows the normali...
Data
Long-term SRRF imaging of microtubule dynamics. EGFP-labeled microtubules in live HeLa cells imaged at 100 frames per second, yielding 1 super resolution frame per second, every 25 minutes for 8 hours. Top panel: TIRF imaging, bottom panel: SRRF rendering. Between 5 and 6 hours the cell lifts from the coverslip, undergoing mitosis. Scale bar is 5 μ...
Data
T cell spreading following drop imaged with SRRF. LifeAct-GFP-labeled actin in a live Jurkat T cell imaged at 100 frames per second, yielding 1 super resolution frame per second. The T cell is dropped onto an anti-CD3 coated coverslip, leading to spreading of the cell and reorganization of the intracellular actin network. Left panel: TIRF movie, ri...
Data
The SRRF algorithm. The SRRF algorithm source code and plugin for ImageJ and Fiji are provided along with a manual providing instructions for installation and use.
Data
Rendering of the radiality transform for various parameters and input point-spread-functions. The radiality transform is shown for the real image (i.e. diffraction-limited image) under a wide range of conditions. In the first half of the movie the radiality transform of an image of a single fluorophore is considered. Firstly, the ring radius over w...
Data
Mitochondrial dynamics imaged with SRRF. Mitotracker Red-labeled mitochondria in live HeLa cells imaged at 100 frames per second, yielding 1 super resolution frame per second. Top panel: TIRF movie, bottom panel: SRRF rendering. Scale bar is 5 μm.
Data
Supplementary Figures 1-12, Supplementary Tables 1- 2, Supplementary Notes 1-3, Supplementary Methods, Supplementary References.
Data
Non-directed actin rearrangement following stimulation with anti-CD28 imaged with SRRF. LifeAct-GFP-labeled actin in a live Jurkat T cell imaged at 100 frames per second, yielding 1 super resolution frame per second. An anti-CD28 coated coverslip is used to stimulate immunological synapse formation. Left panel: TIRF movie, right panel: SRRF renderi...
Data
Retrograde flow of actin during immunological synapse formation upon stimulation with anti-CD3 imaged with SRRF. LifeAct-GFP-labeled actin in a live Jurkat T cell imaged at 100 frames per second, yielding 1 super resolution frame per second. An anti-CD3 coated coverslip is used to stimulate immunological synapse formation. Left panel: TIRF movie, r...
Data
Retrograde flow of actin during immunological synapse formation upon stimulation with anti-CD3&CD28 imaged with SRRF. LifeAct-GFP-labeled actin in a live Jurkat T cell imaged at 100 frames per second, yielding 1 super resolution frame per second. An anti-CD3&CD28 coated coverslip is used to stimulate immunological synapse formation. Left panel: TIR...