An introduction to scanning transmission electron microscopy for the study of protozoans.

Since its inception in the 1930s, transmission electron microscopy (TEM) has been a powerful method to explore the cellular structure of parasites. TEM usually requires samples of <100 nm thick and with protozoans being larger than 1 µm, their study requires resin embedding and ultrathin sectioning. During the past decade, several new methods have been developed to improve, facilitate, and speed up the structural characterisation of biological samples, offering new imaging modalities for the study of protozoans. In particular, scanning transmission electron microscopy (STEM) can be used to observe sample sections as thick as 1 µm thus becoming an alternative to conventional TEM. STEM can also be performed under cryogenic conditions in combination with cryo-electron tomography providing access to the study of thicker samples in their native hydrated states in 3D. This method, called cryo-scanning transmission electron tomography (cryo-STET), was first developed in 2014. This review presents the basic concepts and benefits of STEM methods and provides examples to illustrate the potential for new insights into the structure and ultrastructure of protozoans.

Catabolism of lysosome-related organelles in color-changing spiders supports intracellular turnover of pigments.

Pigment organelles of vertebrates belong to the lysosome-related organelle (LRO) family, of which melanin-producing melanosomes are the prototypes. While their anabolism has been extensively unraveled through the study of melanosomes in skin melanocytes, their catabolism remains poorly known. Here, we tap into the unique ability of crab spiders to reversibly change body coloration to examine the catabolism of their pigment organelles. By combining ultrastructural and metal analyses on high-pressure frozen integuments, we first assess whether pigment organelles of crab spiders belong to the LRO family and second, how their catabolism is intracellularly processed. Using scanning transmission electron microscopy, electron tomography, and nanoscale Synchrotron-based scanning X-ray fluorescence, we show that pigment organelles possess ultrastructural and chemical hallmarks of LROs, including intraluminal vesicles and metal deposits, similar to melanosomes. Monitoring ultrastructural changes during bleaching suggests that the catabolism of pigment organelles involves the degradation and removal of their intraluminal content, possibly through lysosomal mechanisms. In contrast to skin melanosomes, anabolism and catabolism of pigments proceed within the same cell without requiring either cell death or secretion/phagocytosis. Our work hence provides support for the hypothesis that the endolysosomal system is fully functionalized for within-cell turnover of pigments, leading to functional maintenance under adverse conditions and phenotypic plasticity. First formulated for eye melanosomes in the context of human vision, the hypothesis of intracellular turnover of pigments gets unprecedented strong support from pigment organelles of spiders.

AIE Polymer Micelle/Vesicle Photocatalysts Combined with Native Enzymes for Aerobic Photobiocatalysis.

Biocatalytic transformation has attracted increasing attention in the green synthesis of chemicals due to the diversity of enzymes, their high catalytic activities and specificities, and environmentally benign conditions. Most redox enzymes in nature are dependent on nicotinamide cofactors like ß-nicotinamide adenine dinucleotide (NAD+)/reduced nicotinamide adenine dinucleotide (NADH). The use of solar energy, especially visible light, in the regeneration of cofactors through the combination of photocatalysis and biocatalysis provides an extraordinary opportunity to make complete green processes. However, the combination of photocatalysts and enzymes has been challenged by the rapid degradation and deactivation of the enzymatic material by photogenerated reactive oxygen species (ROS). Here, we design core-shell structured polymer micelles and vesicles with aggregation-induced emission (AIE) as visible-light-mediated photocatalysts for highly stable and recyclable photobiocatalysis under aerobic conditions. NAD+ from NADH can be efficiently regenerated by the photoactive hydrophobic core of polymer micelles and the hydrophobic membrane of polymer vesicles, while the enzymatic material (glucose 1-dehydrogenase) is screened from the attack of photogenerated ROS by the hydrophilic surface layer of polymer colloids. After at least 10 regeneration cycles, the enzyme keeps its active state; meanwhile, polymer micelles and vesicles maintain their photocatalytic activity. These polymer colloids show the potential to be developed for the implementation of industrially relevant photobiocatalytic systems.

