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Ardan
Patwardhan
,
Alun
Ashton
,
Robert
Brandt
,
Sarah
Butcher
,
Raffaella
Carzaniga
,
Wah
Chiu
,
Lucy
Collinson
,
Pascal
Doux
,
Elizabeth
Duke
,
Mark H.
Ellisman
,
Erik
Franken
,
Kay
Grunewald
,
Jean-Karim
Heriche
,
Abraham
Koster
,
Werner
Kühlbrandt
,
Ingvar
Lagerstedt
,
Carolyn
Larabell
,
Catherine L.
Lawson
,
Helen
Saibil
,
Eduardo
Sanz-García
,
Sriram
Subramaniam
,
Paul
Verkade
,
Jason R
Swedlow
,
Gerard J
Kleywegt
Open Access
Abstract: We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community.
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Oct 2014
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Abstract: X-rays are used for imaging many different types of biological specimen, ranging from live organisms to the individual cells and proteins from which they are made. The level of detail achieved as a result of the imaging varies depending on both the sample and the technique used. One of the most recent technical developments in X-ray imaging is that of the soft X-ray microscope, designed to allow the internal structure of individual biological cells to be explored. With a field of view of ∼10–20 × ∼10–20 μm, a penetration depth of ∼10 μm and a resolution of ∼40 nm3, the soft X-ray microscope neatly fits between the imaging capabilities of light and electron microscopes.
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Jun 2014
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I02-Macromolecular Crystallography
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Abstract: At the end of cell division, cytokinesis splits the cytoplasm of nascent daughter cells and partitions segregated sister genomes1, 2. To coordinate cell division with chromosome segregation, the mitotic spindle controls cytokinetic events at the cell envelope. The spindle midzone stimulates the actomyosin-driven contraction of the cleavage furrow, which proceeds until the formation of a microtubule-rich intercellular bridge with the midbody at its centre. The midbody directs the final membrane abscission reaction1, 2 and has been proposed to attach the cleavage furrow to the intercellular bridge3. How the mitotic spindle is connected to the plasma membrane during cytokinesis is not understood. Here we identify a plasma membrane tethering activity in the centralspindlin protein complex, a conserved component of the spindle midzone and midbody4. We demonstrate that the C1?domain of the centralspindlin subunit MgcRacGAP associates with the plasma membrane by interacting with polyanionic phosphoinositide lipids. Using X-ray crystallography we determine the structure of this atypical C1?domain. Mutations in the hydrophobic cap and in basic residues of the C1?domain of MgcRacGAP prevent association of the protein with the plasma membrane, and abrogate cytokinesis in human and chicken cells. Artificial membrane tethering of centralspindlin restores cell division in the absence of the C1?domain of MgcRacGAP. Although C1?domain function is dispensable for the formation of the midzone and midbody, it promotes contractility and is required for the attachment of the plasma membrane to the midbody, a long-postulated function of this organelle3. Our analysis suggests that centralspindlin links the mitotic spindle to the plasma membrane to secure the final cut during cytokinesis in animal cells.
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Dec 2012
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B24-Cryo Soft X-ray Tomography
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Abstract: Cryo-soft X-ray tomography (cryo-SXT) is a synchrotron-hosted imaging technique used to analyze the ultrastructure of intact, cryo-prepared cells. Correlation of cryo-fluorescence microscopy and cryo-SXT can be used to localize fluorescent proteins to organelles preserved close to native state. Cryo-correlative light and X-ray microscopy (cryo-CLXM) is particularly useful for the study of organelles that are susceptible to chemical fixation artifacts during sample preparation for electron microscopy. In our recent work, we used cryo-CLXM to characterize GFP-LC3-positive early autophagosomes in nutrient-starved HEK293A cells (Duke et al., 2013). Cup-shaped omegasomes were found to form at “hot-spots” on the endoplasmic reticulum. Furthermore, cryo-SXT image stacks revealed the presence of large complex networks of tubulated mitochondria in the starved cells, which would be challenging to model at this scale and resolution using light or electron microscopy. In this chapter, we detail the cryo-CLXM workflow that we developed and optimized for studying adherent mammalian cells. We show examples of data collected at the three European synchrotrons that currently host cryo-SXT microscopes, and describe how raw cryo-SXT datasets are processed into tomoX stacks, modeled, and correlated with cryo-fluorescence data to identify structures of interest.
