Complete vitrification in pure liquid water and dilute aqueous solutions

Electrified Operando-Freezing of Electrocatalytic CO2 Reduction Cells for Cryogenic Electron Microscopy

The ability to freeze and stabilize reaction intermediates in their metastable states and obtain their structural and chemical information with high spatial resolution is critical to advance materials technologies such as catalysis and batteries. Here, we develop an electrified operando-freezing methodology to preserve these metastable states under electrochemical reaction conditions for cryogenic electron microscopy (cryo-EM) imaging and spectroscopy. Using Cu catalysts for CO2 reduction as a model system, we observe restructuring of the Cu catalyst in a CO2 atmosphere while the same catalyst remains intact in air at the nanometer scale. Furthermore, we discover the existence of a single valence Cu (1+) state and C-O bonding at the electrified liquid-solid interface of the operando-frozen samples, which are key reaction intermediates that traditional ex situ measurements fail to detect. This work highlights our novel technique to study the local structure and chemistry of electrified liquid-solid interfaces, with broad impact beyond catalysis.

Direct comparison of isobaric and isochoric vitrification of two aqueous solutions with photon counting X-ray computed tomography

Vitrification is a promising approach for ice-free cryopreservation of biological material, but progress is hindered by the limited set of experimental tools for studying processes in the interior of the vitrified matter. Isochoric cryopreservation chambers are often metallic, and their opacity prevents direct visual observation. In this study, we introduce photon counting X-ray computed tomography (CT) to compare the effects of rigid isochoric and unconfined isobaric conditions on vitrification and ice formation during cooling of two aqueous solutions: 50 wt% DMSO and a coral vitrification solution, CVS1. Previous studies have only compared vitrification in isochoric systems with isobaric systems that have an exposed air-liquid interface. We use a movable piston to replicate the surface and thermal boundary conditions of the isochoric system yet maintain isobaric conditions. When controlling for the boundary conditions we find that similar ice and vapor volume fractions form during cooling in isochoric and isobaric conditions. Interestingly, we observe distinct ice and vapor cavity morphology in the isochoric systems, possibly due to vapor outgassing or cavitation as rapid cooling causes the pressure to drop in the confined systems. These observations highlight the array of thermal-fluid processes that occur during vitrification in confined aqueous systems and motivate the further application of imaging techniques such as photon counting X-ray CT in fundamental studies of vitrification.

Polarization Amplification in Dynamic Nuclear Polarization Magic-Angle Spinning Solid-State Nuclear Magnetic Resonance by Solubilizing Traditional Ionic Salts

Dynamic nuclear polarization can improve the sensitivity of magic-angle spinning solid-state NMR experiments by 1-2 orders of magnitude. In aqueous media, experiments are usually performed using the so-called DNP juice, a glycerol-d8/D2O/H2O mixture (60/30/10, v/v/v) that can form a homogeneous glass at cryogenic temperatures. This acts as a cryoprotectant and prevents phase separation of the paramagnetic polarizing agents (PAs) that are added to the mixture to provide the source of electron spin polarization required for DNP. Here, we show that relatively high 1H DNP enhancements (∼60) can also be obtained in water without glycerol (or other glass forming agents) simply by dissolving high concentrations of electrolytes (such as NaCl or LiCl), which perturb the otherwise unavoidable ice crystallization observed upon cooling, thereby reducing PA phase separation and restoring DNP efficiency.

Technologies for Vitrification Based Cryopreservation

Cryopreservation is a unique and practical method to facilitate extended access to biological materials. Because of this, cryopreservation of cells, tissues, and organs is essential to modern medical science, including cancer cell therapy, tissue engineering, transplantation, reproductive technologies, and bio-banking. Among diverse cryopreservation methods, significant focus has been placed on vitrification due to low cost and reduced protocol time. However, several factors, including the intracellular ice formation that is suppressed in the conventional cryopreservation method, restrict the achievement of this method. To enhance the viability and functionality of biological samples after storage, a large number of cryoprotocols and cryodevices have been developed and studied. Recently, new technologies have been investigated by considering the physical and thermodynamic aspects of cryopreservation in heat and mass transfer. In this review, we first present an overview of the physiochemical aspects of freezing in cryopreservation. Secondly, we present and catalog classical and novel approaches that seek to capitalize on these physicochemical effects. We conclude with the perspective that interdisciplinary studies provide pieces of the cryopreservation puzzle to achieve sustainability in the biospecimen supply chain.

Nucleation and growth of crystalline ices from amorphous ices

We here review mostly experimental and some computational work devoted to nucleation in amorphous ices. In fact, there are only a handful of studies in which nucleation and growth in amorphous ices are investigated as two separate processes. In most studies, crystallization temperatures T_x or crystallization rates R_JG are accessed for the combined process. Our Review deals with different amorphous ices, namely, vapor-deposited amorphous solid water (ASW) encountered in many astrophysical environments; hyperquenched glassy water (HGW) produced from μm-droplets of liquid water; and low density amorphous (LDA), high density amorphous (HDA), and very high density amorphous (VHDA) ices produced via pressure-induced amorphization of ice I or from high-pressure polymorphs. We cover the pressure range of up to about 6 GPa and the temperature range of up to 270 K, where only the presence of salts allows for the observation of amorphous ices at such high temperatures. In the case of ASW, its microporosity and very high internal surface to volume ratio are the key factors determining its crystallization kinetics. For HGW, the role of interfaces between individual glassy droplets is crucial but mostly neglected in nucleation or crystallization studies. In the case of LDA, HDA, and VHDA, parallel crystallization kinetics to different ice phases is observed, where the fraction of crystallized ices is controlled by the heating rate. A key aspect here is that in different experiments, amorphous ices of different "purities" are obtained, where "purity" here means the "absence of crystalline nuclei." For this reason, "preseeded amorphous ice" and "nuclei-free amorphous ice" should be distinguished carefully, which has not been done properly in most studies. This makes a direct comparison of results obtained in different laboratories very hard, and even results obtained in the same laboratory are affected by very small changes in the preparation protocol. In terms of mechanism, the results are consistent with amorphous ices turning into an ultraviscous, deeply supercooled liquid prior to nucleation. However, especially in preseeded amorphous ices, crystallization from the preexisting nuclei takes place simultaneously. To separate the time scales of crystallization from the time scale of structure relaxation cleanly, the goal needs to be to produce amorphous ices free from crystalline ice nuclei. Such ices have only been produced in very few studies.