Polymersomes with Red/Near-Infrared Emission and Reactive Oxygen Species Generation.

In photodynamic therapy (PDT), the uses of nanoparticles bearing photosensitizers (PSs) can overcome some of the drawbacks of using a PS alone (e.g., poor water solubility and low tumor selectivity). However, numerous nano-formulations are developed by physical encapsulation of PSs through Van der Waals interactions, which have not only a limited load efficiency but also some in vivo biodistribution problems caused by leakage or burst release. Herein, polymersomes made from an amphiphilic block copolymer, in which a PS with aggregation-induced emission (AIE-PS) is covalently attached to its hydrophobic poly(amino acid) block, are reported. These AIE-PS polymersomes dispersed in aqueous solution have a high AIE-PS load efficiency (up to 46% as a mass fraction), a hydrodynamic diameter of 86 nm that is suitable for in vivo applications, and an excellent colloidal stability for at least 1 month. They exhibit a red/near-infrared photoluminescence and ability to generate reactive oxygen species (ROS) under visible light. They are non-cytotoxic in the dark as tested on Hela cells up to concentration of 100 µm. Benefiting from colloidal stability, AIE property and ROS generation capability, such a family of polymersomes can be great candidates for image-guided PDT.

Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodeling by Hfq master regulator.

The bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, due to the association of DNA with proteins called Nucleoid Associated Proteins (NAPs). Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq forms amyloid-like structures through its C-terminal region, hence belonging to the bridging family of NAPs. Here, using cryo soft X-ray tomography imaging of native unlabeled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid. More specifically, Hfq influences nucleoid density especially during the stationary growth phase when it is more abundant. Our results indicate that Hfq could regulate nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNAs. Taken together, our findings reveal a new role for this protein in nucleoid remodeling in vivo, that may serve in response to stress conditions and in adapting to changing environments.

Oxidation-Sensitive Polymersomes Based on Amphiphilic Diblock Copolypeptoids.

Stimuli-responsive polymersomes formed by amphiphilic block copolymers have attracted substantial attention as smart and robust containers for drug delivery and nano/microreactors. Biosourced amphiphilic diblock copolypeptoids were developed that can self-assemble into oxidation-responsive unilamellar vesicles. These vesicles can burst under the action of reactive oxygen species which can be the hydrogen peroxide or the singlet oxygen produced by light-activation of a photosensitizer with spatiotemporal control. Polysarcosine (PSar, also called poly(N-methyl glycine)) was selected as the hydrophilic block because of its resistance to protein adsorption and low toxicity, similar to poly(ethylene glycol) (PEG). We designed and synthesized poly(N-3-(methylthio)propyl glycine) as the hydrophobic block. Its polyglycine backbone is the same as that of PSar, and especially, its hydrophobic N-substituents, thioether side chains, can be oxidized to hydrophilic sulfoxides. These oxidation-responsive polymersomes entirely based on N-substituted poly(amino acid)s were biocompatible as confirmed by cell viability tests and may find applications in drug delivery, biosensing, biodetection, and nano/microreactors.

Correlative infrared nanospectroscopy and transmission electron microscopy to investigate nanometric amyloid fibrils: prospects and challenges.

