Cryofixation during live-imaging enables millisecond time-correlated light and electron microscopy

Structural glycobiology - from enzymes to organelles

Biological carbohydrate polymers represent some of the most complex molecules in life, enabling their participation in a huge range of physiological functions. The complexity of biological carbohydrates arises from an extensive enzymatic repertoire involved in their construction, deconstruction and modification. Over the past decades, structural studies of carbohydrate processing enzymes have driven major insights into their mechanisms, supporting associated applications across medicine and biotechnology. Despite these successes, our understanding of how multienzyme networks function to create complex polysaccharides is still limited. Emerging techniques such as super-resolution microscopy and cryo-electron tomography are now enabling the investigation of native biological systems at near molecular resolutions. Here, we review insights from classical in vitro studies of carbohydrate processing, alongside recent in situ studies of glycosylation-related processes. While considerable technical challenges remain, the integration of molecular mechanisms with true biological context promises to transform our understanding of carbohydrate regulation, shining light upon the processes driving functional complexity in these essential biomolecules.

Model-Based Optimization of Solid-Supported Micro-Hotplates for Microfluidic Cryofixation

Cryofixation by ultra-rapid freezing is widely regarded as the gold standard for preserving cell structure without artefacts for electron microscopy. However, conventional cryofixation technologies are not compatible with live imaging, making it difficult to capture dynamic cellular processes at a precise time. To overcome this limitation, we recently introduced a new technology, called microfluidic cryofixation. The principle is based on micro-hotplates counter-cooled with liquid nitrogen. While the power is on, the sample inside a foil-embedded microchannel on top of the micro-hotplate is kept warm. When the heater is turned off, the thermal energy is drained rapidly and the sample freezes. While this principle has been demonstrated experimentally with small samples (<0.5 mm2), there is an important trade-off between the attainable cooling rate, sample size, and heater power. Here, we elucidate these connections by theoretical modeling and by measurements. Our findings show that cooling rates of 106 K s-1, which are required for the vitrification of pure water, can theoretically be attained in samples up to ∼1 mm wide and 5 μm thick by using diamond substrates. If a heat sink made of silicon or copper is used, the maximum thickness for the same cooling rate is reduced to ∼3 μm. Importantly, cooling rates of 104 K s-1 to 105 K s-1 can theoretically be attained for samples of arbitrary area. Such rates are sufficient for many real biological samples due to the natural cryoprotective effect of the cytosol. Thus, we expect that the vitrification of millimeter-scale specimens with thicknesses in the 10 μm range should be possible using micro-hotplate-based microfluidic cryofixation technology.

Evaluation of heat transfer in porous scaffolds under cryogenic treatment: a numerical study

The present work had evaluated the effect of cryogenic treatment (233 K) on the degradation of polymeric biomaterial using a numerical model. The study on effect of cryogenic temperature on mechanical properties of cell-seeded biomaterials is very limited. However, no study had reported material degradation evaluation. Different structures of silk-fibroin-poly-electrolyte complex (SFPEC) scaffolds had been designed by varying hole distance and hole diameter, with reference to existing literature. The size of scaffolds were maintained at 5 [Formula: see text] 5 mm2. Current study evaluates the effect of cryogenic temperature on mechanical properties (corelated to degradation) of scaffold. Six parameters related to scaffold degradation: heat transfer, deformation gradient, stress, strain, strain tensor, and displacement gradient were analyzed for three different cooling rates (- 5 K/min, - 2 K/min, and - 1 K/min). Scaffold degradation had been evaluated in the presence of water and four different concentrations of cryoprotectant solution. Heat distribution at various points (points_base, point_wall and point_core) on the region of interest (ROI) was found similar for different cooling rates of the system. Thermal stress was found developing proportional to cooling rate, which leads to minimal variation in thermal stress over time. Strain tensor was found gradually decreasing due to attenuating response of deformation gradient. In addition to that, dipping down of cryogenic temperature had prohibited the movement of molecules in the crystalline structure which had restricting the displacement gradient. It was found that uniform distribution of desired heat at different cooling rates has the ability to minimize the responses of other scaffold degradation parameters. It was found that the rates of change in stress, strain, and strain tensor were minimal at different concentrations of cryoprotectant. The present study had predicted the degradation behavior of PEC scaffold under cryogenic temperature on the basis of explicit mechanical properties.