Kinetics and Mechanisms of Pressure-Induced Ice Amorphization and Polyamorphic Transitions in a Machine-Learned Coarse-Grained Water Model

Water glasses have attracted considerable attention due to their potential connection to a liquid-liquid transition in supercooled water. Here we use molecular simulations to investigate the formation and phase behavior of water glasses using the machine-learned bond-order parameter (ML-BOP) water model. We produce glasses through hyperquenching of water, pressure-induced amorphization (PIA) of ice, and pressure-induced polyamorphic transformations. We find that PIA of polycrystalline ice occurs at a lower pressure than that of monocrystalline ice and through a different mechanism. The temperature dependence of the amorphization pressure of polycrystalline ice for ML-BOP agrees with that in experiments. We also find that ML-BOP accurately reproduces the density, coordination number, and structural features of low-density (LDA), high-density (HDA), and very high-density (VHDA) amorphous water glasses. ML-BOP accurately reproduces the experimental radial distribution function of LDA but overpredicts the minimum between the first two shells in high-density glasses. We examine the kinetics and mechanism of the transformation between low-density and high-density glasses and find that the sharp nature of these transitions in ML-BOP is similar to that in experiments and all-atom water models with a liquid-liquid transition. Transitions between ML-BOP glasses occur through a spinodal-like mechanism, similar to ice crystallization from LDA. Both glass-to-glass and glass-to-ice transformations have Avrami-Kolmogorov kinetics with exponent n = 1.5 ± 0.2 in experiments and simulations. Importantly, ML-BOP reproduces the competition between crystallization and HDA→LDA transition above the glass transition temperature T_g, and separation of their time scales below T_g, observed also in experiments. These findings demonstrate the ability of ML-BOP to accurately reproduce water properties across various regimes, making it a promising model for addressing the competition between polyamorphic transitions and crystallization in water and solutions.

Impact of N-heteroaromatic N-termini in Cu(II) ATCUN metallopeptides on their biorelevant redox activity

Cu(II) complexes with ATCUN peptide ligands have been investigated for their ROS (reactive oxygen species) generation and oxidative DNA degradation abilities. The biological activity of most ATCUN complexes such as Cu-GGH (Gly-Gly-His) is, however, low. Tuning the redox chemistry by incorporation of N-heteroaromatics reinstates ROS production which leads to efficient DNA cleavage.

Correlative Cryo-imaging Using Soft X-Ray Tomography for the Study of Virus Biology in Cells and Tissues

Viruses are obligate intracellular pathogens that depend on their host cell machinery and metabolism for their replicative life cycle. Virus entry, replication, and assembly are dynamic processes that lead to the reorganisation of host cell components. Therefore, a complete understanding of the viral processes requires their study in the cellular context where advanced imaging has been proven valuable in providing the necessary information. Among the available imaging techniques, soft X-ray tomography (SXT) at cryogenic temperatures can provide three-dimensional mapping to 25 nm resolution and is ideally suited to visualise the internal organisation of virus-infected cells. In this chapter, the principles and practices of synchrotron-based cryo-soft X-ray tomography (cryo-SXT) in virus research are presented. The potential of the cryo-SXT in correlative microscopy platforms is also demonstrated through working examples of reovirus and hepatitis research at Beamline B24 (Diamond Light Source Synchrotron, UK) and BL09-Mistral beamline (ALBA Synchrotron, Spain), respectively.

Methods of Preparing Nanoscale Vitreous Ice Needles for High-Resolution Cryogenic Characterization

New high-resolution imaging methods for biological samples such as atom probe tomography (APT), facilitated by the invention of laser-pulsed atom probes and cryo-transfer procedures, have recently emerged. However, ensuring the vitreous state of the fabricated aqueous needle-shaped APT samples remains a challenge despite it being crucial for characterizing biomolecules such as proteins and cellular architectures in their near-native state. Our work investigated three potential approaches: (1) open microcapillary (OMC) method, (2) high-pressure freezing method (HPF), and (3) graphene encapsulation method. Diffraction patterns of the needle specimens acquired by cryo-TEM have demonstrated the vitreous state of the ice needles, although limited to the tip regions, has been achieved with the three proposed approaches. With the capability to prepare vitreous ice needles from hydrated samples of up to ∼200 μm thickness (HPF), combined use of the three approaches opens new avenues for future near-atomic imaging of biological cells in their near-native state.

Molecular dynamics analysis of elastic properties and new phase formation during amorphous ices transformations

Unlike conventional first-order phase transitions, the kinetics of amorphous-amorphous transitions has been much less studied. The ultrasonic experiments on the transformations between low-density and high-density amorphous ice induced by pressure or heating provided the pressure and temperature dependencies of elastic moduli. In this article, we make an attempt to build a microscopic picture of these experimentally studied transformations using the molecular dynamics method with the TIP4P/Ice water model. We study carefully the dependence of the results of elastic constants calculations on the deformation rates. The system size effects are considered as well. The comparison with the experimental data enriches our understanding of the transitions observed. Our modeling gives new information about the formation mechanisms of new phase clusters during the transition between low-density and high-density amorphous ices. We analyse the applicability of the term "nucleation" for these processes.

