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Trepout, S.

Publications and source records attributed to Trepout, S..

11 recordsLinked to original sources

Mind the Bend: Curved and Corrugated Cryo-Lamella for Improved Mechanical Resilience

Preparing electron-transparent cryo-lamellae is inherently a serial, low-throughput process. During sample handling, milling, and transfer, cryo-fixed cells and their supporting films are subjected to mechanical forces as well as thermal stresses caused by temperature fluctuations. After milling, these extremely thin lamellae remain vulnerable to both mechanical and thermal stress, often leading to cracking or complete disintegration. Consequently, the loss of valuable lamellae is frequently an unavoidable aspect of working with such fragile specimens. In this work, we reconsider the conventional lamella geometry, which is typically a flat, thin cross-sectional slab. During milling, lamellae often become unintentionally bent, complicating the final polishing step required to achieve uniform thinning across their width. To address this limitation, we propose deliberately fabricating lamellae in a pre-bent configuration, i.e. specifically, adopting an arch-shaped profile instead of the traditional flat geometry. The arch shape is intrinsically more mechanically stable than a flat structure, thereby reducing lamella loss due to mechanical failure. Moreover, pre-bent milling patterns facilitate uniform thinning of bent lamellae, which is difficult to achieve using conventional flat milling approaches. In addition to the arch geometry, we investigate corrugated lamellae, characterised by a sinusoidal variation around the plane of a conventional flat lamella. Similarly to the arch shape, the corrugated design offers enhanced mechanical stability compared to traditional flat lamellae. We fabricated a series of test lamellae incorporating both arches and corrugations. High-resolution cryo-TEM imaging was performed to evaluate these structures, demonstrating that non-flat geometries do not compromise cryo-electron tomography performance. Furthermore, finite element method (FEM) simulations were conducted to provide insight into stress distributions within bent and corrugated lamellae.

biochemistry↗

The IFT-A complex plays a major role in the assembly of anterograde intraflagellar transport trains

Cilia are assembled by intraflagellar transport (IFT), which relies on two protein complexes: IFT-A and IFT-B. It is generally assumed that IFT-B and IFT-A are critical for anterograde and retrograde transport, respectively. However, full deletion of IFT-A genes in several organisms suggests a possible contribution to anterograde transport. In many species, cilia collapse when IFT is altered, hindering functional studies. Here, we investigated the role of IFT-A in the protist Trypanosoma brucei, where IFT is not required for cilium maintenance. Following the inducible knockdown of IFT88 (an IFT-B member) or IFT140 (an IFT-A member), we monitored the fate of several IFT proteins in preassembled cilia using live imaging and evaluated the consequences on train formation by volumetric electron microscopy. Surprisingly, both IFT88 and IFT140 turned out to be essential for anterograde train assembly. Their depletion initially led to the formation of shorter trains and subsequently to an inhibition of train injection. We propose a model to reconcile the diverging phenotypes reported in the literature.

cell biology↗

Mind the crack: Crack-arrest holes and soft-suspension support integration in cryo-lamella preparation for improved resistance to crack formation, fracture and deformation

Preparing electron-transparent cryo-lamellae is inherently a serial and low-throughput process. Once the lamellae are milled, these thin structures endure both mechanical and thermal stress, and as a result many valuable lamellae crack or even disintegrate entirely. This loss is often regarded as a "lamella tax", i.e. an unavoidable cost of working with such fragile specimens. In this work, we introduce two modifications to the standard lamella-preparation workflow aimed at improving lamella mechanical resistance to crack formation and external stress. The first modification involves milling arrays of perforations directly within the lamella body. These perforations are designed to function as crack-arrest holes, intercepting cracks as they appear and preventing, or at least delaying their further propagation. By slowing crack growth, these features increase the likelihood that the lamella remains intact long enough to complete cryo-TEM imaging. The second modification replaces the conventional rigid attachment of the lamella to the surrounding cellular bulk material with a softer suspension using ring-shaped springs formed by ion beam milling. Mounting the lamella on smooth annular springs provides mechanical compliance both across and along the lamella axis, as well as at intermediate angles and in the out-of-plane direction. This flexibility allows the lamella to accommodate larger stresses and deformations without reaching its mechanical failure threshold. We fabricated a series of test lamellae incorporating different crack-arrest hole geometries, as well as lamellae suspended on soft annular springs. We performed high-resolution cryo-TEM imaging to characterise the perforations themselves and characterised the captured crack geometry within the lamellae at the highest level of detail achieved to date. TEM imaging shows crack interception and guided, non-catastrophic failure paths, while simulations confirm lowered stress in suspended lamellae.