Imperative role of electron microscopy in toxicity assessment: A review

Electron microscope (EM) was developed in 1931 and since then microscopical examination of both the biological and non-biological samples has been revolutionized. Modifications in electron microscopy techniques, such as scanning EM and transmission EM, have widened their applicability in the various sectors such as understanding of drug toxicity, development of mechanism, criminal site investigation, and characterization of the nano-molecule. The present review summarizes its role in important aspects such as toxicity assessment and disease diagnosis in special reference to SARS-COV2. In the biological system, EM studies have elucidated the impact of toxicants at the ultra-structural level in various tissue in conformity to physiological alterations. Thus, EM can be concluded as an important tool in toxicity assessment and disease prognosis.

Challenges and triumphs in cryo-electron tomography

Cryo-electron tomography has stepped fully into the spotlight. Enthusiasm is high. Fortunately for us, this is an exciting time to be a cryotomographer, but there is still a way to go before declaring victory. Despite its potential, cryo-electron tomography possesses many inherent challenges. How do we image through thick cell samples, and possibly even tissue? How do we identify a protein of interest amidst the noisy, crowded environment of the cytoplasm? How do we target specific moments of a dynamic cellular process for tomographic imaging? In this review, we cover the history of cryo-electron tomography and how it came to be, roughly speaking, as well as the many approaches that have been developed to overcome its intrinsic limitations.

A cryo-electron tomography workflow reveals protrusion-mediated shedding on injured plasma membrane

Cryo-electron tomography (cryo-ET) provides structural context to molecular mechanisms underlying biological processes. Although straightforward to implement for studying stable macromolecular complexes, using it to locate short-lived structures and events can be impractical. A combination of live-cell microscopy, correlative light and electron microscopy, and cryo-ET will alleviate this issue. We developed a workflow combining the three to study the ubiquitous and dynamic process of shedding in response to plasma membrane damage in HeLa cells. We found filopodia-like protrusions enriched at damage sites and acting as scaffolds for shedding, which involves F-actin dynamics, myosin-1a, and vacuolar protein sorting 4B (a component of the 'endosomal sorting complex required for transport' machinery). Overall, shedding is more complex than current models of vesiculation from flat membranes. Its similarities to constitutive shedding in enterocytes argue for a conserved mechanism. Our workflow can also be adapted to study other damage response pathways and dynamic cellular events.

HPM live μ for a full CLEM workflow

With the development of advanced imaging methods that took place in the last decade, the spatial correlation of microscopic and spectroscopic information-known as multimodal imaging or correlative microscopy (CM)-has become a broadly applied technique to explore biological and biomedical materials at different length scales. Among the many different combinations of techniques, Correlative Light and Electron Microscopy (CLEM) has become the flagship of this revolution. Where light (mainly fluorescence) microscopy can be used directly for the live imaging of cells and tissues, for almost all applications, electron microscopy (EM) requires fixation of the biological materials. Although sample preparation for EM is traditionally done by chemical fixation and embedding in a resin, rapid cryogenic fixation (vitrification) has become a popular way to avoid the formation of artifacts related to the chemical fixation/embedding procedures. During vitrification, the water in the sample transforms into an amorphous ice, keeping the ultrastructure of the biological sample as close as possible to the native state. One immediate benefit of this cryo-arrest is the preservation of protein fluorescence, allowing multi-step multi-modal imaging techniques for CLEM. To minimize the delay separating live imaging from cryo-arrest, we developed a high-pressure freezing (HPF) system directly coupled to a light microscope. We address the optimization of sample preservation and the time needed to capture a biological event, going from live imaging to cryo-arrest using HPF. To further explore the potential of cryo-fixation related to the forthcoming transition from imaging 2D (cell monolayers) to imaging 3D samples (tissue) and the associated importance of homogeneous deep vitrification, the HPF core technology has been revisited to allow easy modification of the environmental parameters during vitrification. Lastly, we will discuss the potential of our HPM within CLEM protocols especially for correlating live imaging using the Zeiss LSM900 with electron microscopy.

Cryo-nanoscale chromosome imaging-future prospects

The high-order structure of mitotic chromosomes remains to be fully elucidated. How nucleosomes compact at various structural levels into a condensed mitotic chromosome is unclear. Cryogenic preservation and imaging have been applied for over three decades, keeping biological structures close to the native in vivo state. Despite being extensively utilized, this field is still wide open for mitotic chromosome research. In this review, we focus specifically on cryogenic efforts for determining the mitotic nanoscale chromatin structures. We describe vitrification methods, current status, and applications of advanced cryo-microscopy including future tools required for resolving the native architecture of these fascinating structures that hold the instructions to life.