A guide into the world of high-resolution 3D imaging: the case of soft X-ray tomography for the life sciences

In the world of bioimaging, every choice made determines the quality and content of the data collected. The choice of imaging techniques for a study could showcase or dampen expected outcomes. Synchrotron radiation is indispensable for biomedical research, driven by the need to see into biological materials and capture intricate biochemical and biophysical details at controlled environments. The same need drives correlative approaches that enable the capture of heterologous but complementary information when studying any one single target subject. Recently, the applicability of one such synchrotron technique in bioimaging, soft X-ray tomography (SXT), facilitates exploratory and basic research and is actively progressing towards filling medical and industrial needs for the rapid screening of biomaterials, reagents and processes of immediate medical significance. Soft X-ray tomography at cryogenic temperatures (cryoSXT) fills the imaging resolution gap between fluorescence microscopy (in the hundreds of nanometers but relatively accessible) and electron microscopy (few nanometers but requires extensive effort and can be difficult to access). CryoSXT currently is accessible, fully documented, can deliver 3D imaging to 25 nm resolution in a high throughput fashion, does not require laborious sample preparation procedures and can be correlated with other imaging techniques. Here, we present the current state of SXT and outline its place within the bioimaging world alongside a guided matrix that aids decision making with regards to the applicability of any given imaging technique to a particular project. Case studies where cryoSXT has facilitated a better understanding of biological processes are highlighted and future directions are discussed.

Bioinspired Ice-Binding Materials for Tissue and Organ Cryopreservation

Cryopreservation of tissues and organs can bring transformative changes to medicine and medical science. In the past decades, limited progress has been achieved, although cryopreservation of tissues and organs has long been intensively pursued. One key reason is that the cryoprotective agents (CPAs) currently used for cell cryopreservation cannot effectively preserve tissues and organs because of their cytotoxicity and tissue destructive effect as well as the low efficiency in controlling ice formation. In stark contrast, nature has its unique ways of controlling ice formation, and many living organisms can effectively prevent freezing damage. Ice-binding proteins (IBPs) are regarded as the essential materials identified in these living organisms for regulating ice nucleation and growth. Note that controversial results have been reported on the utilization of IBPs and their mimics for the cryopreservation of tissues and organs, that is, some groups revealed that IBPs and mimics exhibited unique superiorities in tissues cryopreservation, while other groups showed detrimental effects. In this perspective, we analyze possible reasons for the controversy and predict future research directions in the design and construction of IBP inspired ice-binding materials to be used as new CPAs for tissue cryopreservation after briefly introducing the cryo-injuries and the challenges of conventional CPAs in the cryopreservation of tissues and organs.

Ultra-Rapid Laser Calorimetry for the Assessment of Crystallization in Low-Concentration Cryoprotectants

Cryoprotective agents (CPAs) are routinely used to vitrify, attain an amorphous glass state void of crystallization, and thereby cryopreserve biomaterials. Two vital characteristics of a CPA-loaded system are the critical cooling and warming rates (CCR and CWR), the temperature rates needed to achieve and return from a vitrified state, respectively. Due to the toxicity associated with CPAs, it is often desirable to use the lowest concentrations possible, driving up CWR and making it increasingly difficult to measure. This paper describes a novel method for assessing CWR between the 0.4 × 10⁵ and 10⁷ °C/min in microliter CPA-loaded droplet systems with a new ultrarapid laser calorimetric approach. Cooling was achieved by direct quenching in liquid nitrogen, while warming was achieved by the irradiation of plasmonic gold nanoparticle-loaded vitrified droplets by a high-power 1064 nm millisecond pulsed laser. We assume "apparent" vitrification is achieved provided ice is not visually apparent (i.e., opacity) upon imaging with a camera (CCR) during cooling or highspeed camera (CWR) during warming. Using this approach, we were able to investigate CWRs in single CPA systems such as propylene glycol (PG), glycerol, and Trehalose in water, as well as mixtures of glycerol-trehalose-water and propylene glycol-trehalose-water CPA at low concentrations (20-40 wt %). Further, a phenomenological model for determining the CCRs and CWRs of CPAs was developed which allowed for predictions of CCR or CWR of single component CPA and mixtures (within and outside of the regime their constituents were measured in), providing an avenue for optimizing CCR and CWR and perhaps future CPA cocktail discovery.

Ultrarapid cryo-arrest of living cells on a microscope enables multiscale imaging of out-of-equilibrium molecular patterns

Imaging molecular patterns in cells by fluorescence micro- or nanoscopy has the potential to relate collective molecular behavior to cellular function. However, spatial and spectroscopic resolution is fundamentally limited by motional blur caused by finite photon fluxes and photobleaching. At physiological temperatures, photochemical reactivity does not only limit imaging at multiple scales but is also toxic to biochemical reactions that maintain cellular organization. Here, we present cryoprotectant-free ultrarapid cryo-arrest directly on a multimodal fluorescence microscope that preserves the out-of-equilibrium molecular organization of living cells. This allows the imaging of dynamic processes before cryo-arrest in combination with precise molecular pattern determination at multiple scales within the same cells under cryo-arrest. We both experimentally and theoretically show that ultrarapid cryo-arrest overcomes the fundamental resolution barrier imposed by motional blur and photochemical reactivity, enabling observation of native molecular distributions and reaction patterns that are not resolvable at physiological temperatures.

Kinetics of nonisothermal phase change with arbitrary temperature-time history and initial transformed phase distributions

This paper describes the extension of the classic Avrami equation to nonisothermal systems with arbitrary temperature-time history and arbitrary initial distributions of transformed phase. We start by showing that through examination of phase change in Fourier space, we can decouple the nucleation rate, growth rate, and transformed fraction, leading to the derivation of a nonlinear differential equation relating these three properties. We then consider a population balance partial differential equation (PDE) on the phase size distribution and solve it analytically. Then, by relating this PDE solution to the transformed fraction of phase, we are able to derive initial conditions to the differential equation relating nucleation rate, growth rate, and transformed fraction.