Propagation of structural information through conformational changes in host-encoded amyloid proteins is at the root of many neurodegenerative disorders. Although important breakthroughs have been made in the field, fundamental issues like the 3D-structures of the fibrils involved in some of those disorders are still to be elucidated. To better characterise those nanometric fibrils, a broad range of techniques is currently available. Nevertheless none of them is able to perform direct chemical characterisation of single protein fibrils. In this work, we propose to investigate the structure of the C-terminal region of a bacterial protein called Hfq as a model amyloidogenic protein, using a correlative approach. The complementary techniques used are transmission electron microscopy and a newly developed infrared nanospectroscopy technique called AFM-IR. We introduce and discuss the strategy that we have implemented as well as the protocol, challenges and difficulties encountered during this study to characterise amyloid assemblies at the nearly single-molecule level. LAY DESCRIPTION: Propagation of structural information through conformational changes in amyloid proteins is at the root of many neurodegenerative disorders. Amyloids are nanostructures originating from the aggregation of multiple copies of peptide or protein monomers that eventually form fibrils. Often described as being the cause for the development of various diseases, amyloid fibrils are of major significance in the public health domain. While important breakthroughs have been made in the field, fundamental issues like the 3D-structures of the fibrils implied in some of those disorders are still to be elucidated. To better characterise these fibrils, a broad range of techniques is currently available for the detection and visualisation of amyloid nanostructures. Nevertheless none of them is able to perform direct chemical characterisation of single protein fibrils. In this work, we propose to investigate the structure of model amyloidogenic fibrils using a correlative approach. The complementary techniques used are transmission electron microscopy and a newly developed infrared nanospectroscopy technique called AFM-IR that allows chemical characterisation at the nanometric scale. The strategy, protocol, challenges and difficulties encountered in this approach are introduced and discussed herein.

CO2 -Activated Reversible Transition between Polymersomes and Micelles with AIE Fluorescence.

Fluorescent polymersomes with both aggregation-induced emission (AIE) and CO2 -responsive properties were developed from amphiphilic block copolymer PEG-b-P(DEAEMA-co-TPEMA) in which the hydrophobic block was a copolymer made of tetraphenylethene functionalized methacrylate (TPEMA) and 2-(diethylamino)ethyl methacrylate (DEAEMA) with unspecified sequence arrangement. Four block copolymers with different DEAEMA/TPEMA and hydrophilic/hydrophobic ratios were synthesized, and bright AIE polymersomes were prepared by nanoprecipitation in THF/water and dioxane/water systems. Polymersomes of PEG45 -b-P(DEAEMA36 -co-TPEMA6 ) were chosen to study the CO2 -responsive property. Upon CO2 bubbling vesicles transformed to small spherical micelles, and upon Ar bubbling micelles returned to vesicles with the presence of a few intermediate morphologies. These polymersomes might have promising applications as sensors, nanoreactors, or controlled release systems.

STEM tomography analysis of the trypanosome transition zone.

The protist Trypanosoma brucei is an emerging model for the study of cilia and flagella. Here, we used scanning transmission electron microscopy (STEM) tomography to describe the structure of the trypanosome transition zone (TZ). At the base of the TZ, nine transition fibres irradiate from the B microtubule of each doublet towards the membrane. The TZ adopts a 9 + 0 structure throughout its length of ∼300 nm and its lumen contains an electron-dense structure. The proximal portion of the TZ has an invariant length of 150 nm and is characterised by a collarette surrounding the membrane and the presence of electron-dense material between the membrane and the doublets. The distal portion exhibits more length variation (from 55 to 235 nm) and contains typical Y-links. STEM analysis revealed a more complex organisation of the Y-links compared to what was reported by conventional transmission electron microscopy. Observation of the very early phase of flagellum assembly demonstrated that the proximal portion and the collarette are assembled early during construction. The presence of the flagella connector that maintains the tip of the new flagellum to the side of the old was confirmed and additional filamentous structures making contact with the membrane of the flagellar pocket were also detected. The structure and potential functions of the TZ in trypanosomes are discussed, as well as its mode of assembly.

Poly(ε-caprolactone)-block-polysarcosine by Ring-Opening Polymerization of Sarcosine N-Thiocarboxyanhydride: Synthesis and Thermoresponsive Self-Assembly.