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Oct 2014
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Open Access
Abstract: One of the ultimate aims of imaging in biology is to achieve molecular localisation in the context of the structure of cells in their native state. Here, we review the current state of the art in cryo-soft X-ray tomography (cryo-SXT), which is the only imaging modality that can provide nanoscale 3D information from cryo-preserved, unstained, whole cells thicker than 1 μm. Correlative cryo-fluorescence and cryo-SXT adds functional information to structure, enabling studies of cellular events that cannot be captured using light, electron or X-ray microscopes alone.
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Mar 2014
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I13-2-Diamond Manchester Imaging
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Carles
Bosch
,
Joerg
Lindenau
,
Alexandra
Pacureanu
,
Christopher J.
Peddie
,
Marta
Majkut
,
Andrew C.
Douglas
,
Raffaella
Carzaniga
,
Alexander
Rack
,
Lucy
Collinson
,
Andreas T.
Schaefer
,
Heiko
Stegmann
Diamond Proposal Number(s):
[20274]
Open Access
Abstract: Correlative multimodal imaging is a useful approach to investigate complex structural relations in life sciences across multiple scales. For these experiments, sample preparation workflows that are compatible with multiple imaging techniques must be established. In one such implementation, a fluorescently labeled region of interest in a biological soft tissue sample can be imaged with light microscopy before staining the specimen with heavy metals, enabling follow-up higher resolution structural imaging at the targeted location, bringing context where it is required. Alternatively, or in addition to fluorescence imaging, other microscopy methods, such as synchrotron x-ray computed tomography with propagation-based phase contrast or serial blockface scanning electron microscopy, might also be applied. When combining imaging techniques across scales, it is common that a volumetric region of interest (ROI) needs to be carved from the total sample volume before high resolution imaging with a subsequent technique can be performed. In these situations, the overall success of the correlative workflow depends on the precise targeting of the ROI and the trimming of the sample down to a suitable dimension and geometry for downstream imaging. Here, we showcase the utility of a femtosecond laser (fs laser) device to prepare microscopic samples (1) of an optimized geometry for synchrotron x-ray tomography as well as (2) for volume electron microscopy applications and compatible with correlative multimodal imaging workflows that link both imaging modalities.
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Apr 2023
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I13-2-Diamond Manchester Imaging
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Carles
Bosch
,
Tobias
Ackels
,
Alexandra
Pacureanu
,
Yuxin
Zhang
,
Christopher J.
Peddie
,
Manuel
Berning
,
Norman
Rzepka
,
Marie-Christine
Zdora
,
Isabell
Whiteley
,
Malte
Storm
,
Anne
Bonnin
,
Christoph
Rau
,
Troy
Margrie
,
Lucy
Collinson
,
Andreas T.
Schaefer
Diamond Proposal Number(s):
[20274]
Open Access
Abstract: Understanding the function of biological tissues requires a coordinated study of physiology and structure, exploring volumes that contain complete functional units at a detail that resolves the relevant features. Here, we introduce an approach to address this challenge: Mouse brain tissue sections containing a region where function was recorded using in vivo 2-photon calcium imaging were stained, dehydrated, resin-embedded and imaged with synchrotron X-ray computed tomography with propagation-based phase contrast (SXRT). SXRT provided context at subcellular detail, and could be followed by targeted acquisition of multiple volumes using serial block-face electron microscopy (SBEM). In the olfactory bulb, combining SXRT and SBEM enabled disambiguation of in vivo-assigned regions of interest. In the hippocampus, we found that superficial pyramidal neurons in CA1a displayed a larger density of spine apparati than deeper ones. Altogether, this approach can enable a functional and structural investigation of subcellular features in the context of cells and tissues.