Advances in the study of supercooled water

In this review, we report recent progress in the field of supercooled water. Due to its uniqueness, water presents numerous anomalies with respect to most simple liquids, showing polyamorphism both in the liquid and in the glassy state. We first describe the thermodynamic scenarios hypothesized for the supercooled region and in particular among them the liquid-liquid critical point scenario that has so far received more experimental evidence. We then review the most recent structural indicators, the two-state model picture of water, and the importance of cooperative effects related to the fact that water is a hydrogen-bonded network liquid. We show throughout the review that water's peculiar properties come into play also when water is in solution, confined, and close to biological molecules. Concerning dynamics, upon mild supercooling water behaves as a fragile glass former following the mode coupling theory, and it turns into a strong glass former upon further cooling. Connections between the slow dynamics and the thermodynamics are discussed. The translational relaxation times of density fluctuations show in fact the fragile-to-strong crossover connected to the thermodynamics arising from the existence of two liquids. When considering also rotations, additional crossovers come to play. Mobility-viscosity decoupling is also discussed in supercooled water and aqueous solutions. Finally, the polyamorphism of glassy water is considered through experimental and simulation results both in bulk and in salty aqueous solutions. Grains and grain boundaries are also discussed.

Microscopes, tools, probes, and protocols: A guide in the route of correlative microscopy for biomedical investigation

In the last decades, the advancements of microscopes technology, together with the development of new imaging approaches, are trying to address some biological questions that have been unresolved in the past: the need to combine in the same analysis temporal, functional and morphological information on the biological sample has become pressing. For this reason, the use of correlative microscopy, in which two or more imaging techniques are combined in the same analysis, is getting increasingly widespread. In fact, correlative microscopy can overcome limitations of a single imaging method, giving access to a larger amount of information from the same specimen. However, correlative microscopy can be challenging, and appropriate protocols for sample preparation and imaging methods must be selected. Here we review the state of the art of correlating electron microscopy with different imaging methods, focusing on sample preparation, tools, and labeling methods, with the aim to provide a comprehensive guide for those scientists who are approaching the field of correlative methods.

High-resolution single-particle cryo-EM of samples vitrified in boiling nitro-gen

Based on work by Dubochet and others in the 1980s and 1990s, samples for single-particle cryo-electron microscopy (cryo-EM) have been vitrified using ethane, propane or ethane/propane mixtures. These liquid cryogens have a large difference between their melting and boiling temperatures and so can absorb substantial heat without formation of an insulating vapor layer adjacent to a cooling sample. However, ethane and propane are flammable, they must be liquified in liquid nitro-gen immediately before cryo-EM sample preparation, and cryocooled samples must be transferred to liquid nitro-gen for storage, complicating workflows and increasing the chance of sample damage during handling. Experiments over the last 15 years have shown that cooling rates required to vitrify pure water are only ∼250 000 K s-1, at the low end of earlier estimates, and that the dominant factor that has limited cooling rates of small samples in liquid nitro-gen is sample precooling in cold gas present above the liquid cryogen surface, not the Leidenfrost effect. Using an automated cryocooling instrument developed for cryocrystallography that combines high plunge speeds with efficient removal of cold gas, we show that single-particle cryo-EM samples on commercial grids can be routinely vitrified using only boiling nitro-gen and obtain apoferritin datasets and refined structures with 2.65 Å resolution. The use of liquid nitro-gen as the primary coolant may allow manual and automated workflows to be simplified and may reduce sample stresses that contribute to beam-induced motion.

The role of high-density and low-density amorphous ice on biomolecules at cryogenic temperatures: a case study with polyalanine

Experimental techniques, such as cryo-electron microscopy, require biological samples to be recovered at cryogenic temperatures (T ≈ 100 K) with water being in an amorphous ice state. However, (bulk) water can exist in two amorphous ices at P < 1 GPa, low-density amorphous (LDA) ice at low pressures and high-density amorphous ice (HDA) at high pressures; HDA is ≈20-25% denser than LDA. While fast/plunge cooling at 1 bar brings the sample into LDA, high-pressure cooling (HPC), at sufficiently high pressure, produces HDA. HDA can also be produced by isothermal compression of LDA at cryogenic temperatures. Here, we perform classical molecular dynamics simulations to study the effects of LDA, HDA, and the LDA-HDA transformation on the structure and hydration of a small peptide, polyalanine. We follow thermodynamic paths corresponding to (i) fast/plunge cooling at 1 bar, (ii) HPC at P = 400 MPa, and (iii) compression/decompression cycles at T = 80 K. While process (i) produced LDA in the system, path (iii) produces HDA. Interestingly, the amorphous ice produced in process (ii) is an intermediate amorphous ice (IA) with properties that fall in-between those of LDA and HDA. Remarkably, the structural changes in polyalanine are negligible at all conditions studied (0-2000 MPa, 80-300 K) even when water changes among the low and high-density liquid states as well as the amorphous solids LDA, IA, and HDA. The similarities and differences in the hydration of polyalanine vitrified in LDA, IA, and HDA are described. Since the studied thermodynamic paths are suitable for the cryopreservation of biomolecules, we also study the structure and hydration of polyalanine along isobaric and isochoric heating paths, which can be followed experimentally for the recovery of cryopreserved samples. Upon heating, the structure of polyalanine remains practically unchanged. We conclude with a brief discussion of the practical advantages of (a) using HDA and IA as a cryoprotectant environment (as opposed to LDA), and (b) the use of isochoric heating as a recovery process (as opposed to isobaric heating).