Biocompatible amphiphilic block copolymers composed of polysarcosine (PSar) and poly(ε-caprolactone) (PCL) were synthesized using ring-opening polymerization of sarcosine N-thiocarboxyanhydride initiated by oxyamine-ended PCL and characterized by NMR, SEC, and DSC. Self-assembling of two triblock copolymers PSar8-b-PCL28-b-PSar8 (CS7) and PSar16-b-PCL40-b-PSar16 (CS10) in dilute solution was studied in detail toward polymersome formation using thin-film hydration and nanoprecipitation techniques. A few giant vesicles were obtained by thin-film hydration from both copolymers and visualized by confocal laser scanning microscope. Unilamellar sheets and nanofibers (with 8-10 nm thickness or diameter) were obtained by nanoprecipitation at room temperature and observed by Cryo-TEM. These lamellae and fibrous structures were transformed into worm-like cylinders and spheres (D∼30-100 nm) after heating to 65 °C (>Tm,PCL). Heating CS10 suspensions to 90 °C led eventually to multilamellar polymersomes (D∼100-500 nm). Mechanism II, where micelles expand to vesicles through water diffusion and hydrophilic core forming, was proposed for polymersome formation. A cell viability test confirmed the self-assemblies were not cytotoxic.

GoldDigger and Checkers, computational developments in cryo-scanning transmission electron tomography to improve the quality of reconstructed volumes.

In this work, we present a pair of tools to improve the fiducial tracking and reconstruction quality of cryo-scanning transmission electron tomography (STET) datasets. We then demonstrate the effectiveness of these two tools on experimental cryo-STET data. The first tool, GoldDigger, improves the tracking of fiducials in cryo-STET by accommodating the changed appearance of highly defocussed fiducial markers. Since defocus effects are much stronger in scanning transmission electron microscopy than in conventional transmission electron microscopy, existing alignment tools do not perform well without manual intervention. The second tool, Checkers, combines image inpainting and unsupervised deep learning for denoising tomograms. Existing tools for denoising cryo-tomography often rely on paired noisy image frames, which are unavailable in cryo-STET datasets, necessitating a new approach. Finally, we make the two software tools freely available for the cryo-STET community.

Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates.

The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the threedimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilised through multivalent dynamic interactions of PRC1 with chromatin. Mechanistically, positively charged residues on the internally disordered regions (IDRs) of CBX8 mask negative charges on the DNA to stabilize the condensed state of chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provides a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.

Cryo-electron Microscopy to Analyze the Structure of Bacterial Amyloids In Vitro.

Amyloid fibrils are aggregates of proteins or peptides. In humans, they are associated with various pathologies ranging from neurodegenerative diseases such as Alzheimer's and Parkinson's to systemic diseases like type 2 diabetes. In bacteria, amyloids can exert functional roles such as biofilm formation or gene regulation. Up to now, the aggregation mechanism leading to amyloid fibril formation is poorly understood as proteins with different amino acid sequences can fold into similar 3D structures. Understanding the formation of amyloid fibrils constitutes a central challenge for fighting major human health issues such as neurodegenerative diseases and biofilm formation in ports (implantable chambers). Since the dogma linking protein sequence, 3D structure, and function is increasingly disrupted by the growing understanding of the importance of disordered domains in proteins, it is crucial to possess a method capable of building accurate atomic models of amyloids. Aided by the leap forward of cryo-electron microscopy (cryo-EM), which can now routinely achieve sub-nanometric resolutions, it has become the method of choice for studying amyloids. In this chapter, we use the Hfq protein from Escherichia coli as an example to present general protocols in cryo-EM to unveil the structure of bacterial amyloids and improve our knowledge of their aggregation mechanism.

Coexistence of Transient Liquid Droplets and Amorphous Solid Particles in Nonclassical Crystallization of Cerium Oxalate.