In situ Microfluidic Cryofixation for Cryo Focused Ion Beam Milling and Cryo Electron Tomography

We present a microfluidic platform for studying structure-function relationships at the cellular level by connecting video rate live cell imaging with in situ microfluidic cryofixation and cryo-electron tomography of near natively preserved, unstained specimens. Correlative light and electron microscopy (CLEM) has been limited by the time required to transfer live cells from the light microscope to dedicated cryofixation instruments, such as a plunge freezer or high-pressure freezer. We recently demonstrated a microfluidic based approach that enables sample cryofixation directly in the light microscope with millisecond time resolution, a speed improvement of up to three orders of magnitude. Here we show that this cryofixation method can be combined with cryo-electron tomography (cryo-ET) by using Focused Ion Beam milling at cryogenic temperatures (cryo-FIB) to prepare frozen hydrated electron transparent sections. To make cryo-FIB sectioning of rapidly frozen microfluidic channels achievable, we developed a sacrificial layer technique to fabricate microfluidic devices with a PDMS bottom wall <5 µm thick. We demonstrate the complete workflow by rapidly cryo-freezing Caenorhabditis elegans roundworms L1 larvae during live imaging in the light microscope, followed by cryo-FIB milling and lift out to produce thin, electron transparent sections for cryo-ET imaging. Cryo-ET analysis of initial results show that the structural preservation of the cryofixed C. elegans was suitable for high resolution cryo-ET work. The combination of cryofixation during live imaging enabled by microfluidic cryofixation with the molecular resolution capabilities of cryo-ET offers an exciting avenue to further advance space-time correlative light and electron microscopy (st-CLEM) for investigation of biological processes at high resolution in four dimensions.

Mineralized scale patterns on the cell periphery of the chrysophyte Mallomonas determined by comparative 3D Cryo-FIB SEM data processing

Unicellular protists can biomineralize spatially complex and functional shells. A typical cell of the photosynthetic synurophyte Mallomonas is covered by about 60-100 silica scales. Their geometric arrangement, the so-called scale case, mainly depends on the species and on the cell cycle. In this study, the scale case of the synurophyte Mallomonas was preserved in aqueous suspension using high-pressure freezing (HPF). From this specimen, a three-dimensional (3D) data set spanning a volume of about 25.6 μm × 19.2 μm × 4.2 μm with a voxel size of 12.5 nm × 12.5 nm × 25.0 nm was collected by Cryo-FIB SEM in 3 h and 24 min. SEM imaging using In-lens SE detection allowed to clearly differentiate between mineralized, curved scales of less than 0.2 μm thickness and organic cellular ultrastructure or vitrified ice. The three-dimensional spatial orientations and shapes of a minimum set of scales (N = 13) were identified by visual inspection, and manually segmented. Manual and automated segmentation approaches were comparatively applied to one arbitrarily selected reference scale using the differences in grey level between scales and other constituents. Computational automated routines and principal component analysis of the experimentally extracted data created a realistic mathematical model based on the Fibonacci pattern theory. A complete in silico scale case of Mallomonas was reconstructed showing an optimized scale coverage on the cell surface, similarly as it was observed experimentally. The minimum time requirements from harvesting the living cells to the final scale case determination by Cryo-FIB SEM and computational image processing are discussed.

Towards a mechanistic understanding of cellular processes by cryoEM

A series of recent hardware and software developments have transformed cryo-electron microscopy (cryoEM) from a niche tool into a method that has become indispensable in structural and functional biology. Samples that are rapidly frozen are encased in a near-native state inside a layer of amorphous ice, and then imaged in an electron microscope cooled to cryogenic temperatures. Despite being conceptually simple, cryoEM owns its success to a plethora of technological developments from numerous research groups. Here, we review the key technologies that have made this astonishing transformation possible and highlight recent trends with a focus on cryo-electron tomography. Additionally, we discuss how correlated microscopy is an exciting and perpendicular development route forward in this already rapidly growing field. We specifically discuss microscopy techniques that allow to complement time-dependent information of dynamic processes to the unique high resolution obtained in cryoEM.