molecular biology↗

About the alignment and 3D reconstruction of sparse cryo-scanning transmission electron tomography datasets

In electron microscopy, sparse imaging consists in the collection of a limited subset of the image pixels, which can be used to reduce electron beam damage. Scanning transmission electron microscopy (STEM) is particularly adapted to sparse imaging owing to the scanning nature of the method, scan patterns can be designed where fewer sample locations are targeted. However, since some of the pixels are not scanned, there is an inherent loss of information. Several algorithms were developed to reconstruct missing pixels with high fidelity. Whereas sparse imaging and missing pixel reconstruction in 2D experiments are mature methods, the application of sparse imaging in 3D scanning transmission electron tomography (STET) is rare and still under development. The main difficulty encountered in tomography studies is the tilt-series alignment, which must be accurate to ensure high-quality 3D reconstruction. Because sparse images contain only a certain portion of the original information, the images constituting sparse tilt-series might not share enough mutual information to guarantee an accurate alignment, even after missing pixel reconstruction. This work presents for the first time a thorough analysis of the fiducial alignment and reconstruction of sparse (cryo)STET tilt-series. Furthermore, the limits of sparse imaging are explored to estimate the minimum amount of information required to obtain good-quality 3D reconstructions. The use of a cryo-fixed biological sample is motivated by the fact that cryo-samples are typical highly beam-sensitive samples, and that the intricate nature and structure complexity of biological samples place them among the most difficult to reconstruct with high details.

biophysics↗

Mind the corner: Fillets in cryo-FIB lamella preparation to minimise sample loss caused by stress concentration and lamella breakage

Cryo-FIB milling of biological specimens is a critical and limiting step in the cryo-electron tomography workflow. Preparing electron-transparent cryo-lamellae is a serial, low-throughput process. Even with automation, a skilled operator can typically only produce 15-25 lamellae in a single cryo-FIB session. During sample handling, milling and transfer, the cryo-fixed cells as well as the supporting film layer face various mechanical forces and thermal stresses due to temperature fluctuations. Moreover, after cells are cryo-FIB milled, the resulting thin lamellae continue to endure external forces from mechanical handling and thermal stress. We propose a simple, yet highly effective modification to the standard rectangular milling pattern by implementing "fillets" or corner smoothing providing better mechanical stability. This adjustment helps to avoid sharp corners at the lamella edges, thereby reducing stress concentration. As a result, this modification decreases the likelihood of lamella breakage and improves the overall yield of ready-for-TEM lamellae by 33% as verified experimentally.

biochemistry↗

Accelerated plastic aging in suspension (APAS): A simple, reproducible approach for the generation of model micro- and nanoplastics through simulated environmental forces

The environmental fragmentation of plastic waste leads to the formation of micro- and nanoplastics (MNPs), which pose serious ecological and human health concerns. Despite increasing interest in their biological effects, many studies rely on artificial, uniform particles that fail to mimic the diverse physical and chemical characteristics of real-world MNPs. To address this limitation, we developed the Accelerated Plastic Aging in Suspension (APAS) system--a scalable, reproducible method that mimics natural aging processes by combining ultraviolet (UV) radiation, thermal stress, and mechanical shear to generate environmentally relevant MNPs from commonly used polymers. We used APAS to fragment polyethylene terephthalate (PET), polyamide 6 (Nylon), and polyacrylonitrile (PAN), and observed time-dependent degradation, including the spontaneous formation of nanoplastics (<100 nm). Flow cytometry revealed substantial increases in particle number and reductions in average particle size over 12 weeks. Imaging flow cytometry confirmed consistent generation of heterogeneous, irregular particles across replicate batches. High-resolution imaging via AFM, TEM, and SEM confirmed the presence of nanoplastics with textured and irregular morphologies. Chemical characterization showed APAS aging altered particle surface charge and induced polymer-specific changes in autofluorescence and Raman spectral profiles, consistent with oxidative surface modifications. Laser Direct Infrared (LDIR) imaging further confirmed structural and chemical changes in polymer spectra post-aging. Functionally, under physiologically relevant shear flow conditions, endothelial cells internalized APAS-generated PET MNPs at significantly higher levels than polystyrene (PS) beads of similar size. Uptake was enhanced particularly under oscillatory flow, highlighting the influence of particle physicochemical properties on cellular interactions. Together, these findings demonstrate the ability of the APAS system to produce complex and realistic MNPs for use in environmental and toxicological studies. The system enables generation of nanoplastics and supports more accurate modelling of biological exposure scenarios compared to conventional synthetic particles.

