How to apply the broad toolbox of correlative light and electron microscopy to address a specific biological question.

Correlative light and electron microscopy (CLEM) is an approach that combines the strength of multiple imaging techniques to obtain complementary information about a given specimen. The "toolbox" for CLEM is broad, making it sometimes difficult to choose an appropriate approach for a given biological question. In this chapter, we provide experimental details for three CLEM approaches that can help the interested reader in designing a personalized CLEM strategy for obtaining ultrastructural data by using transmission electron microscopy (TEM).

Future proofing core facilities with a seven-pillar model.

Centralised core facilities have evolved into vital components of life science research, transitioning from a primary focus on centralising equipment to ensuring access to technology experts across all facets of an experimental workflow. Herein, we put forward a seven-pillar model to define what a core facility needs to meet its overarching goal of facilitating research. The seven equally weighted pillars are Technology, Core Facility Team, Training, Career Tracks, Technical Support, Community and Transparency.

Proteomic Landscape of Extracellular Vesicles for Diffuse Large B-Cell Lymphoma Subtyping.

The role of extracellular vesicles (EVs) proteome in diffuse large B-cell lymphoma (DLBCL) pathology, subclassification, and patient screening is unexplored. We analyzed by state-of-the-art mass spectrometry the whole cell and secreted extracellular vesicles (EVs) proteomes of different molecular subtypes of DLBCL, germinal center B cell (GCB subtype), and activated B cell (ABC subtype). After quality control assessment, we compared whole-cell and secreted EVs proteomes of the two cell-of-origin (COO) categories, GCB and ABC subtypes, resulting in 288/1115 significantly differential expressed proteins from the whole-cell proteome and 228/608 proteins from EVs (adjust -value < 0.

The 3D architecture and molecular foundations of de novo centriole assembly via bicentrioles.

Centrioles are structurally conserved organelles, composing both centrosomes and cilia. In animal cycling cells, centrioles often form through a highly characterized process termed canonical duplication. However, a large diversity of eukaryotes assemble centrioles de novo through uncharacterized pathways.

The Histo-CLEM Workflow for tissues of model organisms.

Bridging from the macrostructure to the nanostructure of tissues is often technically challenging. To try to solve this, we developed a flexible CLEM workflow that can be applied to the analysis of tissues from diverse model organisms across various length scales. The Histo-CLEM Workflow combines three main microscopy techniques, namely histology, light microscopy and electron microscopy.

Is the Proteome of Bronchoalveolar Lavage Extracellular Vesicles a Marker of Advanced Lung Cancer?

Acellular bronchoalveolar lavage (BAL) proteomics can partially separate lung cancer from non-lung cancer patients based on principal component analysis and multivariate analysis. Furthermore, the variance in the proteomics data sets is correlated mainly with lung cancer status and, to a lesser extent, smoking status and gender. Despite these advances BAL small and large extracellular vehicles (EVs) proteomes reveal aberrant protein expression in paracrine signaling mechanisms in cancer initiation and progression.

Investigating LGALS3BP/90 K glycoprotein in the cerebrospinal fluid of patients with neurological diseases.

Galectin-3 binding protein (LGALS3BP or 90 K) is a secreted glycoprotein found in human body fluids. Deregulated levels were observed in cancer and infection and its study in neurological diseases is more recent. Here, we have investigated 90 K from human cerebrospinal fluid (CSF) of patients with amyotrophic lateral sclerosis (ALS, n = 35) and other neurological diseases (n = 23).

Temporal and spatial regulation of protein cross-linking by the pre-assembled substrates of a Bacillus subtilis spore coat transglutaminase.

In many cases protein assemblies are stabilized by covalent bonds, one example of which is the formation of intra- or intermolecular ε-(γ-glutamyl)lysil cross-links catalyzed by transglutaminases (TGases). Because of the potential for unwanted cross-linking reactions, the activities of many TGases have been shown to be tightly controlled. Bacterial endospores are highly resilient cells in part because they are surrounded by a complex protein coat.

PLK4 is a microtubule-associated protein that self-assembles promoting MTOC formation.

The centrosome is an important microtubule-organising centre (MTOC) in animal cells. It consists of two barrel-shaped structures, the centrioles, surrounded by the pericentriolar material (PCM), which nucleates microtubules. Centrosomes can form close to an existing structure (canonical duplication) or How centrosomes form is not known.

Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation.

Centrosomes are the major microtubule organising centres of animal cells. Deregulation in their number occurs in cancer and was shown to trigger tumorigenesis in mice. However, the incidence, consequence and origins of this abnormality are poorly understood.

Sympathetic neuron-associated macrophages contribute to obesity by importing and metabolizing norepinephrine.

The cellular mechanism(s) linking macrophages to norepinephrine (NE)-mediated regulation of thermogenesis have been a topic of debate. Here we identify sympathetic neuron-associated macrophages (SAMs) as a population of cells that mediate clearance of NE via expression of solute carrier family 6 member 2 (SLC6A2), an NE transporter, and monoamine oxidase A (MAOA), a degradation enzyme. Optogenetic activation of the sympathetic nervous system (SNS) upregulates NE uptake by SAMs and shifts the SAM profile to a more proinflammatory state.