Crystallization from solution often occurs via "nonclassical" routes; that is, it involves transient, non-crystalline states like reactant-rich liquid droplets and amorphous particles. However, in mineral crystals, the well-defined thermodynamic character of liquid droplets and whether they convert─or not─into amorphous phases have remained unassessed. Here, by combining cryo-transmission electron microscopy and X-ray scattering down to a 250 ms reaction time, we unveil that crystallization of cerium oxalate involves a metastable chemical equilibrium between transient liquid droplets and solid amorphous particles: contrary to the usual expectation, reactant-rich droplets do not evolve into amorphous solids. Instead, at concentrations above 2.5 to 10 mmol L-1, both amorphous and reactant-rich liquid phases coexist for several tens of seconds and their molar fractions remain constant and follow the lever rule in a multicomponent phase diagram. Such a metastable chemical equilibrium between solid and liquid precursors has been so far overlooked in multistep nucleation theories and highlights the interest of rationalizing phase transformations using multicomponent phase diagrams not only when designing and recycling rare earths materials but also more generally when describing nonclassical crystallization.

Evaluation of the Role of Bacterial Amyloid on Nucleoid Structure Using Cryo-Soft X-Ray Tomography.

Bacterial chromosomal DNA is packed within a non-membranous structure, the nucleoid, thanks to nucleoid associated proteins (NAPs). The role of bacterial amyloid has recently emerged among these NAPs, particularly with the nucleoid-associated protein Hfq that plays a direct role in DNA compaction. In this chapter, we present a 3D imaging technique, cryo-soft X-ray tomography (cryo-SXT) to obtain a detailed 3D visualization of subcellular bacterial structures, especially the nucleoid. Cryo-SXT imaging of native unlabeled cells enables observation of the nucleoid in 3D with a high resolution, allowing to evidence in vivo the role of amyloids on DNA compaction. The precise experimental methods to obtain 3D tomograms will be presented.

Breaking photoswitch activation depth limit using ionising radiation stimuli adapted to clinical application.

Electromagnetic radiation-triggered therapeutic effect has attracted a great interest over the last 50 years. However, translation to clinical applications of photoactive molecular systems developed to date is dramatically limited, mainly because their activation requires excitation by low-energy photons from the ultraviolet to near infra-red range, preventing any activation deeper than few millimetres under the skin. Herein we conceive a strategy for photosensitive-system activation potentially adapted to biological tissues without any restriction in depth. High-energy stimuli, such as those employed for radiotherapy, are used to carry energy while molecular activation is provided by local energy conversion. This concept is applied to azobenzene, one of the most established photoswitches, to build a radioswitch. The radiation-responsive molecular system developed is used to trigger cytotoxic effect on cancer cells upon gamma-ray irradiation. This breakthrough activation concept is expected to expand the scope of applications of photosensitive systems and paves the way towards the development of original therapeutic approaches.

Structure of reconstituted bacterial membrane efflux pump by cryo-electron tomography.

Complexes of OprM and MexA, two proteins of the MexA-MexB-OprM multidrug efflux pump from Pseudomonas aeruginosa, an opportunistic Gram-negative bacterium, were reconstituted into proteoliposomes by detergent removal. Stacks of protein layers with a constant height of 21nm, separated by lipid bilayers, were obtained at stoichiometry of 1:1 (w/w). Using cryo-electron microscopy and tomography, we showed that these protein layers were composed of MexA-OprM complexes self-assembled into regular arrays. Image processing of extracted sub-tomograms depicted the architecture of the bipartite complex sandwiched between two lipid bilayers, representing an environment close to that of the native whole pump (i.e. anchored between outer and inner membranes of P. aeruginosa). The MexA-OprM complex appeared as a cylindrical structure in which we were able to identify the OprM molecule and the MexA moiety. MexA molecules have a cylindrical shape prolonging the periplasmic helices of OprM, and widening near the lipid bilayer. The flared part is likely composed of two MexA domains adjacent to the lipid bilayer, although their precise organization was not reachable mainly due to their flexibility. Moreover, the intermembrane distance of 21nm indicated that the height of the bipartite complex is larger than that of the tripartite AcrA-AcrB-TolC built-up model in which TolC and AcrB are docked into contact. We proposed a model of MexA-OprM taking into account features of previous models based on AcrA-AcrB-TolC and our structural results providing clues to a possible mechanism of tripartite system assembly.