pharmacology and toxicology↗

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

Bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, thanks to proteins called Nucleoid Associated Proteins (NAPs). The NAP composition of the nucleoid varies during the bacterial life cycle and is growth phase-dependent. 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 belongs to the bridging family of NAPs. Its bridging mechanism relies on the formation of the amyloid-like structure of Hfq C-terminal region. Here, using cryo soft X-ray tomography imaging of native unlabelled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid, especially during the stationary growth phase. Hfq influences both nucleoid volume and absorbance. Hfq cumulates direct effects and indirect effects due to sRNA-based regulation of other NAPs. Taken together, our findings reveal a new role for this protein in nucleoid remodelling that may serve in response to stress conditions and in adapting to changing environments. This implies that Hfq regulates nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNA.

microbiology↗

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.

cell biology↗

In situ structural analysis of the flagellum attachment zone in Trypanosoma brucei using cryo-scanning transmission electron tomography

The flagellum of Trypanosoma brucei is a 20 {micro}m-long organelle responsible for locomotion and cell morphogenesis. The flagellum attachment zone (FAZ) is a multi-protein complex whose function is to attach the flagellum to the cell body but also to guide cytokinesis. Cryo-transmission electron microscopy is a tool of choice to access the structure of the FAZ in a close-to-native state. However, because of the large dimension of the cell body, the whole FAZ cannot be structurally studied in situ at high resolution in 3D using classical transmission electron microscopy approaches. In the present work, cryo-scanning transmission electron tomography, a new method capable of investigating cryo-fixed thick biological samples, has been used to study whole T. brucei cells at the bloodstream stage. The method has been used to visualise and characterise the structure and organisation of the FAZ filament. It is composed of an array of cytoplasmic stick-like structures. These sticks are heterogeneously distributed between the posterior part and the anterior tip of the cell. This cryo-STET investigation provides new insights in the structure the FAZ filament. In combination with protein structure predictions, this work proposes a new model for the elongation of the FAZ. HighlightsO_LIFlagellar and cellular membranes are in close contact next to the FAZ filament C_LIO_LISticks are heterogeneously distributed along the FAZ filament length C_LIO_LIThin appendages are present between the FAZ filament sticks to neighbouring microtubules C_LIO_LIFAZ elongation could originate from the force exerted by dynein motors on subpellicular microtubules C_LI

cell biology↗

Essential dynamic interdependence of FtsZ and SepF for Z-ring and septum formation in Corynebacterium glutamicum

The mechanisms of Z-ring assembly and regulation in bacteria are poorly understood, particularly in non-model organisms. Actinobacteria, one of the largest bacterial phyla that includes the deadly human pathogen Mycobacterium tuberculosis, lack the canonical FtsZ-membrane anchors as well as all positive and negative Z-ring regulators described for E. coli. Here we investigate the physiological function of Corynebacterium glutamicum SepF, the only cell division-associated protein from Actinobacteria known to directly interact with the conserved C-terminal tail of FtsZ but whose actual mode of action in cytokinesis is yet to be elucidated. We used a mechanistic cell biology approach to unveil the essential interdependence of FtsZ and SepF required for the formation of a functional Z-ring in the actinobacterial model organism C. glutamicum. The crystal structure of the SepF-FtsZ complex reveals a hydrophobic FtsZ-binding pocket, which defines the SepF homodimer as the functional unit, and a reversible oligomerization interface regulated via an alpha helical switch. FtsZ filaments and lipid membranes have opposing effects on SepF polymerization, leading to a complex dynamic role of the protein at the division site, involving FtsZ bundling, Z-ring tethering and membrane reshaping activities that are needed for proper Z-ring assembly and function.

microbiology↗

Bidirectional intraflagellar transport is restricted to only two microtubule doublets in the trypanosome flagellum

Intraflagellar transport (IFT) is the rapid bidirectional movement of large protein complexes driven by kinesin and dynein motors along microtubule doublets of cilia and flagella. Here we used a combination of high-resolution electron and light microscopy to investigate how and where these IFT trains move within the flagellum of the protist Trypanosoma brucei. Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) analysis of trypanosomes showed that trains are found almost exclusively along two sets of doublets (3-4 and 7-8) and distribute in two categories according to their length. High-resolution live imaging of cells expressing mNeonGreen::IFT81 or GFP::IFT52 revealed for the first time IFT trafficking on two parallel lines within the flagellum. Anterograde and retrograde IFT occur on each of these lines. At the distal end, a large individual anterograde IFT train is converted in several smaller retrograde trains in the space of 3-4 seconds while remaining on the same side of the axoneme.

cell biology↗