Wide-angle X-ray scattering and molecular dynamics simulations of supercooled protein hydration water

Understanding the mechanism responsible for the protein low-temperature crossover observed at T≈ 220 K can help us improve current cryopreservation technologies. This crossover is associated with changes in the dynamics of the system, such as in the mean-squared displacement, whereas experimental evidence of structural changes is sparse. Here we investigate hydrated lysozyme proteins by using a combination of wide-angle X-ray scattering and molecular dynamics (MD) simulations. Experimentally we suppress crystallization by accurate control of the protein hydration level, which allows access to temperatures down to T = 175 K. The experimental data indicate that the scattering intensity peak at Q = 1.54 Å-1, attributed to interatomic distances, exhibits temperature-dependent changes upon cooling. In the MD simulations it is possible to decompose the water and protein contributions and we observe that, while the protein component is nearly temperature independent, the hydration water peak shifts in a fashion similar to that of bulk water. The observed trends are analysed by using the water-water and water-protein radial distribution functions, which indicate changes in the local probability density of hydration water.

Experimental evidence for glass polymorphism in vitrified water droplets

The question of whether a first-order liquid-to-liquid transition is at the origin of water’s anomalous properties has been controversial since the pioneering experiments by Mishima et al. in 1985 and molecular simulations by Poole et al. in 1992. Since then, experiments aimed at shedding light on this question have been performed using amorphous ices made from crystalline ice, fueling criticism about their crystal-like nature. In the present study, we avoid crystalline ice at any time of the experiment yet still observe a first-order glass-to-glass transition in vitrified liquid droplets. This makes the strong case for glass polymorphism and the direct thermodynamic connection to the liquid-to-liquid transition at higher temperatures, dismissing the criticism voiced for three decades.

The nature of amorphous ices has been debated for more than 35 years. In essence, the question is whether they are related to ice polymorphs or to liquids. The fact that amorphous ices are traditionally prepared from crystalline ice via pressure-induced amorphization has made a clear distinction tricky. In this work, we vitrify liquid droplets through cooling at ≥10⁶ K ⋅ s⁻¹ and pressurize the glassy deposit. We observe a first order–like densification upon pressurization and recover a high-density glass. The two glasses resemble low- and high-density amorphous ice in terms of both structure and thermal properties. Vitrified water shows all features that have been reported for amorphous ices made from crystalline ice. The only difference is that the hyperquenched and pressurized deposit shows slightly different crystallization kinetics to ice I upon heating at ambient pressure. This implies a thermodynamically continuous connection of amorphous ices with liquids, not crystals.

Principles of Ice-Free Cryopreservation by Vitrification

Vitrification is an alternative to cryopreservation by freezing that enables hydrated living cells to be cooled to cryogenic temperatures in the absence of ice. Vitrification simplifies and frequently improves cryopreservation because it eliminates mechanical injury from ice, eliminates the need to find optimal cooling and warming rates, eliminates the importance of differing optimal cooling and warming rates for cells in mixed cell type populations, eliminates the need to find a frequently imperfect compromise between solution effects injury and intracellular ice formation, and can enable chilling injury to be "outrun" by using rapid cooling without a risk of intracellular ice formation. On the other hand, vitrification requires much higher concentrations of cryoprotectants than cryopreservation by freezing, which introduces greater risks of both osmotic damage and cryoprotectant toxicity. Fortunately, a large number of remedies for the latter problem have been discovered over the past 35 years, and osmotic damage can in most cases be eliminated or adequately controlled by paying careful attention to cryoprotectant introduction and washout techniques. Vitrification therefore has the potential to enable the superior and convenient cryopreservation of a wide range of biological systems (including molecules, cells, tissues, organs, and even some whole organisms), and it is also increasingly recognized as a successful strategy for surviving harsh environmental conditions in nature. But the potential of vitrification is sometimes limited by an insufficient understanding of the complex physical and biological principles involved, and therefore a better understanding may not only help to improve present outcomes but may also point the way to new strategies that may be yet more successful in the future. This chapter accordingly describes the basic principles of vitrification and indicates the broad potential biological relevance of this alternative method of cryopreservation.

Electron Beam-Induced Transformation in High-Density Amorphous Ices

Amorphous ice is commonly used as a noncrystalline matrix for protecting sensitive biological samples in cryogenic electron microscopy (cryo-EM). The amorphization process of water is complex, and at least two amorphous states of different densities are known to exist, high- and low-density amorphous ices (HDA and LDA). These forms are considered to be the counterparts of two distinct liquid states, namely, high- and low-density liquid water. Herein, we investigate the HDA to LDA transition using electron diffraction and cryo-EM. The observed phase transition is induced by the impact of electrons, and we discuss two different mechanisms, namely, local heating and beam-induced motion of water molecules. The temperature increase is estimated by comparison with X-ray scattering experiments on identically prepared samples. Our results suggest that HDA, under the conditions used in our cryo-EM measurements, is locally heated above its glass-transition temperature.

Some Aspects of the Liquid Water Thermodynamic Behavior: From The Stable to the Deep Supercooled Regime

Liquid water is considered to be a peculiar example of glass forming materials because of the possibility of giving rise to amorphous phases with different densities and of the thermodynamic anomalies that characterize its supercooled liquid phase. In the present work, literature data on the density of bulk liquid water are analyzed in a wide temperature-pressure range, also including the glass phases. A careful data analysis, which was performed on different density isobars, made in terms of thermodynamic response functions, like the thermal expansion αP and the specific heat differences CP−CV, proves, exclusively from the experimental data, the thermodynamic consistence of the liquid-liquid transition hypothesis. The study confirms that supercooled bulk water is a mixture of two liquid “phases”, namely the high density (HDL) and the low density (LDL) liquids that characterize different regions of the water phase diagram. Furthermore, the CP−CV isobars behaviors clearly support the existence of both a liquid–liquid transition and of a liquid–liquid critical point.