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May 2022
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Open Access
Abstract: Cryo-soft X-ray tomography (cryo-SXT) is a powerful imaging technique that can extract ultrastructural information from whole, unstained mammalian cells as close to the living state as possible. Subcellular organelles including the nucleus, the Golgi apparatus and mitochondria have been identified by morphology alone, due to the similarity in contrast to transmission electron micrographs. In this study, we used cryo-SXT to image endosomes and autophagosomes, organelles that are particularly susceptible to chemical fixation artefacts during sample preparation for electron microscopy. We used two approaches to identify these compartments. For early and recycling endosomes, which are accessible to externally-loaded markers, we used an anti-transferrin receptor antibody conjugated to 10 nm gold particles. For autophagosomes, which are not accessible to externally-applied markers, we developed a correlative cryo-fluorescence and cryo-SXT workflow (cryo-CLXM) to localise GFP-LC3 and RFP-Atg9. We used a stand-alone cryo-fluorescence stage in the home laboratory to localise the cloned fluorophores, followed by cryo-soft X-ray tomography at the synchrotron to analyse cellular ultrastructure. We mapped the 3D ultrastructure of the endocytic and autophagic structures, and discovered clusters of omegasomes arising from ‘hotspots’ on the ER. Thus, immunogold markers and cryo-CLXM can be used to analyse cellular processes that are inaccessible using other imaging modalities.
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Oct 2013
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Open Access
Abstract: Public participation in research, also known as citizen science, is being increasingly adopted for the analysis of biological volumetric data. Researchers working in this domain are applying online citizen science as a scalable distributed data analysis approach, with recent research demonstrating that non-experts can productively contribute to tasks such as the segmentation of organelles in volume electron microscopy data. This, alongside the growing challenge to rapidly process the large amounts of biological volumetric data now routinely produced, means there is increasing interest within the research community to apply online citizen science for the analysis of data in this context. Here, we synthesise core methodological principles and practices for applying citizen science for analysis of biological volumetric data. We collate and share the knowledge and experience of multiple research teams who have applied online citizen science for the analysis of volumetric biological data using the Zooniverse platform (www.zooniverse.org). We hope this provides inspiration and practical guidance regarding how contributor effort via online citizen science may be usefully applied in this domain.
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Jun 2023
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Ugis
Sarkans
,
Wah
Chiu
,
Lucy M.
Collinson
,
Michele C.
Darrow
,
Jan
Ellenberg
,
David
Grunwald
,
Jean-Karim
Hériché
,
Andrii
Iudin
,
Gabriel G.
Martins
,
Terry
Meehan
,
Kedar
Narayan
,
Ardan
Patwardhan
,
Matthew Robert Geoffrey
Russell
,
Helen R.
Saibil
,
Caterina
Strambio-De-Castillia
,
Jason R.
Swedlow
,
Christian
Tischer
,
Virginie
Uhlmann
,
Paul
Verkade
,
Mary
Barlow
,
Omer
Bayraktar
,
Ewan
Birney
,
Cesare
Catavitello
,
Christopher
Cawthorne
,
Stephan
Wagner-Conrad
,
Elizabeth
Duke
,
Perrine
Paul-Gilloteaux
,
Emmanuel
Gustin
,
Maria
Harkiolaki
,
Pasi
Kankaanpää
,
Thomas
Lemberger
,
Jo
Mcentyre
,
Josh
Moore
,
Andrew W.
Nicholls
,
Shuichi
Onami
,
Helen
Parkinson
,
Maddy
Parsons
,
Marina
Romanchikova
,
Nicholas
Sofroniew
,
Jim
Swoger
,
Nadine
Utz
,
Lenard M.
Voortman
,
Frances
Wong
,
Peijun
Zhang
,
Gerard J.
Kleywegt
,
Alvis
Brazma
Abstract: Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.
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May 2021
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