Light-Gated Nano-Porous Capsules from Stereoisomer-Directed Self-Assemblies.

Structuring pores into stable membrane and controlling their opening is extremely useful for applications that require nanopores as channels for material exchange and transportation. In this work, nanoporous vesicles with aggregation-induced emission (AIE) properties were developed from the amphiphilic polymer PEG550-TPE-Chol, in which the hydrophobic part is composed of a tetraphenylethene (TPE) group and a cholesterol moiety and the hydrophilic block is a poly(ethylene glycol) (PEG, Mn = 550 Da). Two stereoisomers, trans-PEG550-TPE-Chol and cis-PEG550-TPE-Chol, were successfully synthesized. These thermally stable stereoisomers showed distinct self-assembly behavior in water: trans-PEG550-TPE-Chol formed classical vesicles, while cis-PEG550-TPE-Chol self-assembled into cylindrical micelles. Interestingly, trans/cis mixtures of PEG550-TPE-Chol (trans/cis = 60/40), either naturally synthesized without isomers' separation during the synthesis or intentionally mixed using trans- and cis-isomers, constructed perforated vesicles with nanopores. Moreover, under the illumination of high intensity UV light (365 nm, 15 mW/cm2), the classical vesicles of trans-PEG550-TPE-Chol were perforated by its cis counterparts generated from the trans-cis photoisomerization, while the cylindrical micelles of cis-PEG550-TPE-Chol interweaved to form meshes and nanoporous membranes due to the trans-isomers produced by cis-trans photoisomerization. All of these assemblies in water emitted bright cyan fluorescence under UV light, while their constituent molecules were not fluorescent when solubilized in organic solvent. The AIE fluorescent normal vesicles and nanoporous vesicles may find potential applications in biotechnology as light-gated delivery vehicles and capsules with nanochannels for material exchange.

Apomorphine Targets the Pleiotropic Bacterial Regulator Hfq.

Hfq is a bacterial regulator with key roles in gene expression. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, thanks to its binding to small regulatory noncoding RNAs. This property is of primary importance for bacterial adaptation and survival in hosts. Small RNAs and Hfq are, for instance, involved in the response to antibiotics. Previous work has shown that the E. coli Hfq C-terminal region (Hfq-CTR) self-assembles into an amyloid structure. It was also demonstrated that the green tea compound EpiGallo Catechin Gallate (EGCG) binds to Hfq-CTR amyloid fibrils and remodels them into nonamyloid structures. Thus, compounds that target the amyloid region of Hfq may be used as antibacterial agents. Here, we show that another compound that inhibits amyloid formation, apomorphine, may also serve as a new antibacterial. Our results provide an alternative in order to repurpose apomorphine, commonly used in the treatment of Parkinson's disease, as an antibiotic to block bacterial adaptation to treat infections.

Fluorescent polymer cubosomes and hexosomes with aggregation-induced emission.

Fluorescent polymer cubosomes and hexosomes with aggregation-induced emission (AIE) were prepared from amphiphilic block copolymers PEG-b-PTPEMA where the hydrophobic block PTPEMA was a polymethacrylate with tetraphenylethene (TPE) as the AIE side group. Four highly asymmetric block copolymers with hydrophilic block weight ratio f PEG ≤ 20% were synthesized. Cubosomes and hexosomes with strong fluorescence emission were obtained by nanoprecipitation of polymers with f PEG < 9% in dioxane/water and THF/water systems. Their ordered internal structures were studied by electron microscopy (cryo-EM, SEM and TEM) and the X-ray scattering technique (SAXS). To elucidate the formation mechanisms of these inverted colloids, other parameters influencing the morphologies, like the water content during self-assembly and the organic solvent composition, were also investigated. This study not only inspires people to design novel building blocks for the preparation of functional cubosomes and hexosomes, but also presents the first AIE fluorescent polymer cubosome and hexosome with potential applications in bio-related fields.