The Evolution of the Cryopreservation Techniques in Reproductive Medicine—Exploring the Character of the Vitrified State Intra- and Extracellularly to Better Understand Cell Survival after Cryopreservation

Nowadays, cryopreservation of gametes and embryos is a fundamental, integral, and indispensable part of infertility treatment or fertility preservation. Cryopreservation is not only needed for the policy of single embryo transfer and cryopreservation of surplus embryos, but for deferring embryo transfer in the case of ovarian hyperstimulation syndrome, uterine pathologies, and suboptimal endometrium built-up or when preimplantation genetic testing is needed. Several current strategies in assisted reproduction technology (ART) would be inconceivable without highly efficient cryopreservation protocols. Nevertheless, cryopreservation hampered for a long time, especially in terms of low survival rates after freezing and thawing. Only the technical progress during the last decades, namely, in regard to the implementation and advancement of vitrification, leveraged its application, and thus, even allows the cryopreservation of human oocytes—a process that is far from being easy. This review aims to provide a deeper insight into the physical processes of cryopreservation and to explore the character of the vitrified state in the extra and intracellular milieu in order to demonstrate that the common denominator to all cryopreservation procedures is the establishment of an intracellular amorphous condition that hinders the likelihood of crystallization.

Light-coupled cryo-plunger for time-resolved cryo-EM

Proteins are dynamic molecules that can undergo rapid conformational rearrangements in response to stimuli. These structural changes are often critical to protein function, and thus elucidating time-dependent conformational landscapes has been a long-standing goal of structural biology. To harness the power of single particle cryo-EM methods to enable 'time-resolved' structure determination, we have developed a light-coupled cryo-plunger that pairs flash-photolysis of caged ligands with rapid sample vitrification. The 'flash-plunger' consists of a high-power ultraviolet LED coupled with focusing optics and a motorized linear actuator, enabling the user to immobilize protein targets in vitreous ice within a programmable time window - as short as tens of milliseconds - after stimulus delivery. The flash-plunger is a simple, inexpensive and flexible tool to explore short-lived conformational states previously unobtainable by conventional sample preparation methods.

Pair Distribution Function from Electron Diffraction in Cryogenic Electron Microscopy: Revealing Glassy Water Structure

In recent years, cryogenic electron microscopy (Cryo-EM) has revolutionized the structure determination of wet samples and especially that of biological macromolecules. The glassy-water medium in which the molecules are embedded is considered an almost in vivo environment for biological samples. The local structure of amorphous ice is known from neutron- and X-ray-diffraction studies, techniques appropriate for much larger volumes than those used in cryo-EM. We here present a first study of the pair-distribution function g(r) of glassy water under cryo-EM conditions using electron diffraction data. We found g(r) to be between that of low-density amorphous ice and that of supercooled water. Under electron exposure, cubic-ice regions were found to nucleate in thicker glassy-water samples. Our work enables to obtain quantitative structural information using g(r) from cryo-EM.

Paper-Based Cell Cryopreservation

The continuous development of simple and practical cell cryopreservation methods is of great importance to a variety of sectors, especially when considering the efficient short- and long-term storage of cells and their transportation. Although the overall success of such methods has been increased in recent years, there is still need for a unified platform that is highly suitable for efficient cryogenic storage of cells in addition to their easy-to-manage retrieval. Here, a paper-based cell cryopreservation method as an alternative to conventional cryopreservation methods is presented. The method is space-saving, cost-effective, simple and easy to manage, and requires no additional fine-tuning to conventional freezing and thawing procedures to yield comparable recovery of viable cells. It is shown that treating papers with fibronectin solution enhances the release of viable cells post thawing as compared to untreated paper platforms. Additionally, upon release, the remaining cells within the paper lead to the formation and growth of spheroid-like structures. Moreover, it is demonstrated that the developed method works with paper-based 3D cultures, where preformed 3D cultures can be efficiently cryopreserved.

Specific Heat and Transport Functions ofWater

Numerous water characteristics are essentially ascribed to its peculiarity to form strong hydrogen bonds that become progressively more stable on decreasing the temperature. However, the structural and dynamical implications of the molecular rearrangement are still subject of debate and intense studies. In this work, we observe that the thermodynamic characteristics of liquid water are strictly connected to its dynamic characteristics. In particular, we compare the thermal behaviour of the isobaric specific heat of water, measured in different confinement conditions at atmospheric pressure (and evaluated by means of theoretical studies) with its configurational contribution obtained from the values of the measured self-diffusion coefficient through the use of the Adam–Gibbs approach. Our results confirm the existence of a maximum in the specific heat of water at about 225 K and indicate that especially at low temperature the configurational contributions to the entropy are dominant.

A new technical approach for preparing frozen biological samples for electron microscopy

BACKGROUND

Many methodological approaches have focused so far on physiological and molecular responses of plant tissues to freezing but only little knowledge is available on the consequences of extracellular ice-formation on cellular ultrastructure that underlies physiological reactions. In this context, the preservation of a defined frozen state during the entire fixation procedure is an essential prerequisite. However, current techniques are not able to fix frozen plant tissues for transmission electron microscopy (TEM) without interrupting the cold chain. Chemical fixation by glutaraldehyde and osmium tetroxide is not possible at sub-zero temperatures. Cryo-fixation methods, such as high pressure freeze fixation (HPF) representing the state-of-the-art technique for best structural preservation, are not equipped for freezing frozen samples. In order to overcome this obstacle, a novel technical approach for maintaining the cold chain of already frozen plant samples prior and during HPF is presented.

RESULTS

Different algae (Micrasterias denticulata, Klebsormidium crenulatum) and higher plant tissues (Lemna sp., Ranunculus glacialis, Pinus mugo) were successfully frozen and prepared for HPF at freezing temperatures (- 2 °C, - 5 °C, - 6 °C) within a newly developed automatic freezing unit (AFU), that we manufactured from a standard laboratory freezer. Preceding tests on photosynthetic electron transport and ability to plasmolyse show that the temperatures applied did not impair electron transport in PSII nor cell vitality. The transfer of the frozen specimen from the AFU into the HPF-device and subsequently cryo-fixation were performed without intermediate thawing. After cryo-substitution and further processing, the resulting TEM-micrographs showed excellent ultrastructure preservation of the different organisms when compared to specimens fixed at ambient temperature.