Usefulness of zebrafish larvae to evaluate drug-induced functional and morphological renal tubular alterations.

Prediction and management of drug-induced renal injury (DIRI) rely on the knowledge of the mechanisms of drug insult and on the availability of appropriate animal models to explore it. Zebrafish (Danio rerio) offers unique advantages for assessing DIRI because the larval pronephric kidney has a high homology with its human counterpart and it is fully mature at 3.5 days post-fertilization.

Influenza A virus ribonucleoproteins modulate host recycling by competing with Rab11 effectors.

Influenza A virus assembly is an unclear process, whereby individual virion components form an infectious particle. The segmented nature of the influenza A genome imposes a problem to assembly because it requires packaging of eight distinct RNA particles (vRNPs). It also allows genome mixing from distinct parental strains, events associated with influenza pandemic outbreaks.

Automated stitching of microtubule centerlines across serial electron tomograms.

Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation.

Correlative light and electron microscopy for a free-floating spindle in Xenopus laevis egg extracts.

Cryoimmobilization is an optimal method of preserving sample ultrastructure in electron microscopy studies. However, cryoimmobilization is limited to thin samples and this limitation may necessitate the isolation of the structure of interest. For cellular structures that are found in low number, or only during certain phases of the cell cycle, an added benefit of isolation is the possibility to concentrate the structures.

Sialoglycoproteins and N-glycans from secreted exosomes of ovarian carcinoma cells.

Exosomes consist of vesicles that are secreted by several human cells, including tumor cells and neurons, and they are found in several biological fluids. Exosomes have characteristic protein and lipid composition, however, the results concerning glycoprotein composition and glycosylation are scarce. Here, protein glycosylation of exosomes from ovarian carcinoma SKOV3 cells has been studied by lectin blotting, NP-HPLC analysis of 2-aminobenzamide labeled glycans and mass spectrometry.

The ultrastructure of animal atherosclerosis: what has been done, and the electron microscopy advancements that could help scientists answer new biological questions.

Electron microscopy is a powerful technique that has been used to answer numerous structure related research questions in all fields, including atherosclerotic research. Recent technology developments are expanding the capabilities of electron microscopy to address the physiology and pathology of arterial function. The purpose of this review is to describe what was known about the ultrastructure of atherosclerosis in the mid 1990s, what has been added to this knowledge basis since then, and to detail some of the recent electron microscopy techniques that could allow us to shed light on hitherto unaddressed aspects of this disease.

Exposure to diesel exhaust upregulates COX-2 expression in ApoE knockout mice.

Introduction: We have shown that diesel exhaust (DE) inhalation caused progression of atherosclerosis; however, the mechanisms are not fully understood. We hypothesize that exposure to DE upregulates cyclooxygenase (COX) expression and activity, which could play a role in DE-induced atherosclerosis.

Methods: ApoE knockout mice (30-week old) fed with regular chow were exposed to DE (at 200 µg/m(3) of particulate matter) or filtered air (control) for 7 weeks (6 h/day, 5 days/week).

Ultrastructural changes in atherosclerotic plaques following the instillation of airborne particulate matter into the lungs of rabbits.

Background: Epidemiological studies have established that cardiovascular events account for the greatest number of air pollution-related deaths. However, the underlying structural changes are still unknown.

Objective: To investigate changes in the ultrastructure of atherosclerotic plaques in Watanabe heritable hyperlipidemic (WHHL) rabbits following the instillation of ambient particulate matter air pollution (particles smaller than 10 µm in diameter) into the lungs.

Particulate matter air pollution exposure promotes recruitment of monocytes into atherosclerotic plaques.

Epidemiologic studies have shown an association between exposure to ambient particulate air pollution <10 microm in diameter (PM(10)) and increased cardiovascular morbidity and mortality. We previously showed that PM(10) exposure causes progression of atherosclerosis in coronary arteries. We postulate that the recruitment of monocytes from the circulation into atherosclerotic lesions is a key step in this PM(10)-induced acceleration of atherosclerosis.

Fast, cheap and out of control: a zero curation model for ontology development.

During two days at a conference focused on circulatory and respiratory health, 68 volunteers untrained in knowledge engineering participated in an experimental knowledge capture exercise. These volunteers created a shared vocabulary of 661 terms, linking these terms to each other and to a pre-existing upper ontology by adding 245 hyponym relationships and 340 synonym relationships. While ontology-building has proved to be an expensive and labor-intensive process using most existing methodologies, the rudimentary ontology constructed in this study was composed in only two days at a cost of only 3 t-shirts, 4 coffee mugs, and one chocolate moose.

Ultrastructural evidence of early endothelial damage in coronary arteries of rat cardiac allografts.

Background: Events that occur early after transplantation, particularly immune recognition of allo-endothelium, initiate transplant vascular disease (TVD). Previous work suggests an important compromise of endothelial integrity as the allo-immune milieu evolves, although mechanisms by which integrity is altered remain unclear. Increased vascular permeability caused by endothelial damage may allow inflammatory cells, lipoproteins, other proteins, and plasma fluid to enter the sub-endothelial space, thereby contributing to the initiation of atherosclerosis.