CONCLUSIONS

The method presented allows preserving the ultrastructure of plant cells in the frozen state during cryo-fixation. The resulting high quality TEM-images represent an important step towards a better understanding of the consequences of extracellular ice formation on cellular ultrastructure. It has the potential to provide new insights into changes of organelle structure, identification of intracellular injuries during ice formation and may help to understand freezing and thawing processes in plant tissues. It may be combined with analytical TEM such as electron energy loss spectroscopy (EELS), X-ray analyses (EDX) and various other electron microscopic techniques.

Glass polymorphism and liquid-liquid phase transition in aqueous solutions: experiments and computer simulations

One of the most intriguing anomalies of water is its ability to exist as distinct amorphous ice forms (glass polymorphism or polyamorphism). This resonates well with the possible first-order liquid-liquid phase transition (LLPT) in the supercooled state, where ice is the stable phase. In this Perspective, we review experiments and computer simulations that search for LLPT and polyamorphism in aqueous solutions containing salts and alcohols. Most studies on ionic solutes are devoted to NaCl and LiCl; studies on alcohols have mainly focused on glycerol. Less attention has been paid to protein solutions and hydrophobic solutes, even though they reveal promising avenues. While all solutions show polyamorphism and an LLPT only in dilute, sub-eutectic mixtures, there are differences regarding the nature of the transition. Isocompositional transitions for varying mole fractions are observed in alcohol but not in ionic solutions. This is because water can surround alcohol molecules either in a low- or high-density configuration whereas for ionic solutes, the water ion hydration shell is forced into high-density structures. Consequently, the polyamorphic transition and the LLPT are prevented near the ions, but take place in patches of water within the solutions. We highlight discrepancies and different interpretations within the experimental community as well as the key challenges that need consideration when comparing experiments and simulations. We point out where reinterpretation of past studies helps to draw a unified, consistent picture. In addition to the literature review, we provide original experimental results. A list of eleven open questions that need further consideration is identified.

The viral replication organelles within cells studied by electron microscopy

Transmission electron microscopy (TEM) has been crucial to study viral infections. As a result of recent advances in light and electron microscopy, we are starting to be aware of the variety of structures that viruses assemble inside cells. Viruses often remodel cellular compartments to build their replication factories. Remarkably, viruses are also able to induce new membranes and new organelles. Here we revise the most relevant imaging technologies to study the biogenesis of viral replication organelles. Live cell microscopy, correlative light and electron microscopy, cryo-TEM, and three-dimensional imaging methods are unveiling how viruses manipulate cell organization. In particular, methods for molecular mapping in situ in two and three dimensions are revealing how macromolecular complexes build functional replication complexes inside infected cells. The combination of all these imaging approaches is uncovering the viral life cycle events with a detail never seen before.

Some considerations on the water polymorphism and the liquid-liquid transition by the density behavior in the liquid phase

The bulk liquid water density data (ρ) are studied in a very large temperature pressure range including also the glass phases. A thorough analysis of their isobars, together with the suggestions of recent thermodynamical studies, gives evidence of two crossovers at T^* and P^* above which the hydrogen bond interaction is unable to arrange the tetrahedral network that is at the basis of the liquid polymorphism giving rise to the low density liquid (LDL). The curvatures of these isobars, as a function of T, are completely different: concave below P^* (where maxima are) and convex above. In both the cases, a continuity between liquid and glass is observed with P^* as the border of the density evolution toward the two different polymorphic glasses (low and high density amorphous). The experimental data of the densities of these two glasses also show a markedly different pressure dependence. Here, on the basis of these observations in bulk water and by considering a recent study on the growth of the LDL phase, by decreasing temperature, we discuss the water liquid-liquid transition and evaluate the isothermal compressibility inside the deep supercooled regime. Such a quantity shows an additional maximum that is pressure dependent that under ambient conditions agrees with a recent X-ray experiment. In particular, the present analysis suggests the presence of a liquid-liquid critical point located at about 180 MPa and 197 K.

Glass polymorphism in TIP4P/2005 water: A description based on the potential energy landscape formalism

The potential energy landscape (PEL) formalism is a statistical mechanical approach to describe supercooled liquids and glasses. Here, we use the PEL formalism to study the pressure-induced transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA) using computer simulations of the TIP4P/2005 molecular model of water. We find that the properties of the PEL sampled by the system during the LDA-HDA transformation exhibit anomalous behavior. In particular, at conditions where the change in density during the LDA-HDA transformation is approximately discontinuous, reminiscent of a first-order phase transition, we find that (i) the inherent structure (IS) energy, e_IS(V), is a concave function of the volume and (ii) the IS pressure, P_IS(V), exhibits a van der Waals-like loop. In addition, the curvature of the PEL at the IS is anomalous, a nonmonotonic function of V. In agreement with previous studies, our work suggests that conditions (i) and (ii) are necessary (but not sufficient) signatures of the PEL for the LDA-HDA transformation to be reminiscent of a first-order phase transition. We also find that one can identify two different regions of the PEL, one associated with LDA and another with HDA. Our computer simulations are performed using a wide range of compression/decompression and cooling rates. In particular, our slowest cooling rate (0.01 K/ns) is within the experimental rates employed in hyperquenching experiments to produce LDA. Interestingly, the LDA-HDA transformation pressure that we obtain at T = 80 K and at different rates extrapolates remarkably well to the corresponding experimental pressure.

Ice formation and solvent nanoconfinement in protein crystals

Ice formation within protein crystals is a major obstacle to the cryocrystallographic study of protein structure, and has limited studies of how the structural ensemble of a protein evolves with temperature in the biophysically interesting range from ∼260 K to the protein-solvent glass transition near 200 K. Using protein crystals with solvent cavities as large as ∼70 Å, time-resolved X-ray diffraction was used to study the response of protein and internal solvent during rapid cooling. Solvent nanoconfinement suppresses freezing temperatures and ice-nucleation rates so that ice-free, low-mosaicity diffraction data can be reliably collected down to 200 K without the use of cryoprotectants. Hexagonal ice (Ih) forms in external solvent, but internal crystal solvent forms stacking-disordered ice (Isd) with a near-random stacking of cubic and hexagonal planes. Analysis of powder diffraction from internal ice and single-crystal diffraction from the host protein structure shows that the maximum crystallizable solvent fraction decreases with decreasing crystal solvent-cavity size, and that an ∼6 Å thick layer of solvent adjacent to the protein surface cannot crystallize. These results establish protein crystals as excellent model systems for the study of nanoconfined solvent. By combining fast cooling, intense X-ray beams and fast X-ray detectors, complete structural data sets for high-value targets, including membrane proteins and large complexes, may be collected at ∼220-240 K that have much lower mosaicities and comparable B factors, and that may allow more confident identification of ligand binding than in current cryocrystallographic practice.

The Gram-Positive Bacterial Cell Wall

The chapter about the Gram-positive bacterial cell wall gives a brief historical background on the discovery of Gram-positive cell walls and their constituents and microscopic methods applied for studying the Gram-positive cell envelope. Followed by the description of the different chemical building blocks of peptidoglycan and the biosynthesis of the peptidoglycan layers and high turnover of peptidoglycan during bacterial growth. Lipoteichoic acids and wall teichoic acids are highlighted as major components of the cell wall. Characterization of capsules and the formation of extracellular vesicles by Gram-positive bacteria close the section on cell envelopes which have a high impact on bacterial pathogenesis. In addition, the specialized complex and unusual cell wall of mycobacteria is introduced thereafter. Next a short back view is given on the development of electron microscopic examinations for studying bacterial cell walls. Different electron microscopic techniques and methods applied to examine bacterial cell envelopes are discussed in the view that most of the illustrated methods should be available in a well-equipped life sciences orientated electron microscopic laboratory. In addition, newly developed and mostly well-established cryo-methods like high-pressure freezing and freeze-substitution (HPF-FS) and cryo-sections of hydrated vitrified bacteria (CEMOVIS, Cryo-electron microscopy of vitreous sections) are described. At last, modern cryo-methods like cryo-electron tomography (CET) and cryo-FIB-SEM milling (focus ion beam-scanning electron microscopy) are introduced which are available only in specialized institutions, but at present represent the best available methods and techniques to study Gram-positive cell walls under close-to-nature conditions in great detail and at high resolution.

Compositional relaxation on the approach to the glass transition in a model trehalose solution

Molecular dynamics simulation was used to study the temperature dependence of the mutual diffusion coefficient D_{m} and the intermediate scattering function of equilibrium and metastable aqueous solutions of the cryoprotectant molecule trehalose at very low (2.2 and 9wt.%) and very high (80 and 95wt.%) concentrations. The simulations were conducted over a range of temperatures approaching the glass transition temperature T_{g} for each concentration. Similar to a recent observation made on a glass-forming model polydisperse colloidal suspension [Hannam et al., Phys. Rev. E 96, 022609 (2017)2470-004510.1103/PhysRevE.96.022609], we confirmed by a set of independent computations that D_{m} is responsible for the long-time decay of the intermediate scattering function. We observed that D_{m} decreased on the approach to the glass transition temperature, resulting in an extremely slow long-time decay in the intermediate scattering function that culminated in the arrest of compositional fluctuations and a plateau in the intermediate scattering function at T_{g}. In both cases, crystallization requires a change in the composition of the solution, which is a process controlled by D_{m}. This transport coefficient can either increase or decrease as solidification is approached, because it depends on a product of thermodynamic and mobility factors. Our observations show that in both cases, for the glass-forming liquids, it is observed to decrease, while for a previously studied monodisperse colloidal suspension which crystallizes easily, it increases. The similarity in the behavior of these two very different glass-forming systems (the polydisperse colloidal suspension and the sugar solution) shows the importance of the mutual diffusion coefficient to our understanding of vitrification and suggests a possible distinction between between glass-forming and crystallizing solutions.

Theoretical analysis of crystallization by homogeneous nucleation of water droplets

We propose a novel method for analyzing the crystallization process from supercooled water droplets.

Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age

Structural biology is going through a revolution as a result of transformational advances in the field of cryo-electron microscopy (cryo-EM) driven by the development of direct electron detectors and ultrastable electron microscopes. High-resolution cryo-EM images of isolated biomolecules (single particles) suspended in a thin layer of vitrified buffer are subjected to powerful image-processing algorithms, enabling near-atomic resolution structures to be determined in unprecedented numbers. Prior to these advances, electron crystallography of two-dimensional crystals and helical assemblies of proteins had established the feasibility of atomic resolution structure determination using cryo-EM. Atomic resolution single-particle analysis, without the need for crystals, now promises to resolve problems in structural biology that were intractable just a few years ago.

Cryopreservation of Marchantia polymorpha spermatozoa

The liverwort Marchantia polymorpha has become one of the model organisms, since it has less genetic redundancy, sexual and asexual modes of reproduction and a range of genomic and molecular genetic resources. Cryopreservation of fertile spermatozoa eliminates time, space and labor for growing and maintaining male plants in reproductive phase, and also provides an optional way to backup lines. Here we report a protocol to cryopreserve spermatozoa of M. polymorpha in liquid nitrogen. A cryoprotective solution containing sucrose, glycerol and egg yolk and controlled cooling and warming processes led to successful recovery of motile M. polymorpha spermatozoa after the cryogenic process. The survival rate and average motility of spermatozoa after cryopreservation were maintained at 71 and 54% of those before cryopreservation, respectively. Cryopreserved spermatozoa were capable of fertilization to form normal spores. The technique presented here confers more versatility to experiments using M. polymorpha and could be applied to preservation of plant spermatozoa in general.